CiteULike: Group: G4ID - library [2518 articles]

Maternal Footprints of Southeast Asians in North India.

Kumarasamy Thangaraj — 2008-02-19T10:47:18-00:00

Hum Hered, Vol. 66, No. 1. (28 January 2008), pp. 1-9.

We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNA(Lys) region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal. Copyright (c) 2008 S. Karger AG, Basel.

A SINE species from hippopotamus and its distribution among animal species

2007-09-21T15:44:37-00:00

Mammalian Genome, Vol. 9, No. 7. (5 July 1998), pp. 550-555.

Correspondence to: H. Yasue--> Abstract. Thirty sequences of a short interspersed repetitive element (SINE) were isolated from genomic DNA of Hippopotamus amphibius (hippopotamus). RNA polymerase III split promoter sequence was observed in all of the 30 sequences; and poly(A)-like structure at 3'-end, as well as direct repeat flanking to the repetitive sequence in many of the 30 sequences. A comparison of the consensus sequence of the 30 sequences with sequences in a DNA database (DDBJ/GENBANK/EMBL) revealed 93% homology to the consensus sequence of a whale SINE, CHR-2, and 73% homology to mouse glutamic acid tRNA. Phylogenetic analysis of tRNA-related regions of the sequences with all of the mouse tRNAs revealed that glutamic acid tRNA was genetically closest to the hippopotamus SINE. In addition, the tRNA-related region of the consensus sequence was folded into a cloverleaf structure as with mouse glutamic acid tRNA. These findings led us to conclude that the SINE of hippopotamus was genetically related to a whale SINE, CHR-2 [the hippopotamus SINE was named CHR-2(hippo)] and was a retroposon derived from glutamic acid tRNA. Hipo53 and hipo95, which were the genetically most separated CHR-2(hippo) sequences in the present study, were used as a probe for dot-blot hybridization to examine the distribution of their homologous sequences among animal species. Although the distribution spectra of hipo53 and hipo95 homologous sequences in animal species differed to some extent, large amounts of both sequences were found in Hippopotamus amphibius and Globicephala macrorhynchus (whale); and small amounts in most of the animal species in Artiodactyla examined. These findings indicated that the hippopotamus and whale had more recently branched off from the clade that includes chevrotain and pecorans than the other animal species in the clade. The 30 CHR-2(hippo) sequences were aligned, and the substitution rates among the sequences were calculated with a different substitution rate model for transition and for transversion. The calculation combined with the mutation rate of the pseudogenes (r = 4.6 &#50 109) indicated that CHR-2(hippo) sequences diversified at least 132 million years ago (Myr).

Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls.

J Gatesy — 2007-09-21T14:53:13-00:00

Mol Biol Evol, Vol. 13, No. 7. (September 1996), pp. 954-963.

The inferred transition from terrestrial hoofed mammal to fully aquatic cetacean has been intensively studied with fossil evidence. However, large sections of this remarkable evolutionary sequence are missing. Phylogenetic analysis of extant taxa may help to fill in some of these gaps. In this report, kappa-casein (exon 4) and beta-casein (exon 7) milk protein genes from cetaceans and other placental mammals were PCR-amplified, sequenced, and aligned to previously published sequences. Phylogenetic analyses of the casein data suggest that hippopotamid artiodactyls are more closely related to cetaceans than to other artiodactyls (even-toed hoofed mammals). An analysis of the nuclear casein sequences combined with published mitochondrial cytochrome b DNA sequences also supports the Cetacea/Hippopotamidae sister group. This affinity implies that some of the aquatic traits of cetaceans were derived in the common ancestor of Cetacea and Hippopotamidae. An extant "missing link" to Cetacea may have been overlooked by science since the description of the semiaquatic Hippopotamus in 1758. Paleontological information is grossly inconsistent with this hypothesis. If the casein phylogeny is accurate, large gaps in the fossil record as well as extensive morphological reversals and convergences must be acknowledged.

Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade.

BM Ursing — 2007-09-21T14:52:03-00:00

Proc Biol Sci, Vol. 265, No. 1412. (7 December 1998), pp. 2251-2255.

Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.

Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes.

RG Kleineidam — 2007-09-21T14:50:34-00:00

J Mol Evol, Vol. 48, No. 3. (March 1999), pp. 360-368.

