Literature DB >> 30875678

Function and regulation of chromatin insulators in dynamic genome organization.

Dahong Chen1, Elissa P Lei2.   

Abstract

Chromatin insulators are DNA-protein complexes that play a crucial role in regulating chromatin organization. Within the past two years, a plethora of genome-wide conformation capture studies have helped reveal that insulators are necessary for proper genome-wide organization of topologically associating domains, which are formed in a manner distinct from that of compartments. These studies have also provided novel insights into the mechanics of how CTCF/cohesin-dependent loops form in mammals, strongly supporting the loop extrusion model. In combination with single-cell imaging approaches in both Drosophila and mammals, the dynamics of insulator-mediated chromatin interactions are also coming to light. Insulator-dependent structures vary across individual cells and tissues, highlighting the need to study the regulation of insulators in particular temporal and spatial contexts throughout development. Published by Elsevier Ltd.

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Year:  2019        PMID: 30875678      PMCID: PMC6692201          DOI: 10.1016/j.ceb.2019.02.001

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  56 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

2.  Abnormal Microglia and Enhanced Inflammation-Related Gene Transcription in Mice with Conditional Deletion of Ctcf in Camk2a-Cre-Expressing Neurons.

Authors:  Bryan E McGill; Ruteja A Barve; Susan E Maloney; Amy Strickland; Nicholas Rensing; Peter L Wang; Michael Wong; Richard Head; David F Wozniak; Jeffrey Milbrandt
Journal:  J Neurosci       Date:  2017-11-13       Impact factor: 6.167

3.  Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.

Authors:  Kyong-Rim Kieffer-Kwon; Keisuke Nimura; Suhas S P Rao; Jianliang Xu; Seolkyoung Jung; Aleksandra Pekowska; Marei Dose; Evan Stevens; Ewy Mathe; Peng Dong; Su-Chen Huang; Maria Aurelia Ricci; Laura Baranello; Ying Zheng; Francesco Tomassoni Ardori; Wolfgang Resch; Diana Stavreva; Steevenson Nelson; Michael McAndrew; Adriel Casellas; Elizabeth Finn; Charles Gregory; Brian Glenn St Hilaire; Steven M Johnson; Wendy Dubois; Maria Pia Cosma; Eric Batchelor; David Levens; Robert D Phair; Tom Misteli; Lino Tessarollo; Gordon Hager; Melike Lakadamyali; Zhe Liu; Monique Floer; Hari Shroff; Erez Lieberman Aiden; Rafael Casellas
Journal:  Mol Cell       Date:  2017-08-10       Impact factor: 17.970

4.  Architectural Proteins and Pluripotency Factors Cooperate to Orchestrate the Transcriptional Response of hESCs to Temperature Stress.

Authors:  Xiaowen Lyu; M Jordan Rowley; Victor G Corces
Journal:  Mol Cell       Date:  2018-08-16       Impact factor: 17.970

5.  Dual effect of CTCF loss on neuroprogenitor differentiation and survival.

Authors:  L Ashley Watson; Xu Wang; Adrienne Elbert; Kristin D Kernohan; Niels Galjart; Nathalie G Bérubé
Journal:  J Neurosci       Date:  2014-02-19       Impact factor: 6.167

6.  Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF).

Authors:  Somi Kim; Nam-Kyung Yu; Kyu-Won Shim; Ji-Il Kim; Hyopil Kim; Dae Hee Han; Ja Eun Choi; Seung-Woo Lee; Dong Il Choi; Myung Won Kim; Dong-Sung Lee; Kyungmin Lee; Niels Galjart; Yong-Seok Lee; Jae-Hyung Lee; Bong-Kiun Kaang
Journal:  J Neurosci       Date:  2018-04-30       Impact factor: 6.167

7.  Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.

Authors:  Michael R Stadler; Jenna E Haines; Michael B Eisen
Journal:  Elife       Date:  2017-11-17       Impact factor: 8.140

8.  Regulatory Mechanisms of Metamorphic Neuronal Remodeling Revealed Through a Genome-Wide Modifier Screen in Drosophila melanogaster.

