Journal ArticleDOI
Genome-wide nucleosome positioning during embryonic stem cell development
Vladimir B. Teif,Yevhen Vainshtein,Maïwen Caudron-Herger,Jan-Philipp Mallm,Caroline Marth,Thomas Höfer,Karsten Rippe +6 more
TLDR
Nucleosome-depleted regions around transcription start and transcription termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to CpG content or histone methylation marks.Abstract:
Tissue- and disease-specific features of nucleosome positioning have recently been reported. A new study set out to identify features of nucleosome positioning at functional genomic elements during lineage commitment from mouse embryonic stem cells to neural progenitors and embryonic fibroblasts. The results reveal regulatory mechanisms of cell differentiation that involve nucleosome positioning.read more
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Journal Article
The Genomic Code for Nucleosome Positioning
TL;DR: In this article, a nucleosome-DNA interaction model was proposed to predict the genome-wide organization of nucleosomes, and it was shown that genomes encode an intrinsic nucleosomal organization and that this intrinsic organization can explain ∼50% of the in-vivo positions.
Journal ArticleDOI
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P. Nora,Anton Goloborodko,Anne-Laure Valton,Johan H. Gibcus,Alec Uebersohn,Nezar Abdennur,Job Dekker,Leonid A. Mirny,Benoit G. Bruneau +8 more
TL;DR: The data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading, and provides new fundamental insights into the rules governing mammalian genome organization.
Journal ArticleDOI
Cell-free DNA Comprises an in Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin
TL;DR: Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA.
Journal ArticleDOI
Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming
Abdenour Soufi,Meilin Fernandez Garcia,Artur Jaroszewicz,Nebiyu Osman,Matteo Pellegrini,Kenneth S. Zaret +5 more
TL;DR: This work compares the nucleosome and chromatin targeting activities of Oct4, Sox2, and Klf4, which together reprogram somatic cells to pluripotency and provides insight into how pioneer factors can target naive chromatin sites.
Journal ArticleDOI
Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation
Tuncay Baubec,Daniele F Colombo,Christiane Wirbelauer,Juliane Schmidt,Lukas Burger,Arnaud R Krebs,Altuna Akalin,Dirk Schübeler +7 more
TL;DR: Findings reveal how sequence and chromatin cues guide de novo methyltransferase activity to ensure methylome integrity.
References
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Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.