CiteULike: inesdesantiago's library [111 articles]

Transcriptional control of noise in gene expression

Alvaro Sanchez — 2008-03-20T15:15:36-00:00

Proceedings of the National Academy of Sciences (19 March 2008), 0707904105.

Cis-regulatory control of transcription is the dominant form of regulation of gene expression. Recent experimental results suggest that, in addition to the mean expression level, cell-to-cell variability might also be transcriptionally regulated. Here, we develop a stochastic model of transcriptional regulation that allows us to calculate closed-form analytical expressions for the mean and variance of the protein and mRNA distributions for an arbitrarily complex cis-regulatory motif. Our model allows us to investigate how noise may be transcriptionally regulated independently from the mean expression. We show that our approach is in excellent agreement with stochastic simulations and experiment, and leads to an experimentally testable formula for the noise in gene expression as a function of inducer-molecule concentrations. 10.1073/pnas.0707904105

X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations.

Yin Shen — 2008-03-17T00:15:34-00:00

Proc Natl Acad Sci U S A (13 March 2008)

X chromosome inactivation (XCI) is an essential mechanism for dosage compensation of X-linked genes in female cells. We report that subcultures from lines of female human embryonic stem cells (hESCs) exhibit variation (0-100%) for XCI markers, including XIST RNA expression and enrichment of histone H3 lysine 27 trimethylation (H3K27me3) on the inactive X chromosome (Xi). Surprisingly, regardless of the presence or absence of XCI markers in different cultures, all female hESCs we examined (H7, H9, and HSF6 cells) exhibit a monoallelic expression pattern for a majority of X-linked genes. Our results suggest that these established female hESCs have already completed XCI during the process of derivation and/or propagation, and the XCI pattern of lines we investigated is already not random. Moreover, XIST gene expression in subsets of cultured female hESCs is unstable and subject to stable epigenetic silencing by DNA methylation. In the absence of XIST expression, approximately 12% of X-linked promoter CpG islands become hypomethylated and a portion of X-linked alleles on the Xi are reactivated. Because alterations in dosage compensation of X-linked genes could impair somatic cell function, we propose that XCI status should be routinely checked in subcultures of female hESCs, with cultures displaying XCI markers better suited for use in regenerative medicine.

X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells.

Susana S Silva — 2008-03-17T00:18:20-00:00

Proc Natl Acad Sci U S A (13 March 2008)

With the potential to give rise to all somatic cell types, human embryonic stem cells (hESC) have generated enormous interest as agents of cell replacement therapy. One potential limitation is their safety in vivo. Although several studies have focused on concerns over genomic stability ex vivo, few have analyzed epigenetic stability. Here, we use tools of the epigenetic phenomenon, X-chromosome inactivation (XCI), to investigate their epigenetic properties. Among 11 distinct hESC lines, we find a high degree of variability. We show that, like mouse ESC, hESC in principle have the capacity to recapitulate XCI when induced to differentiate in culture (class I lines). However, this capacity is seen in few hESC isolates. Many hESC lines have already undergone XCI (class II and III). Unexpectedly, there is a tendency to lose XIST RNA expression during culture (class III). Despite losing H3-K27 trimethylation, the inactive X of class III lines remains transcriptionally suppressed, as indicated by Cot-1 RNA exclusion. We conclude that hESC lines are subject to dynamic epigenetic reprogramming ex vivo. Given that XCI and cell differentiation are tightly linked, we consider implications for hESC pluripotency and differentiation potential.

GeneTrack--a genomic data processing and visualization framework

Istvan Albert — 2008-05-07T11:06:27-00:00

Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1305-1306.

Motivation: High-throughput ChIP-chip' and ChIP-seq' methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com Contact: iual@psu.edu 10.1093/bioinformatics/btn119

Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Nicole Cloonan — 2008-06-25T20:30:50-00:00

Nature methods (30 May 2008)

We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)(+) transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete.

Systems biology and cancer stem cells.

ND Price — 2008-07-24T15:30:41-00:00

Journal of cellular and molecular medicine, Vol. 12, No. 1. (b 2008), pp. 97-110.

The identification, purification, and characterization of cancer stem cells holds tremendous promise for improving the treatment of cancer. Mounting evidence is demonstrating that only certain tumor cells (i.e. the cancer stem cells) can give rise to tumors when injected and that these purified cell populations generate heterogeneous tumors. While the cell of origin is still not determined definitively, specific molecular markers for populations containing these cancer stem cells have been found for leukemia, brain cancer, and breast cancer, among others. Systems approaches, particularly molecular profiling, have proven to be of great utility for cancer diagnosis and characterization. These approaches also hold significant promise for identifying distinctive properties of the cancer stem cells, and progress is already being made.

Molecular profiling of stem cells.

L Ma — 2008-07-24T15:29:05-00:00

Clinica chimica acta; international journal of clinical chemistry, Vol. 378, No. 1-2. (March 2007), pp. 24-32.

Stem cells, with their profound implication in development and enormous potential in regenerative medicine, have been the subject of extensive molecular profiling studies in search of better markers and regulatory schema governing self-renewal versus differentiation. In this review article, we will discuss current advancement in high throughput technologies dedicated to the transcriptome, proteome and genome-wide localization analyses, and how they have been adopted in molecular profiling of stem cells with an emphasis on embryonic stem cell (ESC), hematopoietic stem cell (HSC) and neural stem cell (NSC).

Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling

Wendy Prudhomme — 2007-09-28T01:32:28-00:00

Proceedings of the National Academy of Sciences, Vol. 101, No. 9. (2 March 2004), pp. 2900-2905.