Mammalian secretory ribonucleases (RNases 1) form a family of extensively studied homologous proteins that were already used for phylogenetic analyses at the protein sequence level previously. In this paper we report the determination of six ribonuclease gene sequences of Artiodactyla and two of Cetacea. These sequences have been used with ruminant homologues in phylogenetic analyses that supported a group including hippopotamus and toothed whales, a group of ruminant pancreatic and brain-type ribonucleases, and a group of tylopod sequences containing the Arabian camel pancreatic ribonuclease gene and Arabian and Bactrian camel and alpaca RNase 1 genes of unknown function. In all analyses the pig was the first diverging artiodactyl. This DNA-based tree is compatible to published trees derived from a number of other genes. The differences to those trees obtained with ribonuclease protein sequences can be explained by the influence of convergence of pancreatic RNases from hippopotamus, camel, and ruminants and by taking into account the information from third codon positions in the DNA-based analyses. The evolution of sequence features of ribonucleases such as the distribution of positively charged amino acids and of potential glycosylation sites is described with regard to increased double-stranded RNA cleavage that is observed in several cetacean and artiodactyl RNases which may have no role in ruminant or ruminant-like digestion.

Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion

JBA Okello — 2005-07-24T00:51:09-00:00

Heredity, Vol. aop, No. current.

Neuroproteomics comes of age

James Butcher — 2007-09-19T10:09:47-00:00

The Lancet Neurology, Vol. 6, No. 10. (October 2007), pp. 850-851.

The evolution of genetic networks by non-adaptive processes

Michael Lynch — 2007-09-19T03:51:54-00:00

Nature Reviews Genetics, Vol. 8, No. 10., pp. 803-813.

How geneticists can help reporters to get their story right

Celeste Condit — 2007-09-19T03:51:53-00:00

Nature Reviews Genetics, Vol. 8, No. 10., pp. 815-820.

Gene conversion: mechanisms, evolution and human disease

Jian-Min Chen — 2007-09-19T03:51:54-00:00

Nature Reviews Genetics, Vol. 8, No. 10. (11 September 2007), pp. 762-775.

Splicing in disease: disruption of the splicing code and the decoding machinery

Guey-Shin Wang — 2007-09-19T03:51:54-00:00

Nature Reviews Genetics, Vol. 8, No. 10. (29 August 2007), pp. 749-761.

Dual-specificity splice sites function alternatively as 5' and 3' splice sites

Chaolin Zhang — 2007-09-19T08:58:41-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 38. (18 September 2007), pp. 15028-15033.

As a result of large-scale sequencing projects and recent splicing-microarray studies, estimates of mammalian genes expressing multiple transcripts continue to increase. This expansion of transcript information makes it possible to better characterize alternative splicing events and gain insights into splicing mechanisms and regulation. Here, we describe a class of splice sites that we call dual-specificity splice sites, which we identified through genome-wide, high-quality alignment of mRNA/EST and genome sequences and experimentally verified by RT-PCR. These splice sites can be alternatively recognized as either 5' or 3' splice sites, and the dual splicing is conceptually similar to a pair of mutually exclusive exons separated by a zero-length intron. The dual-splice-site sequences are essentially a composite of canonical 5' and 3' splice-site consensus sequences, with a CAG|GURAG core. The relative use of a dual site as a 5' or 3' splice site can be accurately predicted by assuming competition for specific binding between spliceosomal components involved in recognition of 5' and 3' splice sites, respectively. Dual-specificity splice sites exist in human and mouse, and possibly in other vertebrate species, although most sites are not conserved, suggesting that their origin is recent. We discuss the implications of this unusual splicing pattern for the diverse mechanisms of exon recognition and for gene evolution. 10.1073/pnas.0703773104

Complexin I is required for mammalian sperm acrosomal exocytosis

Longmei Zhao — 2007-09-19T08:54:39-00:00

Developmental Biology, Vol. 309, No. 2. (15 September 2007), pp. 236-244.

