Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

doi:10.1016/J.MOLCEL.2010.05.004

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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Journal Article•DOI•

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Sven Heinz¹, Christopher Benner¹, Nathanael J. Spann¹, Eric Bertolino², Yin C. Lin¹, Peter Laslo³, Jason X. Cheng², Cornelis Murre¹, Harinder Singh⁴, Harinder Singh², Christopher K. Glass¹ - Show less +7 more•Institutions (4)

University of California, San Diego¹, University of Chicago², University of Leeds³, Genentech⁴

28 May 2010-Molecular Cell (NIH Public Access)-Vol. 38, Iss: 4, pp 576-589

TL;DR: 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.

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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.

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Journal Article•DOI•

A rapid and robust method for single cell chromatin accessibility profiling

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Xi Chen¹, Ricardo J. Miragaia¹, Ricardo J. Miragaia², Kedar Nath Natarajan¹, Sarah A. Teichmann¹, Sarah A. Teichmann³ - Show less +2 more•Institutions (3)

Wellcome Trust Sanger Institute¹, MedImmune², European Bioinformatics Institute³

17 Dec 2018-Nature Communications

TL;DR: A simple and robust plate-based single-cell ATAC-seq method that works in fresh and cryopreserved cells and identifies distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors is developed.

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Abstract: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrate that our method works robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors. ATAC-seq is widely used to identify regulatory regions in the genome. Here the authors develop a simple and robust plate-based single-cell ATAC-seq method that works in fresh and cryopreserved cells.

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1,260 citations

Journal Article•DOI•

Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.

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Wen Xiao¹, Samir Adhikari¹, Samir Adhikari², Ujwal Dahal¹, Ujwal Dahal², Yu-Sheng Chen¹, Yu-Sheng Chen², Ya-Juan Hao¹, Ya-Juan Hao², Bao-Fa Sun², Hui-Ying Sun², Hui-Ying Sun¹, Ang Li², Ang Li¹, Xiao-Li Ping², Weiyi Lai¹, Xing Wang¹, Xing Wang², Hai-Li Ma¹, Hai-Li Ma², Chun-Min Huang², Ying Yang², Niu Huang, Guibin Jiang¹, Hailin Wang¹, Qi Zhou¹, Xiu-Jie Wang¹, Yong-Liang Zhao², Yun-Gui Yang¹, Yun-Gui Yang² - Show less +26 more•Institutions (2)

Chinese Academy of Sciences¹, Beijing Institute of Genomics²

18 Feb 2016-Molecular Cell

TL;DR: The findings provide the direct evidence that m(6)A reader YTHDC1 regulates mRNA splicing through recruiting and modulating pre-mRNA splicing factors for their access to the binding regions of targeted mRNAs.

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1,244 citations

Journal Article•DOI•

Modification of Enhancer Chromatin: What, How, and Why?

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Eliezer Calo¹, Joanna Wysocka¹•Institutions (1)

Stanford University¹

07 Mar 2013-Molecular Cell

TL;DR: An overview of enhancer-associated modifications of histones and DNA is given and enzymatic activities involved in their dynamic deposition and removal are discussed and potential downstream effectors of these marks are described.

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1,215 citations

Journal Article•DOI•

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

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Nobuya Koike¹, Seung Hee Yoo¹, Hung Chung Huang¹, Vivek Kumar¹, Choogon Lee², Tae Kyung Kim¹, Joseph S. Takahashi¹ - Show less +3 more•Institutions (2)

University of Texas Southwestern Medical Center¹, Florida State University²

19 Oct 2012-Science

TL;DR: The transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver is interrogated and a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II recruitment, RNA expression, and chromatin states is found.

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Abstract: The mammalian circadian clock involves a transcriptional feed back loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression, and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of messenger RNA (mRNA) cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.

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1,184 citations

Journal Article•DOI•

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

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Moshe Sade-Feldman¹, Moshe Sade-Feldman², Keren Yizhak¹, Stacey L. Bjorgaard², Stacey L. Bjorgaard¹, John P. Ray¹, Carl G. de Boer¹, Russell W. Jenkins², David J. Lieb¹, Jonathan H. Chen¹, Jonathan H. Chen², Dennie T. Frederick², Michal Barzily-Rokni², Samuel S. Freeman¹, Alexandre Reuben³, Paul Hoover¹, Paul Hoover⁴, Alexandra-Chloé Villani², Alexandra-Chloé Villani¹, Elena Ivanova², Andrew Portell², Patrick H. Lizotte², Amir Reza Aref², Jean Pierre Eliane², Marc R. Hammond², Hans Vitzthum², Shauna M. Blackmon², Bo Li², Bo Li¹, Vancheswaran Gopalakrishnan³, Sangeetha M. Reddy³, Zachary A. Cooper³, Cloud P. Paweletz², David A. Barbie², Anat Stemmer-Rachamimov², Keith T. Flaherty², Jennifer A. Wargo³, Genevieve M. Boland², Ryan J. Sullivan², Gad Getz, Nir Hacohen², Nir Hacohen¹ - Show less +38 more•Institutions (4)

Massachusetts Institute of Technology¹, Harvard University², University of Texas MD Anderson Cancer Center³, Brigham and Women's Hospital⁴

01 Nov 2018-Cell

TL;DR: The study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy by targeting novel combinations of factors in exhausted cells.

