YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Abraham S. Weintraub,Charles H. Li,Alicia V. Zamudio,Alla A. Sigova,Nancy M. Hannett,Daniel S. Day,Brian J. Abraham,Malkiel A. Cohen,Behnam Nabet,Dennis L. Buckley,Yang Eric Guo,Denes Hnisz,Rudolf Jaenisch,James E. Bradner,Nathanael S. Gray,Richard A. Young +15 more
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TLDR
It is shown that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF.About:
This article is published in Cell.The article was published on 2017-12-14 and is currently open access. It has received 654 citations till now. The article focuses on the topics: Enhancer & Regulation of gene expression.read more
Citations
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Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains.
Ann Boija,Isaac A. Klein,Benjamin R. Sabari,Alessandra Dall’Agnese,Eliot L. Coffey,Alicia V. Zamudio,Charles H. Li,Krishna Shrinivas,John C. Manteiga,Nancy M. Hannett,Brian J. Abraham,Lena K. Afeyan,Yang Eric Guo,Jenna K. Rimel,Charli B. Fant,Jurian Schuijers,Tong Ihn Lee,Dylan J. Taatjes,Richard A. Young +18 more
TL;DR: It is reported that diverse ADs form phase- separated condensates with the Mediator coactivator, suggesting that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensate with Mediation is involved in gene activation.
Journal ArticleDOI
Organizational principles of 3D genome architecture
TL;DR: Observations suggest that the 3D organization of the genome is an emergent property of chromatin and its components, and thus may not be only a determinant but also a consequence of its function.
Journal ArticleDOI
Long-range enhancer-promoter contacts in gene expression control.
TL;DR: The latest understanding of long-range enhancer–promoter crosstalk is discussed, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.
Journal ArticleDOI
The dTAG system for immediate and target-specific protein degradation
Behnam Nabet,Justin M. Roberts,Dennis L. Buckley,Dennis L. Buckley,Joshiawa Paulk,Joshiawa Paulk,Shiva Dastjerdi,Annan Yang,Alan L. Leggett,Michael A. Erb,Matthew A. Lawlor,Amanda Souza,Amanda Souza,Thomas G. Scott,Sarah Vittori,Jennifer A. Perry,Jun Qi,Georg E. Winter,Georg E. Winter,Kwok-Kin Wong,Nathanael S. Gray,James E. Bradner,James E. Bradner +22 more
TL;DR: The dTAG system pairs potent heterobifunctional degraders and extensible tagging strategies to achieve immediate and reversible degradation of divergent proteins, facilitating biological investigation and drug target validation in cells and in mice.
Journal ArticleDOI
Chromatin organization by an interplay of loop extrusion and compartmental segregation
TL;DR: The integrated model faithfully reproduces Hi-C data from puzzling experimental observations where altering loop extrusion also led to changes in compartmentalization, and suggests that chromatin organization on the megabase scale emerges from competition of nonequilibrium active loop extrusions and epigenetically defined compartment structure.
References
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TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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