A number of extracellular stimuli, including soluble cytokines and insoluble matrix factors, are known to influence murine embryonic stem cell self-renewal and differentiation behavioral responses via intracellular signaling pathways, but their net effects in combination are difficult to understand. To gain insight concerning key intracellular signals governing these behavioral responses, we employ a multivariate systems analysis of proteomic data generated from combinatorial stimulation of mouse embryonic stem cells by fibronectin, laminin, leukemia-inhibitory factor, and fibroblast growth factor 4. Phosphorylation states of 31 intracellular signaling network components were obtained across 16 different stimulus conditions at three time points by quantitative Western blotting, and partial-least-squares modeling was used to determine which components were most strongly correlated with cell proliferation and differentiation rate constants obtained from flow cytometry measurements of Oct-4 expression levels. This data-driven, multivariate (16 conditions x 31 components x 3 time points = approx1,500 values) proteomic approach identified a set of signaling network components most critically associated (positively or negatively) with differentiation (Stat3, Raf1, MEK, and ERK), proliferation of undifferentiated cells (MEK and ERK), and proliferation of differentiated cells (PKBalpha, Stat3, Src, and PKCepsilon). These predictions were found to be consistent with previous in vivo literature, along with direct in vitro test here by a peptide inhibitor of PKCepsilon. Our results demonstrate how a computational systems biology approach can elucidate key sets of intracellular signaling protein activities that combine to govern cell phenotypic responses to extracellular cues. 10.1073/pnas.0308768101

Nuclear proteomics and directed differentiation of embryonic stem cells.

M Barthelery — 2008-07-24T15:22:07-00:00

Stem cells and development, Vol. 16, No. 6. (December 2007), pp. 905-919.

During the past decade, regenerative medicine has been the subject of intense interest due, in large part, to our growing knowledge of embryonic stem (ES) cell biology. ES cells give rise to cell lineages from the three primordial germ layers--endoderm, mesoderm, and ectoderm. This process needs to be channeled if these cells are to be differentiated efficiently and used subsequently for therapeutic purposes. Indeed, an important area of investigation involves directed differentiation to influence the lineage commitment of these pluripotent cells in vitro. Various strategies involving timely growth factor supplementation, cell co-cultures, and gene transfection are used to drive lineage specific emergence. The underlying goal is to control directly the center of gene expression and cellular programming--the nucleus. Gene expression is enabled, managed, and sustained by the collective actions and interactions of proteins found in the nucleus--the nuclear proteome--in response to extracellular signaling. Nuclear proteomics can inventory these nuclear proteins in differentiating cells and decipher their dynamics during cellular phenotypic commitment. This review details what is currently known about nuclear effectors of stem cell differentiation and describes emerging techniques in the discovery of nuclear proteomics that will illuminate new transcription factors and modulators of gene expression.

Concise Review: Trends in Stem Cell Proteomics

Hossein Baharvand — 2008-07-24T15:20:27-00:00

Stem Cells, Vol. 25, No. 8. (1 August 2007), pp. 1888-1903.

Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including sample heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article. 10.1634/stemcells.2007-0107

Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells

Qiang Tian — 2008-07-24T15:17:07-00:00

Mol Cell Proteomics, Vol. 3, No. 10. (1 October 2004), pp. 960-969.

Using DNA microarrays together with quantitative proteomic techniques (ICAT reagents, two-dimensional DIGE, and MS), we evaluated the correlation of mRNA and protein levels in two hematopoietic cell lines representing distinct stages of myeloid differentiation, as well as in the livers of mice treated for different periods of time with three different peroxisome proliferative activated receptor agonists. We observe that the differential expression of mRNA (up or down) can capture at most 40% of the variation of protein expression. Although the overall pattern of protein expression is similar to that of mRNA expression, the incongruent expression between mRNAs and proteins emphasize the importance of posttranscriptional regulatory mechanisms in cellular development or perturbation that can be unveiled only through integrated analyses of both proteins and mRNAs. 10.1074/mcp.M400055-MCP200

Chromatin in pluripotent embryonic stem cells and differentiation

Eran Meshorer — 2006-06-28T17:44:42-00:00

Nature Reviews Molecular Cell Biology, Vol. 7, No. 7. (17 May 2006), pp. 540-546.

Embryonic stem (ES) cells are unique in that they are pluripotent and have the ability to self-renew. The molecular mechanisms that underlie these two fundamental properties are largely unknown. We discuss how unique properties of chromatin in ES cells contribute to the maintenance of pluripotency and the determination of differentiation properties.

Chromatin remodeling, histone modifications, and DNA methylation - how does it all fit together?

Theresa Geiman — 2008-07-24T15:06:28-00:00

Journal of Cellular Biochemistry, Vol. 87, No. 2. (2002), pp. 117-125.

DNA methylation is important in the control of gene transcription and chromatin structure. The complexities of this process are just beginning to be elucidated in relationship to other epigenetic mechanisms. Exciting new research in the areas of histone methylation and chromatin remodeling make it clear just how important the connections between these various mechanisms and DNA methylation are for the control of chromosome structure and gene expression. Emerging evidence suggests that chromatin remodeling enzymes and histone methylation are essential for proper DNA methylation patterns. Other histone modifications, such as acetylation and phosphorylation, in turn, affect histone methylation and histone methylation also appears to be highly reliant on chromatin remodeling enzymes. This review will summarize what is likely only the beginning of a flood of new information that will ultimately link all epigenetic modifications of the mammalian genome. A model will also be put forth to account for how chromatin modifications lead to genomic DNA methylation patterns. J. Cell. Biochem. 87: 117-125, 2002. Published 2002 Wiley-Liss, Inc.

