ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide
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TLDR
This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin, which can be used to infer regions of increased accessibility, as well as to map regions of transcription‐factor binding and nucleosome position.Abstract:
This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome.read more
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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
M. Ryan Corces,Alexandro E. Trevino,Emily G. Hamilton,Peyton Greenside,Nicholas A Sinnott-Armstrong,Sam Vesuna,Ansuman T. Satpathy,Adam J. Rubin,Kathleen S. Montine,Beijing Wu,Arwa Kathiria,Seung Woo Cho,Maxwell R. Mumbach,Ava C. Carter,Maya Kasowski,Lisa A. Orloff,Viviana I. Risca,Anshul Kundaje,Paul A. Khavari,Thomas J. Montine,William J. Greenleaf,Howard Y. Chang +21 more
TL;DR: The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures.
Journal ArticleDOI
Chromatin accessibility and the regulatory epigenome.
TL;DR: The goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
Journal ArticleDOI
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
M. Ryan Corces,Jason D. Buenrostro,Jason D. Buenrostro,Beijing Wu,Peyton Greenside,Steven M. Chan,Julie L. Koenig,Michael Snyder,Jonathan K. Pritchard,Jonathan K. Pritchard,Anshul Kundaje,William J. Greenleaf,Ravindra Majeti,Howard Y. Chang +13 more
TL;DR: The chromatin accessibility and transcriptional landscapes in 13 human primary blood cell types that span the hematopoietic hierarchy are defined and 'enhancer cytometry' is enabled for enumeration of pure cell types from complex populations.
Journal ArticleDOI
The chromatin accessibility landscape of primary human cancers
M. Ryan Corces,Jeffrey M. Granja,Shadi Shams,Bryan H. Louie,Jose A. Seoane,Wanding Zhou,Tiago C. Silva,Tiago C. Silva,Clarice S. Groeneveld,Christopher K. Wong,Seung Woo Cho,Ansuman T. Satpathy,Maxwell R. Mumbach,Katherine A. Hoadley,A. Gordon Robertson,Nathan C. Sheffield,Ina Felau,Mauro A. A. Castro,Benjamin P. Berman,Louis M. Staudt,Jean C. Zenklusen,Peter W. Laird,Christina Curtis,William J. Greenleaf,Howard Y. Chang +24 more
TL;DR: These chromatin accessibility profiles identify cancer- and tissue-specific DNA regulatory elements that enable classification of tumor subtypes with newly recognized prognostic importance, and identify distinct TF activities in cancer based on differences in the inferred patterns of TF-DNA interaction and gene expression.
Journal ArticleDOI
A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing
Deng Pan,Aya Kobayashi,Aya Kobayashi,Peng Jiang,Lucas Ferrari de Andrade,Rong En Tay,Adrienne M. Luoma,Daphne Tsoucas,Xintao Qiu,Klothilda Lim,Prakash Rao,Henry W. Long,Guo-Cheng Yuan,John G. Doench,Myles Brown,X. Shirley Liu,Kai W. Wucherpfennig +16 more
TL;DR: A genome-scale CRISPR-Cas9 screen was used to identify mechanisms of tumor cell resistance to killing by cytotoxic T cells, the central effectors of antitumor immunity.
References
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