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1,162 citations

Additional excerpts

...…josh/biophysicsweb/ GOMER/index.html CIS-BP database (Weirauch et al., 2014) http://cisbp.ccbr.utoronto.ca/ HOMER version 4.9 (Heinz et al., 2010) http://homer.ucsd.edu/homer/download.html edgeR 3.14.0 (Robinson et al., 2010)…...
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References

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Open Access

More filters

Journal Article•DOI•

High-resolution profiling of histone methylations in the human genome.

[...]

Artem Barski¹, Suresh Cuddapah¹, Kairong Cui¹, Tae-Young Roh¹, Dustin E. Schones¹, Zhibin Wang¹, Gang Wei¹, Iouri Chepelev², Keji Zhao¹ - Show less +5 more•Institutions (2)

National Institutes of Health¹, University of California, Los Angeles²

18 May 2007-Cell

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.

...read moreread less

6,488 citations

"Simple Combinations of Lineage-Dete..." refers background or methods in this paper

...…positions, DNase hypersensitivity, and mononucleosomal ChIP-Seq for a wide range of histone modifications are available, allowing precise determination of nucleosome positions, chromatin accessibility, and histone modifications (Barski et al., 2007; Boyle et al., 2008; Schones et al., 2008)....
[...]
...In this cell type, genome-wide data for nucleosome positions, DNase hypersensitivity, and mononucleosomal ChIP-Seq for a wide range of histone modifications are available, allowing precise determination of nucleosome positions, chromatin accessibility, and histone modifications (Barski et al., 2007; Boyle et al., 2008; Schones et al., 2008)....
[...]
...1 Binding Programs in Macrophages and B Cells We initially performed chromatin immunoprecipitation-coupled deep sequencing (ChIP-Seq) (Barski et al., 2007) to define the PU....
[...]
..., 2008), human CD4 T cells (Barski et al., 2007), and CD36 erythrocyte precursors (Cui et al....
[...]
...…other cell types, we performed de novo motif analysis on H3K4me1/H3K4me3 ChIP-Seq data sets from mouse embryonic stem cells (Meissner et al., 2008; Mikkelsen et al., 2007), liver (Wederell et al., 2008), human CD4+ T cells (Barski et al., 2007), and CD36+ erythrocyte precursors (Cui et al., 2009)....
[...]

Journal Article•DOI•

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

[...]

Tarjei S. Mikkelsen¹, Manching Ku¹, Manching Ku², David B. Jaffe¹, Biju Issac¹, Biju Issac², Erez Lieberman Aiden¹, Erez Lieberman Aiden³, Georgia Giannoukos¹, Pablo Alvarez¹, William Brockman¹, Tae Kyung Kim⁴, Richard Koche², Richard Koche¹, Richard Koche³, William Lee¹, Eric M. Mendenhall¹, Eric M. Mendenhall², Aisling O'Donovan², Aviva Presser¹, Carsten Russ¹, Xiaohui Xie¹, Alexander Meissner³, Marius Wernig³, Rudolf Jaenisch³, Chad Nusbaum¹, Eric S. Lander¹, Eric S. Lander³, Bradley E. Bernstein¹, Bradley E. Bernstein² - Show less +26 more•Institutions (4)

Broad Institute¹, Harvard University², Massachusetts Institute of Technology³, Boston Children's Hospital⁴

02 Aug 2007-Nature

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.

...read moreread less

Abstract: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences Lysine 4 and lysine 9 trimethylation marks imprinting control regions Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations

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4,166 citations

"Simple Combinations of Lineage-Dete..." refers methods in this paper

...To determine whether there is an analogous relationship between promoter-distal H3K4me1 and binding sites for transcription factors in other cell types, we performed de novo motif analysis on H3K4me1/H3K4me3 ChIP-Seq data sets from mouse embryonic stem cells (Meissner et al., 2008; Mikkelsen et al., 2007), liver (Wederell et al....
[...]
...…other cell types, we performed de novo motif analysis on H3K4me1/H3K4me3 ChIP-Seq data sets from mouse embryonic stem cells (Meissner et al., 2008; Mikkelsen et al., 2007), liver (Wederell et al., 2008), human CD4+ T cells (Barski et al., 2007), and CD36+ erythrocyte precursors (Cui et al., 2009)....
[...]

Journal Article•DOI•

RAG-1-deficient mice have no mature B and T lymphocytes

[...]