An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells.

MG Carter — 2008-07-24T15:01:34-00:00

Gene expression patterns : GEP, Vol. 8, No. 3. (February 2008), pp. 181-198.

We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures.

Oct4 Targets Regulatory Nodes to Modulate Stem Cell Function

Pearl Campbell — 2008-07-24T14:58:56-00:00

PLoS ONE, Vol. 2, No. 6. (20 June 2007), e553.

Stem cells are characterized by two defining features, the ability to self-renew and to differentiate into highly specialized cell types. The POU homeodomain transcription factor Oct4 (Pou5f1) is an essential mediator of the embryonic stem cell state and has been implicated in lineage specific differentiation, adult stem cell identity, and cancer. Recent description of the regulatory networks which maintain ‘ES’ have highlighted a dual role for Oct4 in the transcriptional activation of genes required to maintain self-renewal and pluripotency while concomitantly repressing genes which facilitate lineage specific differentiation. However, the molecular mechanism by which Oct4 mediates differential activation or repression at these loci to either maintain stem cell identity or facilitate the emergence of alternate transcriptional programs required for the realization of lineage remains to be elucidated. To further investigate Oct4 function, we employed gene expression profiling together with a robust statistical analysis to identify genes highly correlated to Oct4. Gene Ontology analysis to categorize overrepresented genes has led to the identification of themes which may prove essential to stem cell identity, including chromatin structure, nuclear architecture, cell cycle control, DNA repair, and apoptosis. Our experiments have identified previously unappreciated roles for Oct4 for firstly, regulating chromatin structure in a state consistent with self-renewal and pluripotency, and secondly, facilitating the expression of genes that keeps the cell poised to respond to cues that lead to differentiation. Together, these data define the mechanism by which Oct4 orchestrates cellular regulatory pathways to enforce the stem cell state and provides important insight into stem cell function and cancer.

Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity.

Mitsuhiro Endoh — 2008-03-17T00:22:47-00:00

Development (13 March 2008)

The Polycomb group (PcG) proteins mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes 1 (PRC1) and 2 (PRC2). Although PRC2 has been shown to share target genes with the core transcription network, including Oct3/4, to maintain embryonic stem (ES) cells, it is still unclear whether PcG proteins and the core transcription network are functionally linked. Here, we identify an essential role for the core PRC1 components Ring1A/B in repressing developmental regulators in mouse ES cells and, thereby, in maintaining ES cell identity. A significant proportion of the PRC1 target genes are also repressed by Oct3/4. We demonstrate that engagement of PRC1 at target genes is Oct3/4-dependent, whereas engagement of Oct3/4 is PRC1-independent. Moreover, upon differentiation induced by Gata6 expression, most of the Ring1A/B target genes are derepressed and the binding of Ring1A/B to their target loci is also decreased. Collectively, these results indicate that Ring1A/B-mediated Polycomb silencing functions downstream of the core transcriptional regulatory circuitry to maintain ES cell identity.

Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation.

X Ren — 2008-07-24T14:54:01-00:00

Molecular and cellular biology, Vol. 28, No. 9. (May 2008), pp. 2884-2895.

Polycomb group (PcG) transcription regulatory proteins maintain cell identity by sustained repression of numerous genes. The differentiation of embryonic stem (ES) cells induces a genome-wide shift in PcG target gene expression. We investigated the effects of differentiation and protein interactions on CBX family PcG protein localization and dynamics by using fluorescence imaging. In mouse ES cells, different CBX proteins exhibited distinct distributions and mobilities. Most CBX proteins were enriched in foci known as Polycomb bodies. Focus formation did not affect CBX protein mobilities, and the foci dispersed during ES cell differentiation. The mobilities of CBX proteins increased upon the induction of differentiation and decreased as differentiation progressed. The deletion of the chromobox, which mediates interactions with RING1B, prevented the immobilization of CBX proteins. In contrast, the deletion of the chromodomain, which can bind trimethylated lysine 27 of histone H3, had little effect on CBX protein dynamics. The distributions and mobilities of most CBX proteins corresponded to those of CBX-RING1B complexes detected by using bimolecular fluorescence complementation analysis. Epigenetic reprogramming during ES cell differentiation is therefore associated with global changes in the subnuclear distributions and dynamics of CBX protein complexes.

Fewer Genes, More Noncoding RNA

Jean-Michel Claverie — 2005-09-02T10:35:43-00:00

Science, Vol. 309, No. 5740. (02 September 2005), pp. 1529-1530.

Recent studies showing that most "messenger" RNAs do not encode proteins finally explain the long-standing discrepancy between the small number of protein-coding genes found in vertebrate genomes and the much larger and ever-increasing number of polyadenylated transcripts identified by tag-sampling or microarray-based methods. Exploring the role and diversity of these numerous noncoding RNAs now constitutes a main challenge in transcription research.

Isochores Merit the Prefix 'Iso'

Wentian Li — 2008-07-24T14:49:43-00:00

Genome Biology, Vol. 3, No. 11. (2002), pp. preprint0009.1-preprint0009.15.

The isochore concept in human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in IGHSC analysis concerning the existence of isochore is incorrect, because it had applied an inappropriate statistical test. To test the existence of isochores should be equivalent to a test of homogeneity of windowed GC%. The statistical test applied in the IHGSC's analysis, the binomial test, is however a test of a sequence being random on the base level. For testing the existence of isochore, or homogeneity in GC%, we propose to use another statistical test: the analysis of variance (ANOVA). It can be shown that DNA sequences that are rejected by binomial test may not be rejected by the ANOVA test.