Regulated exocytosis in many cells is controlled by the SNARE complex, whose core includes three proteins that promote membrane fusion. Complexins I and II are highly related cytosolic proteins that bind tightly to the assembled SNARE complex and regulate neuronal exocytosis. Like somatic cells, sperm undergo regulated exocytosis; however, sperm release a single large vesicle, the acrosome, whose release has different characteristics than neuronal exocytosis. Acrosomal release is triggered upon sperm adhesion to the mammalian egg extracellular matrix (zona pellucida) to allow penetration of the egg coat. Membrane fusion occurs at multiple points within the acrosome but how fusion is activated and the formation and progression of fusion points is synchronized is unclear. We show that complexins I and II are found in acrosome-intact mature sperm, bind to SNARE complex proteins, and are not detected in sperm after acrosomal exocytosis (acrosome reaction). Although complexin-I-deficient sperm acrosome-react in response to calcium ionophore, they do not acrosome-react in response to egg zona pellucida proteins and have reduced fertilizing ability, in vitro. Complexin II is present in the complexin-I-deficient sperm and its expression is increased in complexin-I-deficient testes. Therefore, complexin I functions in exocytosis in two related but morphologically distinct secretory processes. Sperm are unusual because they express both complexins I and II but have a unique and specific requirement for complexin I.

Is your ?gene of interest? interesting?

Julie Kiefer — 2007-09-19T08:50:23-00:00

Developmental Dynamics, Vol. 236, No. 10. (2007), pp. 2962-2969.

Has a large-scale screen turned up a potential gene-of-interest that you know nothing about? Your computer is a portal to a wealth of information that can save you valuable time and resources. Freely available data can help to determine whether a particular gene is worthy of further research, and what direction that research should take. Presented here are approaches to mining the Internet, including searching popular model organism databases. The primer covers two typical scenarios: the gene of interest is well characterized, or mostly uncharacterized. Also featured are interviews with Monte Westerfield, PhD, Director of the Zebrafish Information Network (ZFIN) online database, and Principal Investigator of the Human Protein Reference Database (HPRD) project, Akhilesh Pandey, MD, PhD. Developmental Dynamics 236:2962-2969, 2007. © 2007 Wiley-Liss, Inc.

Cell-surface transglutaminase undergoes internalization and lysosomal degradation: an essential role for LRP1

Evgeny Zemskov — 2007-09-18T15:39:37-00:00

J Cell Sci, Vol. 120, No. 18. (15 September 2007), pp. 3188-3199.

Tissue transglutaminase functions as a protein crosslinking enzyme and an integrin-binding adhesion co-receptor for fibronectin on the cell surface. These activities of transglutaminase and the involvement of this protein in cell-matrix adhesion, integrin-mediated signaling, cell migration and matrix organization suggest a precise and efficient control of its cell-surface expression. We report a novel mechanism of regulation of surface transglutaminase through internalization and subsequent lysosomal degradation. Constitutive endocytosis of cell-surface transglutaminase depends on plasma membrane cholesterol and the activity of dynamin-2, and involves both clathrin-coated pits and lipid rafts or caveolae. Furthermore, the key matrix ligands of transglutaminase, fibronectin and platelet-derived growth factor, promote its endocytosis from the cell surface. Our results also indicate that transglutaminase interacts in vitro and on the cell surface with the major endocytic receptor, low-density lipoprotein receptor-related protein 1, and demonstrate the requirement for this receptor in the endocytosis of transglutaminase. Finally, a deficiency of this endocytic receptor or blockade of endo-lysosomal function upregulate transglutaminase expression on the cell surface, leading to increased cell adhesion and matrix crosslinking. These findings characterize a previously unknown pathway of transglutaminase internalization and degradation that might be crucial for regulation of its adhesive and signaling functions on the cell surface and reveal a novel functional link between cell-matrix adhesion and endocytosis. 10.1242/jcs.010397

Evolutionary history of 7SL RNA-derived SINEs in Supraprimates.

JO Kriegs — 2007-09-18T10:46:53-00:00

Trends Genet, Vol. 23, No. 4. (April 2007), pp. 158-161.

The evolutionary relationships of 7SL RNA-derived SINEs such as the primate Alu or the rodent B1 elements have hitherto been obscure. We established an unambiguous phylogenetic tree for Supraprimates, and derived intraordinal relationships of the 7SL RNA-derived SINEs. As well as new elements in Tupaia and primates, we also found that the purported ancestral fossil Alu monomer was restricted to Primates, and provide here the first description of a potential chimeric promoter box region in SINEs.

The forensic use of bioinformation: ethical issues

Nuffield — 2007-09-18T10:31:26-00:00

Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae)

Simone Treplin — 2007-09-18T10:25:17-00:00

Molecular Phylogenetics and Evolution, Vol. 43, No. 1. (April 2007), pp. 328-337.

