Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
Reads0
Chats0
TLDR
It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.About:
This article is published in Molecular Cell.The article was published on 2010-05-28 and is currently open access. It has received 9620 citations till now. The article focuses on the topics: Pioneer factor & General transcription factor.read more
Citations
More filters
Journal ArticleDOI
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Alexander Nord,Matthew J. Blow,Matthew J. Blow,Catia Attanasio,Jennifer A. Akiyama,Amy Holt,Roya Hosseini,Sengthavy Phouanenavong,Ingrid Plajzer-Frick,Malak Shoukry,Veena Afzal,John L.R. Rubenstein,Edward M. Rubin,Edward M. Rubin,Len A. Pennacchio,Len A. Pennacchio,Axel Visel,Axel Visel,Axel Visel +18 more
TL;DR: The dynamic enhancer activities uncovered in this study illuminate rapid and pervasive temporal in vivo changes in enhancer usage that underlie processes central to development and disease.
Journal ArticleDOI
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.
Olivia Corradin,Alina Saiakhova,Batool Akhtar-Zaidi,Lois Myeroff,Joseph Willis,Richard Cowper-Sal·lari,Mathieu Lupien,Sanford D. Markowitz,Peter C. Scacheri +8 more
TL;DR: Evidence is provided that for six common autoimmune disorders, the GWAS association arises from multiple polymorphisms in LD that map to clusters of enhancer elements active in the same cell type, which suggests a "multiple enhancer variant" hypothesis for common traits.
Journal ArticleDOI
N 6 -methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription.
Jun Liu,Jun Liu,Xiaoyang Dou,Xiaoyang Dou,Chuanyuan Chen,Chuanyuan Chen,Chuan Chen,Chang Liu,Chang Liu,Meng Michelle Xu,Siqi Zhao,Siqi Zhao,Bin Shen,Yawei Gao,Dali Han,Chuan He,Chuan He +16 more
TL;DR: Results reveal that m6A on carRNAs can globally tune chromatin state and transcription and that knockout of the m 6A writer Mettl3 or the nuclear reader Ythdc1 in mouse embryonic stem cells increases chromatin accessibility and activates transcription in anm6A-dependent manner.
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.
References
More filters
Journal ArticleDOI
High-resolution profiling of histone methylations in the human genome.
Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen,Manching Ku,Manching Ku,David B. Jaffe,Biju Issac,Biju Issac,Erez Lieberman Aiden,Erez Lieberman Aiden,Georgia Giannoukos,Pablo Alvarez,William Brockman,Tae Kyung Kim,Richard Koche,Richard Koche,Richard Koche,William Lee,Eric M. Mendenhall,Eric M. Mendenhall,Aisling O'Donovan,Aviva Presser,Carsten Russ,Xiaohui Xie,Alexander Meissner,Marius Wernig,Rudolf Jaenisch,Chad Nusbaum,Eric S. Lander,Eric S. Lander,Bradley E. Bernstein,Bradley E. Bernstein +29 more
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.
Journal ArticleDOI
RAG-1-deficient mice have no mature B and T lymphocytes
Peter Mombaerts,John Iacomini,Randall S. Johnson,Karl Herrup,Susumu Tonegawa,Virginia E. Papaioannou +5 more
TL;DR: The introduction of a mutation in RAG-1 into the germline of mice via gene targeting in embryonic stem cells is described and it is shown that this mutation either activates or catalyzes the V(D)J recombination reaction of immunoglobulin and T cell receptor genes.
Journal ArticleDOI
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
Xi Chen,Han Xu,Ping Yuan,Fang Fang,Fang Fang,Mikael Huss,Vinsensius B. Vega,Eleanor Wong,Yuriy L. Orlov,Weiwei Zhang,Weiwei Zhang,Jianming Jiang,Jianming Jiang,Yuin-Han Loh,Yuin-Han Loh,Hock Chuan Yeo,Zhen Xuan Yeo,Vipin Narang,Kunde R Govindarajan,Bernard Leong,Atif Shahab,Yijun Ruan,Guillaume Bourque,Wing-Kin Sung,Neil D. Clarke,Chia-Lin Wei,Huck-Hui Ng,Huck-Hui Ng +27 more
TL;DR: This study uses chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing to map the locations of TF-binding sites and identifies important features of the transcriptional regulatory networks that define ES-cell identity.
Journal ArticleDOI
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Alexander Meissner,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Hongcang Gu,Marius Wernig,Jacob H. Hanna,Andrey Sivachenko,Xiaolan Zhang,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,David B. Jaffe,Andreas Gnirke,Rudolf Jaenisch,Eric S. Lander +14 more
TL;DR: Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.