A Short Genome Primer

Cmels Directorate — 2008-07-24T14:43:39-00:00

Comparative Genomics (5 June 2005), pp. 5-11.

The completion of the Human Genome Project in 2003 marked the most ambitious research effort in the history of life sciences: the sequencing of human DNA. However, the project, which included the participation of Lawrence Livermore biologists and computational scientists, was only the first step in understanding life at the molecular level. “The Human Genome Project gave us the sequence of the human DNA but not the manual that explains what it means,” says Ivan Ovcharenko, a bioinformatics scientist in Livermore’s Computation Directorate.

Antisense starts making more sense

Gordon Carmichael — 2008-07-24T14:29:57-00:00

Nat Biotech, Vol. 21, No. 4. (April 2003), pp. 371-372.

Numerous endogenous antisense RNAs suggest antisense regulation of the human genome is more widespread than first thought

Genome-wide mapping of allele-specific protein-DNA interactions in human cells

Nathaniel Maynard — 2008-03-28T16:35:47-00:00

Nature Methods, Vol. 5, No. 4. (16 March 2008), pp. 307-309.

Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei

Florian Grasser — 2008-07-24T14:02:31-00:00

J Cell Sci, Vol. 121, No. 11. (1 June 2008), pp. 1876-1886.

Using published high-resolution data on S-phase replication timing, we determined the three-dimensional (3D) nuclear arrangement of 33 very-early-replicating and 31 very-late-replicating loci. We analyzed diploid human, non-human primate and rearranged tumor cells by 3D fluorescence in situ hybridization with the aim of investigating the impact of chromosomal structural changes on the nuclear organization of these loci. Overall, their topology was found to be largely conserved between cell types, species and in tumor cells. Early-replicating loci were localized in the nuclear interior, whereas late-replicating loci showed a broader distribution with a higher preference for the periphery than for late-BrdU-incorporation foci. However, differences in the spatial arrangement of early and late loci of chromosome 2, as compared with those from chromosome 5, 7 and 17, argue against replication timing as a major driving force for the 3D radial genome organization in human lymphoblastoid cell nuclei. Instead, genomic properties, and local gene density in particular, were identified as the decisive parameters. Further detailed comparisons of chromosome 7 loci in primate and tumor cells suggest that the inversions analyzed influence nuclear topology to a greater extent than the translocations, thus pointing to geometrical constraints in the 3D conformation of a chromosome territory. 10.1242/jcs.026989

Dissecting the logical types of network control in gene expression profiles.

C Marr — 2008-07-24T14:00:07-00:00

BMC systems biology, Vol. 2 (2008)

BACKGROUND: In the bacterium Escherichia coli the transcriptional regulation of gene expression involves both dedicated regulators binding specific DNA sites with high affinity and also global regulators - abundant DNA architectural proteins of the bacterial nucleoid binding multiple sites with a wide range of affinities and thus modulating the superhelical density of DNA. The first form of transcriptional regulation is predominantly pairwise and specific, representing digitial control, while the second form is (in strength and distribution) continuous, representing analog control. RESULTS: Here we look at the properties of effective networks derived from significant gene expression changes under variation of the two forms of control and find that upon limitations of one type of control (caused e.g. by mutation of a global DNA architectural factor) the other type can compensate for compromised regulation. Mutations of global regulators significantly enhance the digital control, whereas in the presence of global DNA architectural proteins regulation is mostly of the analog type, coupling spatially neighboring genomic loci. Taken together our data suggest that two logically distinct - digital and analog - types of control are balancing each other. CONCLUSION: By revealing two distinct logical types of control, our approach provides basic insights into both the organizational principles of transcriptional regulation and the mechanisms buffering genetic flexibility. We anticipate that the general concept of distinguishing logical types of control will apply to many complex biological networks.

Stem cell self-renewal versus differentiation: Tumor suppressor Mei-P26 and miRNAs control the balance

Run Shen — 2008-07-24T13:56:42-00:00

Cell Res, Vol. 18, No. 7. (0000), pp. 713-715.

Stem cells, which can self-renew and produce different cell types, have been shown to be regulated by extrinsic signals and intrinsic factors. Drosophila ovarian germline stem cells (GSCs), representing one of the well-studied stem cells, continuously proliferate and generate differentiated cystoblasts, which further develop into oocytes. In the Drosophila ovary, cap cells form the GSC niche, which produces the BMP signal for maintaining GSC self-renewal 1. BMP signaling directly represses the transcription of bam, a key differentiation factor, to prevent GSC differentiation and thereby maintain self-renewal. Bam acts with its partner Bgcn to sufficiently drive GSC differentiation. Disruption of BMP signaling leads to GSC premature differentiation and loss, while elimination of Bam/Bgcn function results in accumulation of GSC-like cells. mei-P26, which was initially identified for its role in meiotic recombination, has also been shown to be required for GSC daughter differentiation since its mutant ovaries contain more GSC-like cells 2. As expected, mei-P26 and bam genetically interact with each other to regulate germ cell differentiation. mei-P26 encodes a protein containing a RING finger B-box Coiled-Coil (RBCC) and a NHL (NCL-l, HT2A, and Lin-41) domain 2. Recently, the miRNA pathway is also shown to be required for controlling GSC self-renewal since mutations in Dicer-1, Ago1, and loquacious, which are involved in miRNA production and function in Drosophila, cause rapid loss of GSCs 3, 4, 5. Small 23-25 nt long miRNAs can regulate gene expression through translation repression and mRNA degradation by binding to the 3' untranslated region (UTR) of their target mRNAs 6. Interestingly, the miRNA pathway controls GSC self-renewal not by repressing bam 3, 4, 5. However, it remains unclear how mei-P26 and bam, suppressors of GSC-like tumors, negatively interact with the miRNA pathway to control the balance between self-renewal and differentiation. In a recent issue of Nature, Neumuller et al. have provided the missing link between mei-P26/bam-medatiated differentiation pathway and the self-renewal-promoting miRNA pathway 7.