While the monophyly of the order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, both on morphological and molecular grounds, lower phylogenetic relationships have been a continuous matter of debate, especially within oscines. This is particularly true for the rockfowls (genus Picathartes), which phylogenetic classification has been an ongoing puzzle. Sequence-based molecular studies failed in deriving unambiguously resolved and supported hypotheses. We present here a novel approach: use of retrotransposon insertions as phylogenetic markers in passerine birds. Chicken repeat 1 (CR1) is the most important non-LTR retrotransposon in birds. We present two truncated CR1 loci in passerine birds, not only found in representatives of Corvinae (jays, crows and allies), but also in the West-African Picathartes species which provide new evidence for a closer relationship of these species to Corvidae than has previously been thought. Additionally, we show that not only the absence/presence pattern of a CR1 insertion, but also the CR1 sequences themselves contain phylogenetic information.

Is it genomic imprinting or preferential expression?

Hasan Khatib — 2007-09-18T10:09:52-00:00

BioEssays, Vol. 29, No. 10. (2007), pp. 1022-1028.

Imprinted genes are monoallelically expressed in a parent-of-origin-specific manner, but for many genes reported to be imprinted, the occurrence of preferential expression - where both alleles are expressed but one is expressed more strongly than the other in a parent-of-origin-specific way - has been reported. This preferential expression found in genes described as imprinted has not been thoroughly addressed in genomic imprinting studies. To study this phenomenon, 50 genes, reported to be imprinted in the mouse, were chosen for investigation. Preferential expression was observed for 21 of 27 maternally expressed genes. However, only 5 of 23 paternally expressed genes showed preferential expression. Recently, it has been reported that a remarkable proportion of non-imprinted genes show differential allelic expression. If there is overlap between non-imprinted genes that are differentially expressed and imprinted genes that are preferentially expressed, we need to set new definitions of imprinted genes that, in turn, would probably lead to reassessments of the total number of imprinted genes in mammalian species. BioEssays 29:1022-1028, 2007. © 2007 Wiley Periodicals, Inc.

BBC NEWS | UK | Experts call for DNA restrictions

2007-09-18T10:01:26-00:00

The developmental genetics of homology

Günter Wagner — 2007-05-19T03:15:41-00:00

Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 473-479.

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

Albin Sandelin — 2007-05-19T03:15:41-00:00

Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 424-436.

Genome-wide transcription and the implications for genomic organization.

Philipp Kapranov — 2007-05-10T13:57:03-00:00

Nat Rev Genet (8 May 2007)

Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations suggest that genomic architecture is not colinear, but is instead interleaved and modular, and that the same genomic sequences are multifunctional: that is, used for multiple independently regulated transcripts and as regulatory regions. What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?

ISFG: Recommendations on biostatistics in paternity testing

David Gjertson — 2007-09-17T12:56:30-00:00

Forensic Science International: Genetics, Vol. 1, No. 3-4. (December 2007), pp. 223-231.

The Paternity Testing Commission (PTC) of the International Society for Forensic Genetics has taken up the task of establishing the biostatistical recommendations in accordance with the ISO 17025 standards and a previous set of ISFG recommendations specific to the genetic investigations in paternity cases. In the initial set, the PTC recommended that biostatistical evaluations of paternity are based on a likelihood ratio principle - yielding the paternity index, PI. Here, we have made five supplementary biostatistical recommendations. The first recommendation clarifies and defines basic concepts of genetic hypotheses and calculation concerns needed to produce valid PIs. The second and third recommendations address issues associated with population genetics (allele probabilities, Y-chromosome markers, mtDNA, and population substructuring) and special circumstances (deficiency/reconstruction and immigration cases), respectively. The fourth recommendation considers strategies regarding genetic evidence against paternity. The fifth recommendation covers necessary documentation, reporting details and assumptions underlying calculations. The PTC strongly suggests that these recommendations should be adopted by all laboratories involved in paternity testing as the basis for their biostatistical analysis.

Development of an RNAi-based contraceptive

Z Williams — 2007-09-17T12:21:20-00:00

Fertility and Sterility, Vol. 88, No. Supplement 1. (September 2007), S51.

Rethinking the proximodistal axis of the vertebrate limb in the molecular era

Cliff Tabin — 2007-09-17T12:14:22-00:00

Genes Dev., Vol. 21, No. 12. (15 June 2007), pp. 1433-1442.

10.1101/gad.1547407

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).

