Molecular Cell, volume 76, issue 3, pages 412-42200000

RNA Interactions Are Essential for CTCF-Mediated Genome Organization.

Saldaña Meyer Ricardo ¹

Rodriguez-Hernaez Javier ²

Escobar Thelma ¹

Nishana Mayilaadumveettil ²

Jácome López Karina ³

Nora Elphège P. ^{4, 5}

Bruneau Benoit G.

Tsirigos Aristotelis ^{6, 7}

Furlan-Magaril Mayra ³

Skok Jane ²

Reinberg Danny ¹

Hide authors affiliations Show authors affiliations: 7 affiliations

Howard Hughes Medical Institute, NYU Langone Health, New York, NY, USA |

Department of Pathology, NYULSoM, New York, NY, USA. |

Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, México |

⁴

Gladstone Institutes, San Francisco, CA 94158, USA |

⁵

Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA. |

⁶

Department of Pathology, NYULSoM, New York, NY, USA |

⁷

Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA. |

Publication type: Journal Article

Publication date: 2019-11-01

Elsevier

Journal: Molecular Cell

Quartile SCImago

Quartile WOS

Impact factor: 16

ISSN: 10972765, 10974164

DOI: 10.1016/j.molcel.2019.08.015

Copy DOI

PubMed ID: 31522988

Molecular Biology

Cell Biology

Abstract

The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of 2 of its 11 zinc fingers that are not required for CTCF binding to its cognate DNA site: zinc finger 1 (ZF1) or zinc finger 10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus the ability to insulate chromatin domains and to mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.

By date By citations

Citations by journals

	2 4 6 8 10 12
Molecular Cell	Molecular Cell, 12, 7.06% Molecular Cell 12 publications, 7.06%
Nucleic Acids Research	Nucleic Acids Research, 9, 5.29% Nucleic Acids Research 9 publications, 5.29%
Nature Genetics	Nature Genetics, 7, 4.12% Nature Genetics 7 publications, 4.12%
Nature Communications	Nature Communications, 6, 3.53% Nature Communications 6 publications, 3.53%
Cell Reports	Cell Reports, 6, 3.53% Cell Reports 6 publications, 3.53%
Current Opinion in Genetics and Development	Current Opinion in Genetics and Development, 5, 2.94% Current Opinion in Genetics and Development 5 publications, 2.94%
Frontiers in Cell and Developmental Biology	Frontiers in Cell and Developmental Biology, 4, 2.35% Frontiers in Cell and Developmental Biology 4 publications, 2.35%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 3, 1.76% Proceedings of the National Academy of Sciences of the United States of America 3 publications, 1.76%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 3, 1.76% International Journal of Molecular Sciences 3 publications, 1.76%
Nature Reviews Genetics	Nature Reviews Genetics, 3, 1.76% Nature Reviews Genetics 3 publications, 1.76%
Nature Reviews Molecular Cell Biology	Nature Reviews Molecular Cell Biology, 3, 1.76% Nature Reviews Molecular Cell Biology 3 publications, 1.76%
Nucleus	Nucleus, 3, 1.76% Nucleus 3 publications, 1.76%
Biochemical Society Transactions	Biochemical Society Transactions, 2, 1.18% Biochemical Society Transactions 2 publications, 1.18%
Genes	Genes, 2, 1.18% Genes 2 publications, 1.18%
Nature	Nature, 2, 1.18% Nature 2 publications, 1.18%
Oncogene	Oncogene, 2, 1.18% Oncogene 2 publications, 1.18%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 2, 1.18% Computational and Structural Biotechnology Journal 2 publications, 1.18%
iScience	iScience, 2, 1.18% iScience 2 publications, 1.18%
Trends in Genetics	Trends in Genetics, 2, 1.18% Trends in Genetics 2 publications, 1.18%
Cold Spring Harbor Symposia on Quantitative Biology	Cold Spring Harbor Symposia on Quantitative Biology, 2, 1.18% Cold Spring Harbor Symposia on Quantitative Biology 2 publications, 1.18%
Genome Biology	Genome Biology, 1, 0.59% Genome Biology 1 publication, 0.59%
Nature Immunology	Nature Immunology, 1, 0.59% Nature Immunology 1 publication, 0.59%
Essays in Biochemistry	Essays in Biochemistry, 1, 0.59% Essays in Biochemistry 1 publication, 0.59%
Circulation	Circulation, 1, 0.59% Circulation 1 publication, 0.59%
Neuroscientist	Neuroscientist, 1, 0.59% Neuroscientist 1 publication, 0.59%
Viruses	Viruses, 1, 0.59% Viruses 1 publication, 0.59%
Non-coding RNA	Non-coding RNA, 1, 0.59% Non-coding RNA 1 publication, 0.59%
Critical Reviews in Biochemistry and Molecular Biology	Critical Reviews in Biochemistry and Molecular Biology, 1, 0.59% Critical Reviews in Biochemistry and Molecular Biology 1 publication, 0.59%
Frontiers in Immunology	Frontiers in Immunology, 1, 0.59% Frontiers in Immunology 1 publication, 0.59%
	2 4 6 8 10 12