The three-dimensional structure of human interphase chromosomes is related to the transcriptome map.

S Goetze — 2008-07-24T13:53:37-00:00

Molecular and cellular biology, Vol. 27, No. 12. (June 2007), pp. 4475-4487.

The three-dimensional (3D) organization of the chromosomal fiber in the human interphase nucleus is an important but poorly understood aspect of gene regulation. Here we quantitatively analyze and compare the 3D structures of two types of genomic domains as defined by the human transcriptome map. While ridges are gene dense and show high expression levels, antiridges, on the other hand, are gene poor and carry genes that are expressed at low levels. We show that ridges are in general less condensed, more irregularly shaped, and located more closely to the nuclear center than antiridges. Six human cell lines that display different gene expression patterns and karyotypes share these structural parameters of chromatin. This shows that the chromatin structures of these two types of genomic domains are largely independent of tissue-specific variations in gene expression and differentiation state. Moreover, we show that there is remarkably little intermingling of chromatin from different parts of the same chromosome in a chromosome territory, neither from adjacent nor from distant parts. This suggests that the chromosomal fiber has a compact structure that sterically suppresses intermingling. Together, our results reveal novel general aspects of 3D chromosome architecture that are related to genome structure and function.

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Xi Chen — 2008-06-13T18:29:13-00:00

Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117.

Summary Transcription factors (TFs) and their specific interactions with targets are crucial for specifying gene-expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of 13 sequence-specific TFs (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1, and CTCF) and 2 transcription regulators (p300 and Suz12). These factors are known to play different roles in ES-cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators, and key reprogramming factors. Our study provides insights into the integration of the signaling pathways into the ES-cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different TFs. Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.

Polycomb complexes repress developmental regulators in murine embryonic stem cells

Laurie Boyer — 2006-04-20T00:45:33-00:00

Nature (19 April 2006)

The mechanisms by which embryonic stem (ES) cells self-renew while maintaining the ability to differentiate into virtually all adult cell types are not well understood. Polycomb group (PcG) proteins are transcriptional repressors that help to maintain cellular identity during metazoan development by epigenetic modification of chromatin structure1. PcG proteins have essential roles in early embryonic development2, 3, 4, 5, 6 and have been implicated in ES cell pluripotency2, but few of their target genes are known in mammals. Here we show that PcG proteins directly repress a large cohort of developmental regulators in murine ES cells, the expression of which would otherwise promote differentiation. Using genome-wide location analysis in murine ES cells, we found that the Polycomb repressive complexes PRC1 and PRC2 co-occupied 512 genes, many of which encode transcription factors with important roles in development. All of the co-occupied genes contained modified nucleosomes (trimethylated Lys 27 on histone H3). Consistent with a causal role in gene silencing in ES cells, PcG target genes were de-repressed in cells deficient for the PRC2 component Eed, and were preferentially activated on induction of differentiation. Our results indicate that dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development.

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Alexander Meissner — 2008-07-07T18:29:24-00:00

Nature (06 July 2008)

DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.

R Versteeg — 2006-12-20T01:59:30-00:00

Genome Res, Vol. 13, No. 9. (September 2003), pp. 1998-2004.

The chromosomal gene expression profiles established by the Human Transcriptome Map (HTM) revealed a clustering of highly expressed genes in about 30 domains, called ridges. To physically characterize ridges, we constructed a new HTM based on the draft human genome sequence (HTMseq). Expression of 25,003 genes can be analyzed online in a multitude of tissues (http://bioinfo.amc.uva.nl/HTMseq). Ridges are found to be very gene-dense domains with a high GC content, a high SINE repeat density, and a low LINE repeat density. Genes in ridges have significantly shorter introns than genes outside of ridges. The HTMseq also identifies a significant clustering of weakly expressed genes in domains with fully opposite characteristics (antiridges). Both types of domains are open to tissue-specific expression regulation, but the maximal expression levels in ridges are considerably higher than in antiridges. Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation.

Control of developmental regulators by polycomb in human embryonic stem cells.

TI Lee — 2006-04-26T09:09:08-00:00

Cell, Vol. 125, No. 2. (21 April 2006), pp. 301-313.

Polycomb group proteins are essential for early development in metazoans, but their contributions to human development are not well understood. We have mapped the Polycomb Repressive Complex 2 (PRC2) subunit SUZ12 across the entire nonrepeat portion of the genome in human embryonic stem (ES) cells. We found that SUZ12 is distributed across large portions of over two hundred genes encoding key developmental regulators. These genes are occupied by nucleosomes trimethylated at histone H3K27, are transcriptionally repressed, and contain some of the most highly conserved noncoding elements in the genome. We found that PRC2 target genes are preferentially activated during ES cell differentiation and that the ES cell regulators OCT4, SOX2, and NANOG cooccupy a significant subset of these genes. These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation.