Y Ruan — 2007-06-16T07:38:42-00:00

Genome Res, Vol. 17, No. 6. (June 2007), pp. 828-838.

Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5' and 3' transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution.

D Zheng — 2007-06-21T08:59:41-00:00

Genome Res, Vol. 17, No. 6. (June 2007), pp. 839-851.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott Margulies — 2007-06-14T00:04:53-00:00

Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774.

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. 10.1101/gr.6034307

Origin of phenotypes: Genes and transcripts.

TR Gingeras — 2007-06-21T09:01:25-00:00

Genome Res, Vol. 17, No. 6. (June 2007), pp. 682-690.

While the concept of a gene has been helpful in defining the relationship of a portion of a genome to a phenotype, this traditional term may not be as useful as it once was. Currently, "gene" has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physical boundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes on the same (sense) and opposite strand (antisense). Moreover, they are often located in intergenic regions, making the genic portions of the human genome an interleaved network of both annotated polyadenylated and nonpolyadenylated transcripts, including splice variants with novel 5' ends extending hundreds of kilobases. This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term "gene" and suggests that transcripts may be used to define the operational unit of a genome.

What is a gene, post-ENCODE? History and updated definition.

MB Gerstein — 2007-06-15T21:49:06-00:00

Genome Res, Vol. 17, No. 6. (June 2007), pp. 669-681.

While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century-from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.

ENCODE: More genomic empowerment.

GM Weinstock — 2007-06-21T09:01:34-00:00

Genome Res, Vol. 17, No. 6. (June 2007), pp. 667-668.

Evolutionarily conserved genes preferentially accumulate introns.

Liran Carmel — 2007-05-30T13:21:59-00:00

Genome Res (10 May 2007)

Introns that interrupt eukaryotic protein-coding sequences are generally thought to be nonfunctional. However, for reasons still poorly understood, positions of many introns are highly conserved in evolution. Previous reconstructions of intron gain and loss events during eukaryotic evolution used a variety of simplified evolutionary models that yielded contradicting conclusions and are not suited to reveal some of the key underlying processes. We combine a comprehensive probabilistic model and an extended data set, including 391 conserved genes from 19 eukaryotes, to uncover previously unnoticed aspects of intron evolution-in particular, to assign intron gain and loss rates to individual genes. The rates of intron gain and loss in a gene show moderate positive correlation. A gene's intron gain rate shows a highly significant negative correlation with the coding-sequence evolution rate; intron loss rate also significantly, but positively, correlates with the sequence evolution rate. Correlations of the opposite signs, albeit less significant ones, are observed between intron gain and loss rates and gene expression level. It is proposed that intron evolution includes a neutral component, which is manifest in the positive correlation between the gain and loss rates and a selection-driven component as reflected in the links between intron gain and loss and sequence evolution. The increased intron gain and decreased intron loss in evolutionarily conserved genes indicate that intron insertion often might be adaptive, whereas some of the intron losses might be deleterious. This apparent functional importance of introns is likely to be due, at least in part, to their multiple effects on gene expression.

Three distinct modes of intron dynamics in the evolution of eukaryotes.

Liran Carmel — 2007-05-30T13:22:45-00:00

Genome Res (10 May 2007)

Several contrasting scenarios have been proposed for the origin and evolution of spliceosomal introns, a hallmark of eukaryotic genes. A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species. It is inferred that a relatively high intron density was reached early, i.e., the last common ancestor of eukaryotes contained >2.15 introns/kilobase, and the last common ancestor of multicellular life forms harbored approximately 3.4 introns/kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last approximately 1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution of the intron-exon structure. The primary, balanced mode, apparently, operates in all lineages. In this mode, intron gain and loss are strongly and positively correlated, in contrast to previous reports on inverse correlation between these processes. The second mode involves an elevated rate of intron loss and is prevalent in several lineages, such as fungi and insects. The third mode, characterized by elevated rate of intron gain, is seen only in deep branches of the tree, indicating that bursts of intron invasion occurred at key points in eukaryotic evolution, such as the origin of animals. Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features.

A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing.