Citations by publishers

	5 10 15 20 25 30 35 40 45
Springer Nature	Springer Nature, 44, 25.88% Springer Nature 44 publications, 25.88%
Elsevier	Elsevier, 38, 22.35% Elsevier 38 publications, 22.35%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 10, 5.88% Multidisciplinary Digital Publishing Institute (MDPI) 10 publications, 5.88%
Oxford University Press	Oxford University Press, 10, 5.88% Oxford University Press 10 publications, 5.88%
Frontiers Media S.A.	Frontiers Media S.A., 6, 3.53% Frontiers Media S.A. 6 publications, 3.53%
Wiley	Wiley, 5, 2.94% Wiley 5 publications, 2.94%
Taylor & Francis	Taylor & Francis, 4, 2.35% Taylor & Francis 4 publications, 2.35%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 4, 2.35% Cold Spring Harbor Laboratory 4 publications, 2.35%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 3, 1.76% Proceedings of the National Academy of Sciences (PNAS) 3 publications, 1.76%
Portland Press	Portland Press, 3, 1.76% Portland Press 3 publications, 1.76%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 2, 1.18% Public Library of Science (PLoS) 2 publications, 1.18%
EMBO press	EMBO press, 2, 1.18% EMBO press 2 publications, 1.18%
Wolters Kluwer Health	Wolters Kluwer Health, 1, 0.59% Wolters Kluwer Health 1 publication, 0.59%
SAGE	SAGE, 1, 0.59% SAGE 1 publication, 0.59%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 1, 0.59% American Society for Biochemistry and Molecular Biology 1 publication, 0.59%
Genetics Society of America	Genetics Society of America, 1, 0.59% Genetics Society of America 1 publication, 0.59%
American Society of Hematology	American Society of Hematology, 1, 0.59% American Society of Hematology 1 publication, 0.59%
Walter de Gruyter	Walter de Gruyter, 1, 0.59% Walter de Gruyter 1 publication, 0.59%
Bioscientifica	Bioscientifica, 1, 0.59% Bioscientifica 1 publication, 0.59%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 1, 0.59% American Association for the Advancement of Science (AAAS) 1 publication, 0.59%
	5 10 15 20 25 30 35 40 45