A chromatin landmark and transcription initiation at most promoters in human cells.

MG Guenther — 2008-03-19T18:19:40-00:00

Cell, Vol. 130, No. 1. (13 July 2007), pp. 77-88.

We describe the results of a genome-wide analysis of human cells that suggests that most protein-coding genes, including most genes thought to be transcriptionally inactive, experience transcription initiation. We found that nucleosomes with H3K4me3 and H3K9,14Ac modifications, together with RNA polymerase II, occupy the promoters of most protein-coding genes in human embryonic stem cells. Only a subset of these genes produce detectable full-length transcripts and are occupied by nucleosomes with H3K36me3 modifications, a hallmark of elongation. The other genes experience transcription initiation but show no evidence of elongation, suggesting that they are predominantly regulated at postinitiation steps. Genes encoding most developmental regulators fall into this group. Our results also identify a class of genes that are excluded from experiencing transcription initiation, at which mechanisms that prevent initiation must predominate. These observations extend to differentiated cells, suggesting that transcription initiation at most genes is a general phenomenon in human cells.

Gene dynamics and nuclear architecture during differentiation

Schofer — 2008-01-14T18:35:36-00:00

Differentiation, Vol. 76, No. 1. (January 2008), pp. 41-56.

The complexity of the mammalian transcriptome

Gustincich — 2006-08-25T23:36:59-00:00

The Journal of Physiology, Vol. 575, No. 2. (September 2006), pp. 321-332.

A comprehensive understanding of protein and regulatory networks is strictly dependent on the complete description of the transcriptome of cells. After the determination of the genome sequence of several mammalian species, gene identification is based on in silico predictions followed by evidence of transcription. Conservative estimates suggest that there are about 20 000 protein-encoding genes in the mammalian genome. In the last few years the combination of full-length cDNA cloning, cap-analysis gene expression (CAGE) tag sequencing and tiling arrays experiments have unveiled unexpected additional complexities in the transcriptome. Here we describe the current view of the mammalian transcriptome focusing on transcripts diversity, the growing non-coding RNA world, the organization of transcriptional units in the genome and promoter structures. In-depth analysis of the brain transcriptome has been challenging due to the cellular complexity of this organ. Here we present a computational analysis of CAGE data from different regions of the central nervous system, suggesting distinctive mechanisms of brain-specific transcription

Gene activation and deactivation related changes in the three-dimensional structure of chromatin.

E Wegel — 2006-07-28T14:15:09-00:00

Chromosoma, Vol. 114, No. 5. (November 2005), pp. 331-337.

Chromatin in the interphase nucleus is dynamic, decondensing where genes are activated and condensing where they are silenced. Local chromatin remodelling to a more open structure during gene activation is followed by changes in nucleosome distribution through the action of the transcriptional machinery. This leads to chromatin expansion and looping out of whole genomic regions. Such chromatin loops can extend beyond the chromosome territory. As several studies point to the location of transcription sites inside chromosome territories as well as at their periphery, extraterritorial loops cannot simply be a mechanism for making transcribed genes accessible to the transcriptional machinery and must occur for other reasons. The level of decondensation within an activated region varies greatly and probably depends on the density of activated genes and the number of engaged RNA polymerases. Genes that are silenced during development form a more closed chromatin structure. Specific histone modifications are correlated with gene activation and silencing, and silenced genes may become associated with heterochromatin protein 1 homologues or with polycomb group complexes. Several levels of chromatin packaging are found in the nucleus relating to the different functions of and performed by active genes; euchromatic and heterochromatic regions and the models explaining higher-order chromatin structure are still disputed.

Dynamics and interplay of nuclear architecture, genome organization, and gene expression.

R Schneider — 2007-12-10T16:46:59-00:00

Genes Dev, Vol. 21, No. 23. (1 December 2007), pp. 3027-3043.

The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions

Christian Lanctot — 2007-01-18T11:53:14-00:00

Nat Rev Genet, Vol. 8, No. 2. (February 2007), pp. 104-115.

The living test-tube: imaging of real-time gene expression

Yaron Shav-Tal — 2008-07-24T13:17:47-00:00

Soft Matter, Vol. 2, No. 5. (2006), pp. 361-370.

Cells are dynamic entities. Not only are some cells motile but there is constant motion of organelles, proteins, nucleic acids and other molecules within every living cell. These complex molecular pathways control the life cycle of a cell and all come down to the basic players of the gene expression pathway: DNA, RNA and protein. It is therefore imperative to study biological processes as they naturally occur-in living cells, and to unravel the biophysical rules that govern intracellular dynamics. Towards this end, genetically encoded fluorescent proteins have become one of the major tools available for the study of kinetic processes taking place in real-time. This review will focus on the technical developments available for the study of gene activity in living cells and will summarize the novel biological information extracted from these approaches.

Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis.

SJ Clark — 2008-07-24T13:14:53-00:00

Human molecular genetics, Vol. 16 Spec No 1 (15 April 2007)

Despite the completion of the Human Genome Project, we are still far from understanding the molecular events underlying epigenetic change in cancer. Cancer is a disease of the DNA with both genetic and epigenetic changes contributing to changes in gene expression. Epigenetics involves the interplay between DNA methylation, histone modifications and expression of non-coding RNAs in the regulation of gene transcription. We now know that tumour suppressor genes, with CpG island-associated promoters, are commonly hypermethylated and silenced in cancer, but we do not understood what triggers this process or when it occurs during carcinogenesis. Epigenetic gene silencing has always been envisaged as a local event silencing discrete genes, but recent data now indicates that large regions of chromosomes can be co-coordinately suppressed; a process termed long range epigenetic silencing (LRES). LRES can span megabases of DNA and involves broad heterochromatin formation accompanied by hypermethylation of clusters of contiguous CpG islands within the region. It is not clear if LRES is initiated by one critical gene target that spreads and conscripts innocent bystanders, analogous to large genetic deletions or if coordinate silencing of multiple genes is important in carcinogenesis? Over the next decade with the exciting new genomic approaches to epigenome analysis and the initiation of a Human Epigenome Project, we will understand more about the interplay between DNA methylation and chromatin modifications and the expression of non-coding RNAs, promising a new range of molecular diagnostic cancer markers and molecular targets for cancer epigenetic therapy.

