Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription
Minna U. Kaikkonen,Nathanael J. Spann,Sven Heinz,Casey E. Romanoski,Karmel A. Allison,Joshua D. Stender,Hyun B. Chun,David F. Tough,Rab K. Prinjha,Christopher Benner,Christopher K. Glass +10 more
TLDR
An essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts is suggested.About:
This article is published in Molecular Cell.The article was published on 2013-08-08 and is currently open access. It has received 584 citations till now. The article focuses on the topics: Enhancer RNAs & Enhancer.read more
Citations
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Trained immunity: A program of innate immune memory in health and disease
Mihai G. Netea,Leo A. B. Joosten,Eicke Latz,Kingston H. G. Mills,Gioacchino Natoli,Hendrik G. Stunnenberg,Luke A. J. O'Neill,Ramnik J. Xavier +7 more
TL;DR: Proof-of-principle experimental studies support the hypothesis that trained immunity is one of the main immunological processes that mediate the nonspecific protective effects against infections induced by vaccines, such as bacillus Calmette-Guérin or measles vaccination.
Journal ArticleDOI
Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities
David Gosselin,Verena M. Link,Casey E. Romanoski,Gregory J. Fonseca,Dawn Z Eichenfield,Nathanael J. Spann,Joshua D. Stender,Hyun B. Chun,Hannah Garner,Frederic Geissmann,Christopher K. Glass +10 more
TL;DR: It is found that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers.
Journal ArticleDOI
The selection and function of cell type-specific enhancers
TL;DR: The human body contains several hundred cell types, all of which share the same genome, and much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers, which influences the functions of enhancers and super-enhancers.
Journal ArticleDOI
An environment-dependent transcriptional network specifies human microglia identity
David Gosselin,Dylan Skola,Nicole G. Coufal,Nicole G. Coufal,Inge R. Holtman,Inge R. Holtman,Johannes C. M. Schlachetzki,Eniko Sajti,Baptiste N. Jaeger,Carolyn O’Connor,Conor Fitzpatrick,Martina P. Pasillas,Monique Pena,Amy Adair,David D. Gonda,Michael J. Levy,Richard M. Ransohoff,Fred H. Gage,Christopher K. Glass +18 more
TL;DR: The transcriptomes and DNA regulatory elements of human microglia ex vivo and in vitro in comparison to the mouse are defined and systematically relate these features to expression of genes associated with genome-wide association study (GWAS) risk alleles or exhibiting altered expression in neurodegenerative diseases and psychiatric disorders.
Journal ArticleDOI
The multidimensional mechanisms of long noncoding RNA function
TL;DR: The functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function are discussed and some mechanisms are shared with other types of genes.
References
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An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
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
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.
Journal ArticleDOI
Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing
Ru Cao,Liangjun Wang,Hengbin Wang,Li Xia,Hediye Erdjument-Bromage,Paul Tempst,Richard S. Jones,Yi Zhang +7 more
TL;DR: The purification and characterization of an EED-EZH2 complex, the human counterpart of the Drosophila ESC-E(Z) complex, is reported, and it is demonstrated that the complex specifically methylates nucleosomal histone H3 at lysine 27 (H3-K27).
Journal ArticleDOI
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Menno P. Creyghton,Albert W. Cheng,G. Grant Welstead,Tristan Kooistra,Bryce W. Carey,Eveline J. Steine,Jacob H. Hanna,Michael A. Lodato,Garrett M. Frampton,Phillip A. Sharp,Laurie A. Boyer,Richard A. Young,Rudolf Jaenisch +12 more
TL;DR: The epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse is interrogated and it is found that histone H3K27ac distinguishes active enhancers from inactive/poised enhancers and poised enhancer networks provide clues to unrealized developmental programs.
Journal ArticleDOI
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
TL;DR: A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.
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