CTCF looping is established during gastrulation in medaka embryos.

Animals CCCTC-Binding Factor / genetics Cell Cycle Proteins / genetics Chromatin / genetics Gastrulation / genetics Mice Oryzias / genetics Zebrafish / genetics

Journal

Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021

Informations de publication

Date de publication:
06 2021
Historique:
received: 06 08 2020
accepted: 30 03 2021
pubmed: 20 5 2021
medline: 11 3 2022
entrez: 19 5 2021
Statut: ppublish

Résumé

Chromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely challenging in mammalian early embryos, the developmental stage at which cohesin-mediated loops form remains unknown. Here, we study early development in medaka (the Japanese killifish,

Identifiants

DOI: 10.1101/gr.269951.120 PMID: 34006570 PMC: PMC8168583
pubmed: 34006570
pii: gr.269951.120
doi: 10.1101/gr.269951.120
pmc: PMC8168583
doi:

Substances chimiques

CCCTC-Binding Factor 0
Cell Cycle Proteins 0
Chromatin 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

968-980

Informations de copyright

© 2021 Nakamura et al.; Published by Cold Spring Harbor Laboratory Press.

Références

Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nature. 2019 Dec;576(7786):306-310
pubmed: 31801998
Nature. 2015 Jul 9;523(7559):240-4
pubmed: 26030525
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Cell Rep. 2018 Jul 3;24(1):1-10.e4
pubmed: 29972771
Elife. 2014 Oct 14;3:
pubmed: 25313869
Nat Commun. 2017 Nov 28;8(1):1833
pubmed: 29184138
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Science. 2019 Dec 13;366(6471):1338-1345
pubmed: 31753851
Cell. 2017 Oct 5;171(2):305-320.e24
pubmed: 28985562
Cell Syst. 2018 Nov 28;7(5):482-495.e10
pubmed: 30414923
Nature. 2019 Dec;576(7785):158-162
pubmed: 31776509
Annu Rev Cell Dev Biol. 2014;30:581-613
pubmed: 25150012
Nature. 2016 Jan 7;529(7584):110-4
pubmed: 26700815
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Dev Cell. 2017 Aug 21;42(4):316-332
pubmed: 28829942
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Dev Cell. 2014 Jan 13;28(1):94-101
pubmed: 24374176
Cell Rep. 2016 May 31;15(9):2038-49
pubmed: 27210764
Cell. 2015 May 21;161(5):1012-1025
pubmed: 25959774
EMBO J. 2017 Dec 15;36(24):3600-3618
pubmed: 29217590
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
pubmed: 26499245
Genome Res. 2017 Nov;27(11):1939-1949
pubmed: 28855260
Annu Rev Genet. 2010;44:217-41
pubmed: 20731603
Mech Dev. 2004 Jul;121(7-8):629-37
pubmed: 15210172
Genome Res. 2014 Jul;24(7):1157-68
pubmed: 24709819
Nat Cell Biol. 2019 Nov;21(11):1393-1402
pubmed: 31685986
Cell. 2017 May 18;169(5):930-944.e22
pubmed: 28525758
Cell Stem Cell. 2016 Feb 4;18(2):262-75
pubmed: 26686465
Curr Top Dev Biol. 2016;116:273-97
pubmed: 26970624
Nature. 2012 Apr 11;485(7398):381-5
pubmed: 22495304
Cell. 2017 Jul 13;170(2):367-381.e20
pubmed: 28709003
Cell. 2017 Apr 6;169(2):216-228.e19
pubmed: 28388407
Nature. 2017 Apr 6;544(7648):110-114
pubmed: 28355183
Nature. 2017 Jul 12;547(7662):232-235
pubmed: 28703188
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Science. 2019 Dec 13;366(6471):1345-1349
pubmed: 31780627
Mech Dev. 2004 Jul;121(7-8):605-18
pubmed: 15210170
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Dec;9(12):1185-8
pubmed: 23103880
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Development. 2009 Sep;136(18):3033-42
pubmed: 19700615
Nat Commun. 2011;2:310
pubmed: 21556064
Nat Biotechnol. 2014 Apr;32(4):381-386
pubmed: 24658644
Development. 2014 Jul;141(13):2568-80
pubmed: 24924192
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
Nat Rev Mol Cell Biol. 2019 Sep;20(9):535-550
pubmed: 31197269
Nature. 2020 Apr;580(7801):142-146
pubmed: 32238933
Cell Rep. 2014 Nov 6;9(3):1163-70
pubmed: 25437568
Adv Genet. 2016;95:161-94
pubmed: 27503357
Bioinformatics. 2017 Jul 15;33(14):i369-i378
pubmed: 28881993
Cell. 2012 Feb 3;148(3):458-72
pubmed: 22265598
Nature. 2002 Dec 5;420(6915):520-62
pubmed: 12466850
Genome Res. 2021 Jun;31(6):981-994
pubmed: 34006569

Auteurs

Ryohei Nakamura (R)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan.
ORCID: 0000-0002-7812-8034

Yuichi Motai (Y)

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan.

Masahiko Kumagai (M)

Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan.

Candice L Wike (CL)

Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

Haruyo Nishiyama (H)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan.

Yoichiro Nakatani (Y)

Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan.
ORCID: 0000-0001-7604-0242

Neva C Durand (NC)

The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.
Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139 USA.
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA.

Kaori Kondo (K)

RIKEN-IMS, Laboratory for Developmental Genetics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Takashi Kondo (T)

RIKEN-IMS, Laboratory for Developmental Genetics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Tatsuya Tsukahara (T)

Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Atsuko Shimada (A)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan.

Bradley R Cairns (BR)

Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

Erez Lieberman Aiden (EL)

The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.
Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139 USA.
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA.

Shinichi Morishita (S)

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan.

Hiroyuki Takeda (H)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033 Japan.

Articles similaires

Evaluating the efficacy of telesurgery with dual console SSI Mantra Surgical Robotic System: experiment on animal model and clinical trials.

Sudhir Prem Srivastava, Vishwajyoti Pascual Srivastava, Avinesh Singh et al.
1.00
Robotic Surgical Procedures Animals Humans Telemedicine Models, Animal

Odour generalisation and detection dog training.

Lyn Caldicott, Thomas W Pike, Helen E Zulch et al.
1.00
Animals Odorants Dogs Generalization, Psychological Smell

FBXO22 inhibits colitis and colorectal carcinogenesis by regulating the degradation of the S2448-phosphorylated form of mTOR.

Minle Li, Xuan Chen, Pengfei Qu et al.
1.00
Animals TOR Serine-Threonine Kinases Colorectal Neoplasms Colitis Mice

Use of organic material provided by an automatic enrichment device by weaner pigs and its influence on tail lesions.

Philipp Heseker, Jeanette Probst, Stefanie Ammer et al.
1.00
Animals Tail Swine Behavior, Animal Animal Husbandry

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › CTCF looping is established during...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Protéines de répression › Facteur de liaison à la séquence CCCTC › CTCF looping is established during...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines du cycle cellulaire › CTCF looping is established during...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › CTCF looping is established during...
questionsmedicales.fr › Phénomènes physiologiques › Croissance et développement › Morphogenèse › Gastrulation › CTCF looping is established during...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › CTCF looping is established during...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Poissons › Smegmamorpha › Beloniformes › Oryzias › CTCF looping is established during...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Poissons › Cypriniformes › Cyprinidae › Danio zébré › CTCF looping is established during...