Rodger B Voelker — 2007-05-30T13:20:57-00:00

Genome Res (24 May 2007)

Orthologous mammalian introns contain many highly conserved sequences. Of these sequences, many are likely to represent protein binding sites that are under strong positive selection. In order to identify conserved protein binding sites that are important for splicing, we analyzed the composition of intronic sequences that are conserved between human and six eutherian mammals. We focused on all completely conserved sequences of seven or more nucleotides located in the regions adjacent to splice-junctions. We found that these conserved intronic sequences are enriched in specific motifs, and that many of these motifs are statistically associated with either alternative or constitutive splicing. In validation of our methods, we identified several motifs that are known to play important roles in alternative splicing. In addition, we identified several novel motifs containing GCT that are abundant and are associated with alternative splicing. Furthermore, we demonstrate that, for some of these motifs, conservation is a strong indicator of potential functionality since conserved instances are associated with alternative splicing while nonconserved instances are not. A surprising outcome of this analysis was the identification of a large number of AT-rich motifs that are strongly associated with constitutive splicing. Many of these appear to be novel and may represent conserved intronic splicing enhancers (ISEs). Together these data show that conservation provides important insights into the identification and possible roles of cis-acting intronic sequences important for alternative and constitutive splicing.

Differing patterns of selection in alternative and constitutive splice sites

Kavita Garg — 2007-06-07T21:13:11-00:00

Genome Res. (7 June 2007), gr.6347907.

In addition to allowing identification of putative functional elements as regions having reduced substitution rates, comparison of genome sequences can also provide insights into these elements at the nucleotide level, by indicating the pattern of tolerated substitutions. We created data sets of orthologous alternative and constitutive splice sites in mouse, rat, and human and analyzed the substitutions occurring within them. Our results illuminate differences between alternative and constitutive sites and, in particular, strongly support the idea that alternative sites are under selection to be weak. 10.1101/gr.6347907

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

Andrew Gentles — 2007-09-17T11:57:35-00:00

Genome Res., Vol. 17, No. 7. (1 July 2007), pp. 992-1004.

The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size ([~]3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They cover [~]52% of the genome, higher than in any other amniotic lineage studied to date, and may account for the unusually large genome size. In comparison to other mammals, Monodelphis is significantly rich in non-LTR retrotransposons from the LINE-1, CR1, and RTE families, with >29% of the genome sequence comprised of copies of these elements. Monodelphis has at least four families of RTE, and we report support for horizontal transfer of this non-LTR retrotransposon. In addition to short interspersed elements (SINEs) mobilized by L1, we found several families of SINEs that appear to use RTE elements for mobilization. In contrast to L1-mobilized SINEs, the RTE-mobilized SINEs in Monodelphis appear to shift from G+C-rich to G+C-low regions with time. Endogenous retroviruses have colonized [~]10% of the opossum genome. We found that their density is enhanced in centromeric and/or telomeric regions of most Monodelphis chromosomes. We identified 83 new families of ancient repeats that are highly conserved across amniotic lineages, including 14 LINE-derived repeats; and a novel SINE element, MER131, that may have been exapted as a highly conserved functional noncoding RNA, and whose emergence dates back to [~]300 million years ago. Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals. 10.1101/gr.6070707

Promoting transcriptome diversity

Strausberg — 2007-09-17T11:54:14-00:00

Genome Res., Vol. 17, No. 7. (1 July 2007), pp. 965-968.

Although the number of protein-encoding human genes is more limited than many had estimated, the human transcript repertoire is much more diverse than anticipated. In part, transcript diversity is generated through the use of alternative promoters and alternate splicing. In addition, based on discoveries using technologies such as full-length cDNA libraries and whole genome tiling microarrays, it is now likely that non-protein-encoding transcripts comprise a substantial fraction of the human RNA population. Much attention is currently focused on understanding the role of alternative promoters in generating transcript diversity, both for non-protein-encoding (ncRNAs) and protein-encoding RNAs. 10.1101/gr.6499807

A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids

Daria Babushok — 2007-08-02T08:23:23-00:00

Genome Res., Vol. 17, No. 8. (1 August 2007), pp. 1129-1138.

Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of functional domains are assembled at the RNA level from distinct genes, and the resulting chimera is then reverse transcribed and integrated into the genome by the L1 retrotransposon. We characterized a novel gene, which we termed PIP5K1A and PSMD4-like (PIPSL), created by this mechanism from an intergenic transcript between the phosphatidylinositol-4-phosphate 5-kinase (PIP5K1A) and the 26S proteasome subunit (PSMD4) genes in a hominoid ancestor. PIPSL is transcribed specifically in the testis both in humans and chimpanzees, and is post-transcriptionally repressed by independent mechanisms in these primate lineages. The PIPSL gene encodes a chimeric protein combining the lipid kinase domain of PIP5K1A and the ubiquitin-binding motifs of PSMD4. Strong positive selection on PIPSL led to its rapid divergence from the parental genes PIP5K1A and PSMD4, forming a chimeric protein with a distinct cellular localization and minimal lipid kinase activity, but significant affinity for cellular ubiquitinated proteins. PIPSL is a tightly regulated, testis-specific novel ubiquitin-binding protein formed by an unusual exon-shuffling mechanism in hominoid primates and represents a key example of rapid evolution of a testis-specific gene. 10.1101/gr.6252107

Heritability of alternative splicing in the human genome

Tony Kwan — 2007-08-02T08:27:15-00:00

Genome Res., Vol. 17, No. 8. (1 August 2007), pp. 1210-1218.

Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genome-wide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblastoid cell lines (LCLs) derived from the CEPH HapMap population. We show the identification of transcripts containing sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals. A number of novel alternative splicing events with no previous annotations in either the RefSeq and EST databases were identified, indicating that we are able to discover de novo splicing events. Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes: OAS1, CAST, and CRTAP. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population. In one candidate, we identified a regulatory polymorphism that disrupts a 5' splice site of an exon in the CAST gene, resulting in its exclusion in the mutant allele. This report illustrates that our approach can detect both annotated and novel alternatively spliced variants, and that such variation among individuals is heritable and genetically controlled. 10.1101/gr.6281007

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

Gene copy number variation spanning 60 million years of human and primate evolution.

Laura Dumas — 2007-08-03T01:29:54-00:00

Genome Res (31 July 2007)

Given the evolutionary importance of gene duplication to the emergence of species-specific traits, we have extended the application of cDNA array-based comparative genomic hybridization (aCGH) to survey gene duplications and losses genome-wide across 10 primate species, including human. Using human cDNA arrays that contained 41,126 cDNAs, corresponding to 24,473 unique human genes, we identified 4159 genes that likely represent most of the major lineage-specific gene copy number gains and losses that have occurred in these species over the past 60 million years. We analyzed 1,233,780 gene-to-gene data points and found that gene gains typically outnumbered losses (ratio of gains/losses = 2.34) and these frequently cluster in complex and dynamic genomic regions that are likely to serve as gene nurseries. Almost one-third of all human genes (6696) exhibit an aCGH- predicted change in copy number in one or more of these species, and within-species gene amplification is also evident. Many of the genes identified here are likely to be important to lineage-specific traits including, for example, human-specific duplications of the AQP7 gene, which represent intriguing candidates to underlie the key physiological adaptations in thermoregulation and energy utilization that permitted human endurance running.

Evolution and multilevel optimization of the genetic code.

Tobias Bollenbach — 2007-04-03T05:24:27-00:00

Genome Res (9 March 2007)

The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors.

How similar are amino acid mutations in human genetic diseases and evolution

Hao Wu — 2007-09-17T10:49:50-00:00

Biochemical and Biophysical Research Communications, Vol. 362, No. 2. (19 October 2007), pp. 233-237.

Accumulating evidence indicates that some deleterious mutations responsible for genetic diseases may offer benefits for human to prevent other diseases. Therefore, human genetic diseases and evolution were tentatively regarded as the two sides of the same coin, which stimulated our interest to explore how similar are amino acid mutations in human genetic diseases and evolution. Through a large-scale analysis on amino acid mutation patterns of genetic diseases and evolution of Hominidae (Homo sapiens and Pan troglodytes), it was found that there exist significant correlations between two mutation patterns. Besides, there also exist some evident differences between both mutations, especially those associated with four amino acids C, G, R, and L. These findings are of significance to understanding the subtle connections between human genetic diseases and evolution.

Fluorescent protein FRET: the good, the bad and the ugly

David Piston — 2007-09-17T10:26:58-00:00

Trends in Biochemical Sciences, Vol. 32, No. 9. (September 2007), pp. 407-414.

Dynamic protein interactions play a significant part in many cellular processes. A technique that shows considerable promise in elucidating such interactions is Forster resonance energy transfer (FRET). When combined with multiple, colored fluorescent proteins, FRET permits high spatial resolution assays of protein-protein interactions in living cells. Because FRET signals are usually small, however, their measurement requires careful interpretation and several control experiments. Nevertheless, the use of FRET in cell biological experiments has exploded over the past few years. Here we describe the physical basis of FRET and the fluorescent proteins appropriate for these experiments. We also review the approaches that can be used to measure FRET, with particular emphasis on the potential artifacts associated with each approach.