Radial chromatin positioning is shaped by local gene density, not by gene expression.

K Küpper — 2008-07-24T13:07:15-00:00

Chromosoma, Vol. 116, No. 3. (June 2007), pp. 285-306.

G- and R-bands of metaphase chromosomes are characterized by profound differences in gene density, CG content, replication timing, and chromatin compaction. The preferential localization of gene-dense, transcriptionally active, and early replicating chromatin in the nuclear interior and of gene-poor, later replicating chromatin at the nuclear envelope has been demonstrated to be evolutionary-conserved in various cell types. Yet, the impact of different local chromatin features on the radial nuclear arrangement of chromatin is still not well understood. In particular, it is not known whether radial chromatin positioning is preferentially shaped by local gene density per se or by other related parameters such as replication timing or transcriptional activity. The interdependence of these distinct chromatin features on the linear deoxyribonucleic acid (DNA) sequence precludes a simple dissection of these parameters with respect to their importance for the reorganization of the linear DNA organization into the distinct radial chromatin arrangements observed in the nuclear space. To analyze this problem, we generated probe sets of pooled bacterial artificial chromosome (BAC) clones from HSA 11, 12, 18, and 19 representing R/G-band-assigned chromatin, segments with different gene density and gene loci with different expression levels. Using multicolor 3D flourescent in situ hybridization (FISH) and 3D image analysis, we determined their localization in the nucleus and their positions within or outside the corresponding chromosome territory (CT). For each BAC data on local gene density within 2- and 10-Mb windows, as well as GC (guanine and cytosine) content, replication timing and expression levels were determined. A correlation analysis of these parameters with nuclear positioning revealed regional gene density as the decisive parameter determining the radial positioning of chromatin in the nucleus in contrast to band assignment, replication timing, and transcriptional activity. We demonstrate a polarized distribution of gene-dense vs gene-poor chromatin within CTs with respect to the nuclear border. Whereas we confirm previous reports that a particular gene-dense and transcriptionally highly active region of about 2 Mb on 11p15.5 often loops out from the territory surface, gene-dense and highly expressed sequences were not generally found preferentially at the CT surface as previously suggested.

Domain-wide regulation of gene expression in the human genome

Hinco Gierman — 2007-09-04T18:25:14-00:00

Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1286-1295.

Transcription factor complexes bind to regulatory sequences of genes, providing a system of individual expression regulation. Targets of distinct transcription factors usually map throughout the genome, without clustering. Nevertheless, highly and weakly expressed genes do cluster in separate chromosomal domains with an average size of 8090 genes. We therefore asked whether, besides transcription factors, an additional level of gene expression regulation exists that acts on chromosomal domains. Here we show that identical green fluorescent protein (GFP) reporter constructs integrated at 90 different chromosomal positions obtain expression levels that correspond to the activity of the domains of integration. These domains are up to 80 genes long and can exert an eightfold effect on the expression levels of integrated genes. 3D-FISH shows that active domains of integration have a more open chromatin structure than integration domains with weak activity. These results reveal a novel domain-wide regulatory mechanism that, together with transcription factors, exerts a dual control over gene transcription. 10.1101/gr.6276007

Evolutionary Origin and Maintenance of Coexpressed Gene Clusters in Mammals

Marie Semon — 2006-08-02T10:14:47-00:00

Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1715-1723.

Gene order is not random with regard to gene expression in mammals: coexpressed genes, and in particular housekeeping genes, are clustered along chromosomes more often than expected by chance. To understand the origin of these clusters and to quantify the impact of this phenomenon on genome organization, we analyzed clusters of coexpressed genes in the human and mouse genomes. We show that neighboring genes experience continuous concerted expression changes during evolution, which leads to the formation of coexpressed gene clusters. The pattern of expression within these clusters evolves more slowly than the genomic average. Moreover, by studying gene order evolution, we show that some clusters are maintained by natural selection and, therefore, have a functional significance. However, we also demonstrate that some coexpressed gene clusters are the result of neutral coevolution effects, as illustrated by the clustering of genes escaping inactivation on the X chromosome. Moreover, we show that, although statistically significant, constraints on gene orders have a limited impact on mammalian genome organization, affecting only 3-5% of the pool of human and murine genes. It had been hypothesized that coexpressed gene clusters might correspond to large chromatin domains. In contradiction, we find that most of these clusters contain only 2 genes whose coexpression may be due to transcriptional read-through or the activity of bidirectional promoters. 10.1093/molbev/msl034

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.

