23 papers · ranked by Valyu relevance
L.G Nikolaev, S.B Akopov, D.A Didych, E.D Sverdlov
The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently…
Judith Hyle, Yang Zhang, Shaela Wright, Beisi Xu + 6 more
'John Easton' 'Liqing Tian' 'Ruopeng Feng' 'Peng Xu' 'Chunliang Li'] Title: Abstract Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated…
Eleftherios Bochalis, Ilias Georgakopoulos-Soares
CCCTC-binding factor (CTCF) is a master regulator of the human genome, directly modulating both transcription and 3D genome organization. However, previous human genome-wide maps of its binding sites have been built on an incomplete assembly, leaving out many repetitive, difficult-to-sequence regions. Here, we leverage…
Clélia Laitem, Justyna Zaborowska, Michael Tellier, Yuki Yamaguchi + 4 more
'Qingfu Cao' 'Sylvain Egloff' 'Hiroshi Handa' 'Shona Murphy'] CTCF is a versatile transcription factor with well-established roles in chromatin organization and insulator function. Recent findings also implicate CTCF in the control of elongation by RNA polymerase (RNAP) II. Here we show that CTCF knockdown abrogates…
Sarion R. Bowers, Peter N. Cockerill
CCCTC-binding Factor (CCTF) is the only known vertebrate protein that functions to organise the genome into distinct functional chromatin domains. A subset of CTCF sites also provide insulator activity and barrier activity to block inappropriate enhancer-promoter communication and spreading of histone modifications and…
Hongshan Zhang, Zhubing Shi, Edward J. Banigan, Yoori Kim + 3 more
Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging…
Martin Franke, Elisa De la Calle-Mustienes, Ana Neto, Rafael D. Acemel + 3 more
CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding^1–5^. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains, which are sub-megabase…
Mayilaadumveettil Nishana, Javier Rodriguez-Hernaez, Caryn Ha, Erica Chio + 6 more
Ubiquitously expressed CTCF is involved in numerous cellular functions, some of which involve organizing chromatin into TAD structures and others to its role as a transcription factor. In contrast, its paralog, CTCFL is normally only present in testis. However, it is also aberrantly expressed in many cancers. While it…
Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran + 7 more
'Ali Ranjbaran' 'Erica Chio' 'Elphege P. Nora' 'Sana B. Badri' 'Andreas Kloetgen' 'Benoit G. Bruneau' 'Aristotelis Tsirigos' 'Jane A. Skok'] Background Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally…
Nestor Norio Oiwa, Kunhe Li, C. E. Cordeiro, Dieter W. Heermann
We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence…
Brian C Del Rosario, Andrea J Kriz, Amanda M Del Rosario, Anthony Anselmo + 6 more
'Anthony Anselmo' 'Christopher J Fry' 'Forest M White' 'Ruslan I Sadreyev' 'Jeannie T Lee' 'Jessica K Tyler' 'Jessica K Tyler'] The zinc finger CCCTC-binding protein (CTCF) carries out many functions in the cell. Although previous studies sought to explain CTCF multivalency based on sequence composition of binding…
Boyi Yang, Nabil Aounallah
Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we utilize previously published ChIP-seq and RNA-seq data to investigate the effects…
Frank Sleutels, Widia Soochit, Marek Bartkuhn, Helen Heath + 15 more
'Sven Dienstbach' 'Philipp Bergmaier' 'Vedran Franke' 'Manuel Rosa-Garrido' 'Suzanne van de Nobelen' 'Lisa Caesar' 'Michael van der Reijden' 'Jan Christian Bryne' 'Wilfred van IJcken' 'J Anton Grootegoed' 'M Dolores Delgado' 'Boris Lenhard' 'Rainer Renkawitz' 'Frank Grosveld' 'Niels Galjart'] Background CTCF is a…
Lian Liu, Yuanxiao Tang, Qiang Wu
As an essential regulator of higher-order chromatin structures, CTCF is a highly-conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the…
Lian Liu, Yuanxiao Tang, Yan Zhang, Qiang Wu
Title: Summary As an essential regulator of higher-order chromatin structures, CCCTC-binding factor (CTCF) is a highly conserved protein with a central DNA-binding domain of 11 tandem zinc fingers (ZFs), which are flanked by amino (N-) and carboxy (C-) terminal domains of intrinsically disordered regions. Here we…
Ivan Junier, Ryan Dale, Chunhui Hou, François Képès + 1 more
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional folding of a 1 Mbp region of human chromosome 11 containing the β-globin genes by…
Martin Oti, Jonas Falck, Martijn A. Huynen, Huiqing Zhou
Background The CCTC-binding factor (CTCF) protein is involved in genome organization, including mediating three-dimensional chromatin interactions. Human patient lymphocytes with mutations in a single copy of the CTCF gene have reduced expression of enhancer-associated genes involved in response to stimuli. We…
Chris A. Brackley, James Johnson, Davide Michieletto, A. N. Morozov + 3 more
'Mario Nicodemi' 'Peter R. Cook' 'Davide Marenduzzo'] We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with the CTCF protein, stabilize…
Gennadi V. Glinsky
Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF and STAT1, identifies non-random highly correlated patterns of density distributions along the chromosome length…
Martina Crippa, Yinxiu Zhan, Guido Tiana
An active loop-extrusion mechanism is regarded as the main out–of–equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by solving the kinetic equations associated with the motion of the extruder. By averaging…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
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Membrane fusion underpins many fundamental cellular processes, yet the design of artificial fusogens that can interact with specific cell surface markers in a precise and predictable manner remains a major challenge. Here we demonstrate that cholera toxin B-subunit (CTB), a naturally occurring glycolipid-binding…