Nucleosome positioning signals in genomic DNA Export

@article{Peckham2007, abstract = {10.1101/gr.6101007 Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of whose nucleosome binding affinities have been experimentally determined () to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of and identified strong periodicity within 199 center-aligned mononucleosomes studied recently () despite there being no periodicity information used to train the support vector machine. Our analysis suggests that only a subset of nucleosomes are likely to be positioned by intrinsic sequence signals. This observation is consistent with the available experimental data and is inconsistent with the proposal of a nucleosome positioning code. Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in .}, author = {Peckham, Heather E. and Thurman, Robert E. and Fu, Yutao and Stamatoyannopoulos, John A. and Noble, William S. and Struhl, Kevin and Weng, Zhiping}, citeulike-article-id = {1446924}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.6101007}, citeulike-linkout-1 = {http://genome.cshlp.org/content/17/8/1170.full.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/17/8/1170.full.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/17/8/1170}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17620451}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17620451}, day = {9}, doi = {10.1101/gr.6101007}, journal = {Genome Research}, keywords = {nucleosome, simulation, statistics}, month = {August}, number = {8}, pages = {1170--1177}, posted-at = {2009-04-28 12:30:26}, priority = {2}, title = {Nucleosome positioning signals in genomic DNA}, url = {http://dx.doi.org/10.1101/gr.6101007}, volume = {17}, year = {2007} }

TY - JOUR ID - Peckham2007 L3 - citeulike-article-id:1446924 N2 - 10.1101/gr.6101007 Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of whose nucleosome binding affinities have been experimentally determined () to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of and identified strong periodicity within 199 center-aligned mononucleosomes studied recently () despite there being no periodicity information used to train the support vector machine. Our analysis suggests that only a subset of nucleosomes are likely to be positioned by intrinsic sequence signals. This observation is consistent with the available experimental data and is inconsistent with the proposal of a nucleosome positioning code. Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in . IS - 8 JF - Genome Research EP - 1177 TI - Nucleosome positioning signals in genomic DNA VL - 17 SP - 1170 KW - nucleosome KW - simulation KW - statistics AU - Peckham, Heather AU - Thurman, Robert AU - Fu, Yutao AU - Stamatoyannopoulos, John AU - Noble, William AU - Struhl, Kevin AU - Weng, Zhiping PY - 2007/08/09/ UR - http://dx.doi.org/10.1101/gr.6101007 ER -