Katleen De Preter — 2008-03-20T08:18:07-00:00

Nucleic Acids Res (16 March 2008)

The search for feature enrichment is a widely used method to characterize a set of genes. While several tools have been designed for nominal features such as Gene Ontology annotations or KEGG Pathways, very little has been proposed to tackle numerical features such as the chromosomal positions of genes. For instance, microarray studies typically generate gene lists that are differentially expressed in the sample subgroups under investigation, and when studying diseases caused by genome alterations, it is of great interest to delineate the chromosomal regions that are significantly enriched in these lists. In this article, we present a positional gene enrichment analysis method (PGE) for the identification of chromosomal regions that are significantly enriched in a given set of genes. The strength of our method relies on an original query optimization approach that allows to virtually consider all the possible chromosomal regions for enrichment, and on the multiple testing correction which discriminates truly enriched regions versus those that can occur by chance. We have developed a Web tool implementing this method applied to the human genome (http://www.esat.kuleuven.be/ approximately bioiuser/pge). We validated PGE on published lists of differentially expressed genes. These analyses showed significant overrepresentation of known aberrant chromosomal regions.

Spatial genome organization in the formation of chromosomal translocations.

KJ Meaburn — 2008-07-24T12:43:33-00:00

Seminars in cancer biology, Vol. 17, No. 1. (February 2007), pp. 80-90.

Chromosomal translocations and genomic instability are universal hallmarks of tumor cells. While the molecular mechanisms leading to the formation of translocations are rapidly being elucidated, a cell biological understanding of how chromosomes undergo translocations in the context of the cell nucleus in vivo is largely lacking. The recent realization that genomes are non-randomly arranged within the nuclear space has profound consequences for mechanisms of chromosome translocations. We review here the emerging principles of spatial genome organization and discuss the implications of non-random spatial genome organization for the genesis and specificity of cancerous chromosomal translocations.

Spatial organization of the eukaryotic genome and the action of epigenetic mechanisms

Razin — 2007-02-26T16:37:14-00:00

Russian Journal of Genetics, Vol. 42, No. 12. (December 2006), pp. 1353-1361.

Developmentally-poised chromatin of embryonic stem cells.

TP Rasmussen — 2008-07-24T12:37:54-00:00

Frontiers in bioscience : a journal and virtual library, Vol. 13 (2008), pp. 1568-1577.

Embryonic stem (ES) cells proliferate indefinitely while maintaining pluripotency. The ability of ES cells to form all cell-types of the embryo can occur because they maintain their genome in an epigenetically-potentiated state that is amenable to a broad series of changes in gene expression. Epigenetic stasis and change occur at a molecular level largely through mechanisms involving chromatin and its modification. This review outlines current knowledge of chromatin homeostasis in undifferentiated ES cells, and the remodeling of chromatin during the course of ES cell differentiation. Furthermore, recent evidence shows that the chromatin of many genes in ES cells is configured in developmentally-potentiated states that index them for later transcriptional outcomes. ES cell chromatin also has dynamic physical and kinetic properties that are probably necessary for rapid and pervasive remodeling upon differentiation. Finally, knowledge of nuclear reprogramming activities in oocytes and ES cells are considered, since these activities may also function in the maintenance of pluripotent ES cell chromatin and are also likely involved in subsequent differentiation.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

Leah Barrera — 2007-11-30T07:05:35-00:00

Genome Res. (27 November 2007), gr.6654808.

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified [~]24,000 promoters across these samples, including 16,976 annotated mRNA 5' ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5' end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals. 10.1101/gr.6654808

Early replication and the apoptotic pathway.

SM Cohen — 2008-02-10T04:16:16-00:00

J Cell Physiol, Vol. 213, No. 2. (November 2007), pp. 434-439.

In higher eukaryotes there is a link between time of replication and transcription. It is generally accepted that genes that are actively transcribed are replicated in the first half of S phase while inactive genes replicate in the second half of S phase. We have recently reported that in normal human fibroblasts there are some functionally related genes that replicate at the same time in S phase. This had been previously reported for functionally related genes that are located in clusters, for example the alpha- and beta-globin complexes. We have shown, however, that this also occurs with some functionally related genes that are not organized in a cluster, but rather are distributed throughout the genome. For example, using GOstat analysis of data from our and other groups, we found an overrepresentation of genes involved in the apoptotic process among sequences that are replicated very early (approximately in the first hour of S phase) in both fibroblasts and lymphoblastoid cells. This finding leads us to question how and why the replication of genes in the apoptotic pathway is temporally organized in this manner. Here we discuss the possible explanations and implications of this observation.

Gene Regulation in the Third Dimension

Job Dekker — 2008-03-28T03:07:50-00:00

Science, Vol. 319, No. 5871. (28 March 2008), pp. 1793-1794.

Analysis of the spatial organization of chromosomes reveals complex three-dimensional networks of chromosomal interactions. These interactions affect gene expression at multiple levels, including long-range control by distant enhancers and repressors, coordinated expression of genes, and modification of epigenetic states. Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations. 10.1126/science.1152850

Whole-genome views of chromatin structure

Martin Loden — 2005-05-06T02:10:49-00:00

Chromosome Research, Vol. 13, No. 3. (January 2005), pp. 289-298.

DNA in eukaryotes is packed into chromatin. The basic component of chromatin is the nucleosome consisting of DNA wrapped around a histone octamer. Inside the cell nucleus, chromatin is folded into higher-order structures through various mechanisms, including repositioning of nucleosomes along the DNA, packing of nucleosomes into more condensed 3-dimensional configurations, looping of chromatin fibres, and tethering of chromosomal regions to nuclear structures. Over the past few years, new microarray-based methods have been developed for the genome-wide mapping of various aspects of chromatin structure. These methods are beginning to provide insights into the different types of chromatin and the architectural principles that govern the 3-dimensional organisation of the genome inside the nucleus.