We do not take into account publications that without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2019,2020,2021,2022,2023,2024],"ids":[0,0,0,0,0,0],"codes":[0,0,0,0,0,0],"imageUrls":["","","","","",""],"datasets":[{"label":"Citations number","data":[7,37,40,34,40,12],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["4.12","21.76","23.53","20","23.53","7.06"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Molecular Cell","Nucleic Acids Research","Nature Genetics","Nature Communications","Cell Reports","Current Opinion in Genetics and Development","Frontiers in Cell and Developmental Biology","Proceedings of the National Academy of Sciences of the United States of America","International Journal of Molecular Sciences","Nature Reviews Genetics","Nature Reviews Molecular Cell Biology","Nucleus","Biochemical Society Transactions","Genes","Nature","Oncogene","Computational and Structural Biotechnology Journal","iScience","Trends in Genetics","Cold Spring Harbor Symposia on Quantitative Biology","Genome Biology","Nature Immunology","Essays in Biochemistry","Circulation","Neuroscientist","Viruses","Non-coding RNA","Critical Reviews in Biochemistry and Molecular Biology","Frontiers in Immunology"],"ids":[19820,23904,5840,3231,9130,11302,12128,306,14627,13955,10207,5407,10198,8879,14611,20423,4268,6073,14739,7565,22171,6848,7813,25062,11561,2455,18908,19938,1699],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/yNSijlgQghQF53VZuyFLA30CKDe4j3HK74Vtpnxa_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/mxFdPe9qujsfvfYfcN0QOclAiYORFb0xrRlwV8gs_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/5YZtvLvkPZuc2JHOaZsjCvGSHFCuC3drUwN3YAc5_medium.webp","\/storage\/images\/resized\/nUqNrP9GnM1t0BrAIXp1LBodjU8aIJ2Fk4pLfGhZ_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/hg4jJjT8wVGtHstBCc0zk465Mg9pLx3G4odCDOqE_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/nUqNrP9GnM1t0BrAIXp1LBodjU8aIJ2Fk4pLfGhZ_medium.webp","\/storage\/images\/resized\/6QE8LXWrLpkoy5A2te6hw7who46GeCoTYIstuoAz_medium.webp","\/storage\/images\/resized\/ruydfaB80LDjlkYqsfOeUAZohOIODyq7bQzis5O7_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/5YZtvLvkPZuc2JHOaZsjCvGSHFCuC3drUwN3YAc5_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp"],"datasets":[{"label":"","data":[12,9,7,6,6,5,4,3,3,3,3,3,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[7.06,5.29,4.12,3.53,3.53,2.94,2.35,1.76,1.76,1.76,1.76,1.76,1.18,1.18,1.18,1.18,1.18,1.18,1.18,1.18,0.59,0.59,0.59,0.59,0.59,0.59,0.59,0.59,0.59],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Springer Nature","Elsevier","Multidisciplinary Digital Publishing Institute (MDPI)","Oxford University Press","Frontiers Media S.A.","Wiley","Taylor & Francis","Cold Spring Harbor Laboratory","Proceedings of the National Academy of Sciences (PNAS)","Portland Press","Public Library of Science (PLoS)","EMBO press","Wolters Kluwer Health","SAGE","American Society for Biochemistry and Molecular Biology","Genetics Society of America","American Society of Hematology","Walter de Gruyter","Bioscientifica","American Association for the Advancement of Science (AAAS)"],"ids":[8,17,202,19,208,11,18,6909,162,801,344,9415,32,31,2090,3356,2252,4,7773,189],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/yNSijlgQghQF53VZuyFLA30CKDe4j3HK74Vtpnxa_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/5YZtvLvkPZuc2JHOaZsjCvGSHFCuC3drUwN3YAc5_medium.webp","\/storage\/images\/resized\/hg4jJjT8wVGtHstBCc0zk465Mg9pLx3G4odCDOqE_medium.webp","\/storage\/images\/resized\/mxFdPe9qujsfvfYfcN0QOclAiYORFb0xrRlwV8gs_medium.webp","\/storage\/images\/resized\/nUqNrP9GnM1t0BrAIXp1LBodjU8aIJ2Fk4pLfGhZ_medium.webp","\/storage\/images\/resized\/PRGhlgB4OKRltSNtT39eA6wlnOTGRap1QQ6FQHih_medium.webp","\/storage\/images\/resized\/1UiI5HycPsvulDeXOySNp0OuaMMmIKfPnsdKPyH0_medium.webp","\/storage\/images\/resized\/6QE8LXWrLpkoy5A2te6hw7who46GeCoTYIstuoAz_medium.webp","\/storage\/images\/resized\/ruydfaB80LDjlkYqsfOeUAZohOIODyq7bQzis5O7_medium.webp","\/storage\/images\/resized\/OuA6WPZekwEiUM99mP2pSqj4yHPxHezM6xgLhAjO_medium.webp","\/storage\/images\/resized\/9EVpRifnnUJt6oHGY5GfsfSXTEz5wzbdgnZqiF5m_medium.webp","\/storage\/images\/resized\/QMhhcrIUiVtFnND3WWZ7hIbu6GYeoRoA2zoVsMEX_medium.webp","\/storage\/images\/resized\/3SpVxcYL33bOvPq4sHxJLH2NeKNeDloahSUpNiO4_medium.webp","\/storage\/images\/resized\/gI2YSALZRdW7QrL82nSGMnE18gGeSacV0cvz6ORd_medium.webp","\/storage\/images\/resized\/s10mcsCV4OAUg9O2KrqOquQC0PhyLMI8hUUkuflM_medium.webp"],"datasets":[{"label":"","data":[44,38,10,10,6,5,4,4,3,3,2,2,1,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[25.88,22.35,5.88,5.88,3.53,2.94,2.35,2.35,1.76,1.76,1.18,1.18,0.59,0.59,0.59,0.59,0.59,0.59,0.59,0.59],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}

