Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Hideharu Hashimoto,Dongxue Wang,John R. Horton,John R. Horton,Xing Zhang,Xing Zhang,Victor G. Corces,Xiaodong Cheng,Xiaodong Cheng +8 more
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TLDR
The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers, modulates the three-dimensional organization of chromatin and is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence.About:
This article is published in Molecular Cell.The article was published on 2017-06-01 and is currently open access. It has received 195 citations till now. The article focuses on the topics: CTCF & Consensus sequence.read more
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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian L. Sanborn,Suhas S.P. Rao,Su-Chen Huang,Neva C. Durand,Miriam H. Huntley,Andrew I. Jewett,Ivan D. Bochkov,Dharmaraj Chinnappan,Ashok Cutkosky,Jian Li,Kristopher Geeting,Doug McKenna,Elena K. Stamenova,Andreas Gnirke,Alexandre Melnikov,Eric S. Lander,Erez Lieberman Aiden +16 more
TL;DR: In this article, high-resolution spatial proximity maps are consistent with a model in which a complex, including the proteins CCCTC-binding factor (CTCF) and cohesin, mediates the formation of loops by a process of extrusion.
Journal ArticleDOI
Dynamic DNA methylation: In the right place at the right time
TL;DR: Recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments are reviewed as well as discuss the molecular mechanisms that connect transcriptional regulation and5mC.
Journal ArticleDOI
The roles of DNA, RNA and histone methylation in ageing and cancer.
Ewa M. Michalak,Ewa M. Michalak,Marian L. Burr,Marian L. Burr,Marian L. Burr,Andrew J. Bannister,Mark A. Dawson,Mark A. Dawson +7 more
TL;DR: The cellular functions of chromatin methylation are discussed and a perspective on the emerging data from early-phase clinical trial therapies that target regulators of DNA and histone methylation is provided.
Journal ArticleDOI
Emerging Evidence of Chromosome Folding by Loop Extrusion.
TL;DR: Predictions from polymer models of loop extrusion with barrier elements and recent experimental studies that provide strong support for loop extrusions are reviewed, focusing on perturbations to CTCF and cohesin assayed via Hi-C in interphase.
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Genome folding through loop extrusion by SMC complexes
TL;DR: The loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of chromosomes (SMC) complexes, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination.
References
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Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
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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 Article
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
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao,Miriam H. Huntley,Neva C. Durand,Elena K. Stamenova,Ivan D. Bochkov,James T. Robinson,James T. Robinson,Adrian L. Sanborn,Ido Machol,Ido Machol,Arina D. Omer,Arina D. Omer,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +15 more
TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
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