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
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TLDR
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.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci
Kambiz Mousavi,Hossein Zare,Stefania Dell'Orso,Lars Grøntved,Gustavo Gutierrez-Cruz,Assia Derfoul,Gordon L. Hager,Vittorio Sartorelli +7 more
TL;DR: The data suggest that eRNAs contribute to establishing a cell-type-specific transcriptional circuitry by directing chromatin-remodeling events by regulating genomic access of the transcriptional complex to defined regulatory regions.
Journal ArticleDOI
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
Krishanpal Karmodiya,Arnaud R Krebs,Arnaud R Krebs,Mustapha Oulad-Abdelghani,Hiroshi Kimura,Laszlo Tora +5 more
TL;DR: It is suggested that chromatin modifications, such as H3K9ac and H2K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3 k9 and H3k14 acetylation could be driven by cis regulatory elements such as CpG content at promoters.
Journal ArticleDOI
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
TL;DR: Analysis of chromatin conformation during Drosophila embryogenesis offers insight into when spatial genome organization is first established during development and identifies a key factor that helps trigger this architecture.
Journal ArticleDOI
Modulation of cytokine receptors by IL-2 broadly regulates differentiation into helper T cell lineages
TL;DR: IL-2 influences helper T cell differentiation by modulating the expression of cytokine receptors to help specify and maintain differentiated states.
Journal ArticleDOI
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency
Yael Costa,Junjun Ding,Thorold W. Theunissen,Francesco Faiola,Timothy A. Hore,Pavel V. Shliaha,Miguel Fidalgo,Arven Saunders,Moyra Lawrence,Sabine Dietmann,Satyabrata Das,Dana N. Levasseur,Zhe Li,Mingjiang Xu,Wolf Reik,Wolf Reik,José C. R. Silva,Jianlong Wang +17 more
TL;DR: It is proposed that TET1 is recruited by NANOG to enhance the expression of a subset of key reprogramming target genes, and a new role for 5-methylcytosine hydroxylases in the establishment of naive pluripotency is uncovered.
References
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David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
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Genome-wide location and function of dna binding proteins
TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.