Peter Mombaerts¹, John Iacomini¹, Randall S. Johnson², Karl Herrup, Susumu Tonegawa¹, Virginia E. Papaioannou³ - Show less +2 more•Institutions (3)

Massachusetts Institute of Technology¹, Harvard University², Tufts University³

06 Mar 1992-Cell

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.

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2,821 citations

"Simple Combinations of Lineage-Dete..." refers background in this paper

...…in B lineage progenitors devoid of both E2A and EBF (E2A / ), EBF only (EBF / ), or control cells that express both factors (Rag1 / ), which are arrested at successive stages in B cell development (Dias et al., 2008; Ikawa et al., 2004; Lin and Grosschedl, 1995; Mombaerts et al., 1992) (Figure 1A)....
[...]
...We addressed this question in B lineage progenitors devoid of both E2A and EBF (E2A / ), EBF only (EBF / ), or control cells that express both factors (Rag1 / ), which are arrested at successive stages in B cell development (Dias et al., 2008; Ikawa et al., 2004; Lin and Grosschedl, 1995; Mombaerts et al., 1992) (Figure 1A)....
[...]

Journal Article•DOI•

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

[...]

Xi Chen¹, Han Xu¹, Ping Yuan¹, Fang Fang¹, Fang Fang², Mikael Huss¹, Vinsensius B. Vega¹, Eleanor Wong¹, Yuriy L. Orlov¹, Weiwei Zhang², Weiwei Zhang¹, Jianming Jiang², Jianming Jiang¹, Yuin-Han Loh¹, Yuin-Han Loh², Hock Chuan Yeo¹, Zhen Xuan Yeo¹, Vipin Narang¹, Kunde R Govindarajan¹, Bernard Leong¹, Atif Shahab¹, Yijun Ruan¹, Guillaume Bourque¹, Wing-Kin Sung¹, Neil D. Clarke¹, Chia-Lin Wei¹, Huck-Hui Ng², Huck-Hui Ng¹ - Show less +24 more•Institutions (2)

Genome Institute of Singapore¹, National University of Singapore²

13 Jun 2008-Cell

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.

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2,519 citations

"Simple Combinations of Lineage-Dete..." refers background in this paper

...This model offers an explanation for the extensive genome-wide and cell typespecific colocalization of transcription factors observed in various previous studies (Chen et al., 2008; MacArthur et al., 2009) and provides insights into how simple combinations of lineage-restricted transcription factors on a genome-wide scale can specify promoter-distal cis-regulatory elements ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs....
[...]
...…an explanation for the extensive genome-wide and cell typespecific colocalization of transcription factors observed in various previous studies (Chen et al., 2008; MacArthur et al., 2009) and provides insights into how simple combinations of lineage-restricted transcription factors on a…...
[...]
...Comparisons of the genome-wide binding patterns of different transcription factors in a variety of species and cell types have generated two major insights regarding transcription factor binding patterns: (1) different factors in the same cell type tend to colocalize on a genome-wide scale (Chen et al., 2008; MacArthur et al., 2009), and (2) the same factor in different cell types or at different stages of development exhibits different genome-wide binding patterns (Lupien et al....
[...]
...…insights regarding transcription factor binding patterns: (1) different factors in the same cell type tend to colocalize on a genome-wide scale (Chen et al., 2008; MacArthur et al., 2009), and (2) the same factor in different cell types or at different stages of development exhibits different…...
[...]

Journal Article•DOI•

Genome-scale DNA methylation maps of pluripotent and differentiated cells

[...]

Alexander Meissner¹, Tarjei S. Mikkelsen², Tarjei S. Mikkelsen¹, Hongcang Gu², Marius Wernig¹, Jacob H. Hanna¹, Andrey Sivachenko², Xiaolan Zhang², Bradley E. Bernstein³, Bradley E. Bernstein², Chad Nusbaum², David B. Jaffe², Andreas Gnirke², Rudolf Jaenisch¹, Eric S. Lander - Show less +11 more•Institutions (3)

Massachusetts Institute of Technology¹, Broad Institute², Harvard University³

07 Aug 2008-Nature

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.

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Abstract: DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

...read moreread less

2,482 citations

"Simple Combinations of Lineage-Dete..." refers methods in this paper

...To determine whether there is an analogous relationship between promoter-distal H3K4me1 and binding sites for transcription factors in other cell types, we performed de novo motif analysis on H3K4me1/H3K4me3 ChIP-Seq data sets from mouse embryonic stem cells (Meissner et al., 2008; Mikkelsen et al., 2007), liver (Wederell et al....
[...]
...…factors in other cell types, we performed de novo motif analysis on H3K4me1/H3K4me3 ChIP-Seq data sets from mouse embryonic stem cells (Meissner et al., 2008; Mikkelsen et al., 2007), liver (Wederell et al., 2008), human CD4+ T cells (Barski et al., 2007), and CD36+ erythrocyte…...
[...]