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Literature DB >> 26276625

A CTCF Code for 3D Genome Architecture.

Abstract

The architectural protein CTCF plays a complex role in decoding the functional output of the genome. Guo et al. now show that the orientation of a CTCF site restricts its choice of interacting partner, thus creating a code that predicts the three-dimensional organization of the genome. We propose a DNA extrusion model to account for orientation-specific loop formation.

Entities: Chemical Gene Species

Mesh：

Substances：
Repressor Proteins

Year: 2015 PMID： 26276625 PMCID： PMC4745123 DOI： 10.1016/j.cell.2015.07.053

Source DB: PubMed Journal: Cell ISSN： 0092-8674 Impact factor: 41.582

10 in total

1. Real-time detection of single-molecule DNA compaction by condensin I.

Authors: Terence R Strick; Tatsuhiko Kawaguchi; Tatsuya Hirano
Journal: Curr Biol Date: 2004-05-25 Impact factor: 10.834

2. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Authors: Ya Guo; Quan Xu; Daniele Canzio; Jia Shou; Jinhuan Li; David U Gorkin; Inkyung Jung; Haiyang Wu; Yanan Zhai; Yuanxiao Tang; Yichao Lu; Yonghu Wu; Zhilian Jia; Wei Li; Michael Q Zhang; Bing Ren; Adrian R Krainer; Tom Maniatis; Qiang Wu
Journal: Cell Date: 2015-08-13 Impact factor: 41.582

Review 3. CTCF: an architectural protein bridging genome topology and function.

Authors: Chin-Tong Ong; Victor G Corces
Journal: Nat Rev Genet Date: 2014-03-11 Impact factor: 53.242

4. Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Authors: Elphège P Nora; Bryan R Lajoie; Edda G Schulz; Luca Giorgetti; Ikuhiro Okamoto; Nicolas Servant; Tristan Piolot; Nynke L van Berkum; Johannes Meisig; John Sedat; Joost Gribnau; Emmanuel Barillot; Nils Blüthgen; Job Dekker; Edith Heard
Journal: Nature Date: 2012-04-11 Impact factor: 49.962

5. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors: Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal: Cell Date: 2014-12-11 Impact factor: 41.582

6. Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Authors: Jennifer E Phillips-Cremins; Michael E G Sauria; Amartya Sanyal; Tatiana I Gerasimova; Bryan R Lajoie; Joshua S K Bell; Chin-Tong Ong; Tracy A Hookway; Changying Guo; Yuhua Sun; Michael J Bland; William Wagstaff; Stephen Dalton; Todd C McDevitt; Ranjan Sen; Job Dekker; James Taylor; Victor G Corces
Journal: Cell Date: 2013-05-23 Impact factor: 41.582

7. The CTCF insulator protein forms an unusual DNA structure.

Authors: Melissa J MacPherson; Paul D Sadowski
Journal: BMC Mol Biol Date: 2010-12-21 Impact factor: 2.946

8. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Authors: Matteo Vietri Rudan; Christopher Barrington; Stephen Henderson; Christina Ernst; Duncan T Odom; Amos Tanay; Suzana Hadjur
Journal: Cell Rep Date: 2015-02-26 Impact factor: 9.423

9. Cohesin relocation from sites of chromosomal loading to places of convergent transcription.

Authors: Armelle Lengronne; Yuki Katou; Saori Mori; Shihori Yokobayashi; Gavin P Kelly; Takehiko Itoh; Yoshinori Watanabe; Katsuhiko Shirahige; Frank Uhlmann
Journal: Nature Date: 2004-06-30 Impact factor: 49.962

10. Self-organization of domain structures by DNA-loop-extruding enzymes.

Authors: Elnaz Alipour; John F Marko
Journal: Nucleic Acids Res Date: 2012-10-15 Impact factor: 16.971

10 in total

77 in total

1. The Energetics and Physiological Impact of Cohesin Extrusion.

Authors: Laura Vian; Aleksandra Pękowska; Suhas S P Rao; Kyong-Rim Kieffer-Kwon; Seolkyoung Jung; Laura Baranello; Su-Chen Huang; Laila El Khattabi; Marei Dose; Nathanael Pruett; Adrian L Sanborn; Andres Canela; Yaakov Maman; Anna Oksanen; Wolfgang Resch; Xingwang Li; Byoungkoo Lee; Alexander L Kovalchuk; Zhonghui Tang; Steevenson Nelson; Michele Di Pierro; Ryan R Cheng; Ido Machol; Brian Glenn St Hilaire; Neva C Durand; Muhammad S Shamim; Elena K Stamenova; José N Onuchic; Yijun Ruan; Andre Nussenzweig; David Levens; Erez Lieberman Aiden; Rafael Casellas
Journal: Cell Date: 2018-04-26 Impact factor: 41.582

Review 2. Genome folding through loop extrusion by SMC complexes.

Authors: Iain F Davidson; Jan-Michael Peters
Journal: Nat Rev Mol Cell Biol Date: 2021-03-25 Impact factor: 94.444

3. Genome Organization Drives Chromosome Fragility.

Authors: Andres Canela; Yaakov Maman; Seolkyoung Jung; Nancy Wong; Elsa Callen; Amanda Day; Kyong-Rim Kieffer-Kwon; Aleksandra Pekowska; Hongliang Zhang; Suhas S P Rao; Su-Chen Huang; Peter J Mckinnon; Peter D Aplan; Yves Pommier; Erez Lieberman Aiden; Rafael Casellas; André Nussenzweig
Journal: Cell Date: 2017-07-20 Impact factor: 41.582

4. A kidney-specific genetic control module in mice governs endocrine regulation of the cytochrome P450 gene Cyp27b1 essential for vitamin D₃ activation.

Authors: Mark B Meyer; Nancy A Benkusky; Martin Kaufmann; Seong Min Lee; Melda Onal; Glenville Jones; J Wesley Pike
Journal: J Biol Chem Date: 2017-08-14 Impact factor: 5.157

Review 5. One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease.

Authors: Michal Lazniewski; Wayne K Dawson; Anna Maria Rusek; Dariusz Plewczynski
Journal: Semin Cell Dev Biol Date: 2018-10-11 Impact factor: 7.727

Review 6. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.

Authors: Rachel Patton McCord; Noam Kaplan; Luca Giorgetti
Journal: Mol Cell Date: 2020-01-27 Impact factor: 17.970

Review 7. Cohesin Mutations in Cancer.

Authors: Magali De Koninck; Ana Losada
Journal: Cold Spring Harb Perspect Med Date: 2016-12-01 Impact factor: 6.915