Journal ArticleDOI
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Stefan Bonn,Robert P. Zinzen,Charles Girardot,E. Hilary Gustafson,Alexis Perez-Gonzalez,Nicolas Delhomme,Yad Ghavi-Helm,Bartek Wilczyński,Andrew Riddell,Eileen E. M. Furlong +9 more
TLDR
This new approach to obtain cell type–specific information on chromatin state and RNA polymerase II (Pol II) occupancy within the multicellular Drosophila melanogaster embryo identifies dynamic enhancer usage, an essential step in deciphering developmental networks.Abstract:
Chromatin modifications are associated with many aspects of gene expression, yet their role in cellular transitions during development remains elusive. Here, we use a new approach to obtain cell type-specific information on chromatin state and RNA polymerase II (Pol II) occupancy within the multicellular Drosophila melanogaster embryo. We directly assessed the relationship between chromatin modifications and the spatio-temporal activity of enhancers. Rather than having a unique chromatin state, active developmental enhancers show heterogeneous histone modifications and Pol II occupancy. Despite this complexity, combined chromatin signatures and Pol II presence are sufficient to predict enhancer activity de novo. Pol II recruitment is highly predictive of the timing of enhancer activity and seems dependent on the timing and location of transcription factor binding. Chromatin modifications typically demarcate large regulatory regions encompassing multiple enhancers, whereas local changes in nucleosome positioning and Pol II occupancy delineate single active enhancers. This cell type-specific view identifies dynamic enhancer usage, an essential step in deciphering developmental networks.read more
Citations
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Journal ArticleDOI
Transcription factors: from enhancer binding to developmental control.
TL;DR: Current knowledge of transcription factor function from genomic and genetic studies is reviewed and how different strategies, including extensive cooperative regulation, progressive priming of regulatory elements, and the integration of activities from multiple enhancers, confer specificity and robustness to transcriptional regulation during development are discussed.
Journal ArticleDOI
Modification of Enhancer Chromatin: What, How, and Why?
Eliezer Calo,Joanna Wysocka +1 more
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.
Journal ArticleDOI
Transcriptional enhancers: from properties to genome-wide predictions.
TL;DR: How properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies are discussed and recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity are covered.
Journal ArticleDOI
Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Cosmas D. Arnold,Daniel Gerlach,Christoph Stelzer,Łukasz M. Boryń,Martina Rath,Alexander Stark +5 more
TL;DR: STARR-seq identifies thousands of cell type–specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map, revealing the highly complex regulation of transcription.
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.
References
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Journal ArticleDOI
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Journal ArticleDOI
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Journal ArticleDOI
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TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
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
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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
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Jason Ernst,Pouya Kheradpour,Pouya Kheradpour,Tarjei S. Mikkelsen,Noam Shoresh,Lucas D. Ward,Lucas D. Ward,Charles B. Epstein,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Manching Ku,Manching Ku,Manching Ku,Timothy Durham,Manolis Kellis,Manolis Kellis,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein +20 more