Authors:  Dahong Chen; Tingting Gu; Tom N Pham; Montgomery J Zachary; Randall S Hewes
Journal:  Genetics       Date:  2017-05-05       Impact factor: 4.562

9.  Successive gain of insulator proteins in arthropod evolution.

Authors:  Peter Heger; Rebecca George; Thomas Wiehe
Journal:  Evolution       Date:  2013-06-04       Impact factor: 3.694

10.  Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells.

Authors:  Qi Wang; Qiu Sun; Daniel M Czajkowsky; Zhifeng Shao
Journal:  Nat Commun       Date:  2018-01-15       Impact factor: 14.919

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  10 in total

1.  Distinct Elements Confer the Blocking and Bypass Functions of the Bithorax Fab-8 Boundary.

Authors:  Olga Kyrchanova; Daniel Wolle; Marat Sabirov; Amina Kurbidaeva; Tsutomu Aoki; Oksana Maksimenko; Maria Kyrchanova; Pavel Georgiev; Paul Schedl
Journal:  Genetics       Date:  2019-09-24       Impact factor: 4.562

2.  NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization.

Authors:  Shue Chen; Leah F Rosin; Gianluca Pegoraro; Nellie Moshkovich; Patrick J Murphy; Guoyun Yu; Elissa P Lei
Journal:  Nucleic Acids Res       Date:  2022-08-12       Impact factor: 19.160

3.  Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function.

Authors:  Indira Bag; Yang Chen; Karole D'Orazio; Prisma Lopez; Sabine Wenzel; Yuichiro Takagi; Elissa P Lei
Journal:  G3 (Bethesda)       Date:  2022-08-25       Impact factor: 3.542

Review 4.  ArcRNAs and the formation of nuclear bodies.

Authors:  Shinichi Nakagawa; Tomohiro Yamazaki; Taro Mannen; Tetsuro Hirose
Journal:  Mamm Genome       Date:  2021-06-03       Impact factor: 2.957

5.  Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2.

Authors:  Gizem Guzelsoy; Cansu Akkaya; Dila Atak; Cory D Dunn; Alkan Kabakcioglu; Nurhan Ozlu; Gulayse Ince-Dunn
Journal:  Sci Rep       Date:  2019-12-23       Impact factor: 4.379

6.  The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes.

Authors:  L S Melnikova; P G Georgiev; A K Golovnin
Journal:  Acta Naturae       Date:  2020 Oct-Dec       Impact factor: 1.845

7.  Asthma-associated genetic variants induce IL33 differential expression through an enhancer-blocking regulatory region.

Authors:  Ivy Aneas; Donna C Decker; Anne I Sperling; Marcelo A Nóbrega; Chanie L Howard; Débora R Sobreira; Noboru J Sakabe; Kelly M Blaine; Michelle M Stein; Cara L Hrusch; Lindsey E Montefiori; Juan Tena; Kevin M Magnaye; Selene M Clay; James E Gern; Daniel J Jackson; Matthew C Altman; Edward T Naureckas; Douglas K Hogarth; Steven R White; Jose Luis Gomez-Skarmeta; Nathan Schoetler; Carole Ober
Journal:  Nat Commun       Date:  2021-10-21       Impact factor: 17.694

Review 8.  REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics.

Authors:  Soile V E Keränen; Angel Villahoz-Baleta; Andrew E Bruno; Marc S Halfon
Journal:  Insects       Date:  2022-07-11       Impact factor: 3.139

9.  Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.

Authors:  Pengyu Ni; Joshua Moe; Zhengchang Su
Journal:  BMC Biol       Date:  2022-10-05       Impact factor: 7.364

10.  M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.

Authors:  Shue Chen; Leah F Rosin; Indira Bag; Yang Chen; Chen-Yu Liu; Guo-Yun Yu; Elissa P Lei
Journal:  Nat Commun       Date:  2021-07-07       Impact factor: 14.919

  10 in total

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