Metrics

Cite this

GOST |

Cite this

GOST Copy

Saldaña Meyer R. et al. RNA Interactions Are Essential for CTCF-Mediated Genome Organization. // Molecular Cell. 2019. Vol. 76. No. 3. pp. 412-42200000.

GOST all authors (up to 50) Copy

Saldaña Meyer R., Rodriguez-Hernaez J., Escobar T., Nishana M., Jácome López K., Nora E. P., Bruneau B. G., Tsirigos A., Furlan-Magaril M., Skok J., Reinberg D. RNA Interactions Are Essential for CTCF-Mediated Genome Organization. // Molecular Cell. 2019. Vol. 76. No. 3. pp. 412-42200000.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1016/j.molcel.2019.08.015

UR - https://doi.org/10.1016%2Fj.molcel.2019.08.015

TI - RNA Interactions Are Essential for CTCF-Mediated Genome Organization.

T2 - Molecular Cell

AU - Saldaña Meyer, Ricardo

AU - Rodriguez-Hernaez, Javier

AU - Escobar, Thelma

AU - Nishana, Mayilaadumveettil

AU - Jácome López, Karina

AU - Nora, Elphège P.

AU - Bruneau, Benoit G.

AU - Tsirigos, Aristotelis

AU - Furlan-Magaril, Mayra

AU - Skok, Jane

AU - Reinberg, Danny

PY - 2019

DA - 2019/11/01 00:00:00

PB - Elsevier

SP - 412-42200000

IS - 3

VL - 76

PMID - 31522988

SN - 1097-2765

SN - 1097-4164

ER -

BibTex |

Cite this

BibTex Copy

@article{2019_Saldaña Meyer,

author = {Ricardo Saldaña Meyer and Javier Rodriguez-Hernaez and Thelma Escobar and Mayilaadumveettil Nishana and Karina Jácome López and Elphège P. Nora and Benoit G. Bruneau and Aristotelis Tsirigos and Mayra Furlan-Magaril and Jane Skok and Danny Reinberg},

title = {RNA Interactions Are Essential for CTCF-Mediated Genome Organization.},

journal = {Molecular Cell},

year = {2019},

volume = {76},

publisher = {Elsevier},

month = {nov},

url = {https://doi.org/10.1016%2Fj.molcel.2019.08.015},

number = {3},

pages = {412--42200000},

doi = {10.1016/j.molcel.2019.08.015}

}

MLA

Cite this

MLA Copy

Saldaña Meyer, Ricardo, et al. “RNA Interactions Are Essential for CTCF-Mediated Genome Organization..” Molecular Cell, vol. 76, no. 3, Nov. 2019, pp. 412-42200000. https://doi.org/10.1016%2Fj.molcel.2019.08.015.

Found error?

Publisher

Elsevier

Journal

Molecular Cell

Quartile SCImago

Quartile WOS

Impact factor

ISSN

10972765 (Print)
10974164 (Electronic)