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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Chromatin accessibility: a window into the genome
Maria Tsompana,Michael J. Buck +1 more
TL;DR: The limitations and advantages of current genome-wide chromatin accessibility assays are discussed with especial attention on experimental precautions and sequence data analysis and the perspective on future improvements necessary for moving the field of chromatin profiling forward is concluded.
Journal ArticleDOI
The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming
Abed AlFatah Mansour,Ohad Gafni,Leehee Weinberger,Asaf Zviran,Muneef Ayyash,Yoach Rais,Vladislav Krupalnik,Mirie Zerbib,Daniela Amann-Zalcenstein,Itay Maza,Shay Geula,Sergey Viukov,Liad Holtzman,Ariel Pribluda,Eli Canaani,Shirley Horn-Saban,Ido Amit,Noa Novershtern,Jacob H. Hanna +18 more
TL;DR: It is shown in mice and humans that the histone H3 methylated Lys’27 (H3K27) demethylase Utx regulates the efficient induction, rather than maintenance, of pluripotency, and highlights the principle that molecular regulators mediating loss of repressive chromatin during in vivo germ cell reprograming can be co-opted during in vitro reprogramming towards ground state pluripOTency.
Journal ArticleDOI
A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia
Daniel Herranz,Alberto Ambesi-Impiombato,Teresa Palomero,Stephanie A. Schnell,Laura Belver,Agnieszka A. Wendorff,Luyao Xu,Mireia Castillo-Martin,David Llobet-Navas,Carlos Cordon-Cardo,Emmanuelle Clappier,Jean Soulier,Jean Soulier,Adolfo A. Ferrando +13 more
TL;DR: This work identifies N-Me as a long-range oncogenic enhancer implicated directly in the pathogenesis of human leukemia and highlights the importance of the NOTCH1-MYC regulatory axis in T cell transformation and as a therapeutic target in T-ALL.
Journal ArticleDOI
Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types
Kyle M. Loh,Angela Chen,Pang Wei Koh,Tianda Z. Deng,Rahul Sinha,Jonathan M. Tsai,Amira A. Barkal,Kimberle Shen,Rajan Jain,Rachel M. Morganti,Ng Shyh-Chang,Nathaniel B. Fernhoff,Benson M. George,Gerlinde Wernig,Rachel E.A. Salomon,Zhenghao Chen,Hannes Vogel,Jonathan A. Epstein,Anshul Kundaje,William S. Talbot,Philip A. Beachy,Lay Teng Ang,Irving L. Weissman +22 more
TL;DR: The extrinsic signals controlling each binary lineage decision were defined, enabling us to logically block differentiation toward unwanted fates and rapidly steer pluripotent stem cells toward 80%-99% pure human mesodermal lineages at most branchpoints.
Journal ArticleDOI
An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.
Bernard Ng,Charles C. White,Hans-Ulrich Klein,Hans-Ulrich Klein,Solveig K. Sieberts,Cristin McCabe,Ellis Patrick,Jishu Xu,Lei Yu,Chris Gaiteri,David A. Bennett,Sara Mostafavi,Sara Mostafavi,Philip L. De Jager,Philip L. De Jager +14 more
TL;DR: A multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types is reported.
References
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TL;DR: The application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells is reported and it is shown that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms.
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Genome-Wide Mapping of in Vivo Protein-DNA Interactions
David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
PatentDOI
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.