Marking histone H3 variants: How, when and why?

Alejandra Loyola — 2007-09-17T10:30:39-00:00

Trends in Biochemical Sciences, Vol. 32, No. 9. (September 2007), pp. 425-433.

DNA in eukaryotic cells is compacted into chromatin, a regular repeated structure in which the nucleosome represents the basic unit. The nucleosome not only serves to compact the genetic material but also provides information that affects nuclear functions including DNA replication, repair and transcription. This information is conveyed through numerous combinations of histone post-translational modifications (PTMs) and histone variants. A recent challenge has been to understand how and when these combinations of PTMs are imposed and to what extent they are determined by the choice of a specific histone variant. Here we focus on histone H3 variants and the PTMs that they carry before and after their assembly into chromatin. We review and discuss recent knowledge about how the choice and initial modifications of a specific variant might affect PTM states and eventually the final epigenetic state of a chromosomal domain.

Characterization of human control region sequences for Spanish individuals in a forensic mtDNA data set

Carlos Alvarez — 2007-09-17T10:24:47-00:00

Legal Medicine, Vol. 9, No. 6. (November 2007), pp. 293-304.

Population data on the hypervariable regions of the mitochondrial DNA (mtDNA) genome are used to convey the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, mtDNA profiles of Spanish individuals (n = 312) were analyzed to describe haplogroup distributions and to determine relevant single nucleotide polymorphisms (SNPs) of those haplogroups. All nine common European haplogroups were observed in the sample, and these were divided into subgroups when possible. Haplogroup H was the most common haplogroup. The haplogroups U, J, T, and V were the next most frequent groups, each occurring at a frequency of 6.4% or greater. In addition, African and Asian sequences were present though rare in the samples. The data were compared with and found to be similar to other published data sets. There were 109 SNPs observed in the data set, including 10 positions not previously reported. The most variable sites are consistent with other studies.

Identification of a rare mutation in a TH01 primer binding site

Tomohiro Takayama — 2007-09-17T10:18:59-00:00

Legal Medicine, Vol. 9, No. 6. (November 2007), pp. 289-292.

We experienced a difficult case of TH01 typing. Instability of TH01 allele 9.3 was observed using GenePrint STR System TH01. Allele dropout was observed when an AmpFlSTR Profiler Kit was subsequently used for confirmation of the TH01 type. Use of the PowerPlex 16 System made it possible to detect allele 9.3. As a result of sequencing, a single point mutation (G-to-A transition) located 37 bases upstream of the first TCAT motif of the repeat region was identified as the cause of the allele dropout during use of the AmpFlSTR Profiler Kit. This mutation was located at the 3' end of the forward primers of the AmpFlSTR Profiler Kit and GenePrint STR System TH01.

BBC NEWS | Health | Concern over DNA database access

2007-09-17T10:04:17-00:00

DNA-testing for immigration cases: The risk of erroneous conclusions

Andreas Karlsson — 2007-09-17T10:00:12-00:00

Forensic Science International, Vol. 172, No. 2-3. (25 October 2007), pp. 144-149.

Making the correct decision based on results from DNA analyses and other information in family reunification cases can be complicated for a number of reasons. These include stratified populations, cultural differences in family constellations, families with different population origin, and complicated family relations giving complex pedigrees. The aim of this study was to analyze the risk of erroneous conclusions in immigration cases and to propose alternative procedures to current methods to reduce the risk of making such errors. A simulation model was used to study different issues. For simplicity, we focus on cases which can be formulated as questions about paternity. We present an overview of error rates (of falsely included men as the true father and of falsely excluded true fathers) for fairly standard computations, and we show how these are affected by different factors. For example, adding more DNA markers to a case will decrease the error rates, as will the inclusion of more children. We found that using inappropriate population frequency databases had just minor effects on the error rates, but the likelihood ratios varied from an underestimation of 100 times up to an overestimation of 100,000 times. To reduce the risk of falsely including a man related to the true father we propose a more refined prior including five hypotheses instead of the two normally used. Simulations showed that this method gave reduced error rates compared with standard computations, even when the prior does not exactly correspond to reality.