CTCF: an architectural protein bridging genome topology and function
Chin-Tong Ong,Victor G. Corces +1 more
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TLDR
Although CTCF has been assigned various roles that are often contradictory, new results now help to draw a unifying model to explain the many functions of this protein.Abstract:
CCCTC-binding factor (CTCF) is a DNA-binding protein that has various, often seemingly contradictory, roles in gene regulation. This Review describes these disparate functions and how the context-dependent looping of DNA regions by CTCF is emerging as a potential unifying mechanism that underpins these diverse roles.read more
Citations
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Journal ArticleDOI
Cell-free DNA Comprises an in Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin
TL;DR: Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA.
Journal ArticleDOI
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
Zhonghui Tang,Oscar Junhong Luo,Xingwang Li,Meizhen Zheng,Jacqueline Jufen Zhu,Przemyslaw Szalaj,Pawel Trzaskoma,Adriana Magalska,Jakub Wlodarczyk,Blazej Ruszczycki,Paul J. Michalski,Emaly Piecuch,Ping Wang,Danjuan Wang,Simon Zhongyuan Tian,May Penrad-Mobayed,Laurent M. Sachs,Xiaoan Ruan,Chia-Lin Wei,Edison T. Liu,Grzegorz M. Wilczynski,Dariusz Plewczynski,Guoliang Li,Yijun Ruan,Yijun Ruan +24 more
TL;DR: 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation, and provides unique insights in the topological mechanism of human variations and diseases.
Journal ArticleDOI
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
Ya Guo,Quan Xu,Quan Xu,Daniele Canzio,Jia Shou,Jia Shou,Li Jinhuan,Li Jinhuan,David U. Gorkin,Inkyung Jung,Haiyang Wu,Haiyang Wu,Yanan Zhai,Yanan Zhai,Yuanxiao Tang,Yuanxiao Tang,Yichao Lu,Yichao Lu,Yonghu Wu,Yonghu Wu,Zhilian Jia,Zhilian Jia,Wei Li,Wei Li,Michael Q. Zhang,Bing Ren,Adrian R. Krainer,Tom Maniatis,Qiang Wu,Qiang Wu +29 more
TL;DR: Although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context, the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity.
Journal ArticleDOI
Organization and function of the 3D genome.
TL;DR: The insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches are discussed and how these new concepts have been used to address important biological questions in development and disease are explained.
Journal ArticleDOI
Activation of proto-oncogenes by disruption of chromosome neighborhoods
Denes Hnisz,Abraham S. Weintraub,Daniel S. Day,Anne-Laure Valton,Rasmus O. Bak,Charles H. Li,Johanna Goldmann,Bryan R. Lajoie,Zi Peng Fan,Alla A. Sigova,Jessica Reddy,Diego Borges-Rivera,Tong Ihn Lee,Rudolf Jaenisch,Matthew H. Porteus,Job Dekker,Job Dekker,Richard A. Young +17 more
TL;DR: Insulated neighborhoods in T cell acute lymphoblastic leukemia (T-ALL) are mapped and it is found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes.
References
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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
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
Journal ArticleDOI
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Mamta Tahiliani,Kian Peng Koh,Yinghua Shen,William A. Pastor,Hozefa S. Bandukwala,Yevgeny Brudno,Suneet Agarwal,Lakshminarayan M. Iyer,David R. Liu,L. Aravind,Anjana Rao +10 more
TL;DR: It is shown here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro.
Journal ArticleDOI
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Shinsuke Ito,Li Shen,Qing Dai,Susan C. Wu,Leonard B. Collins,James A. Swenberg,Chuan He,Yi Zhang +7 more
TL;DR: This study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation, and identifies two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins.
Journal ArticleDOI
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphège P. Nora,Bryan R. Lajoie,Edda G. Schulz,Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Ikuhiro Okamoto,Ikuhiro Okamoto,Ikuhiro Okamoto,Nicolas Servant,Nicolas Servant,Nicolas Servant,Tristan Piolot,Tristan Piolot,Tristan Piolot,Nynke L. van Berkum,Johannes Meisig,John W. Sedat,Joost Gribnau,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Nils Blüthgen,Job Dekker,Edith Heard,Edith Heard,Edith Heard +26 more
TL;DR: In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, this study sets the stage for the full genetic dissection of the mouse X-inactivation centre.
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