Literature DB >> 27111891

TAD disruption as oncogenic driver.

Anne-Laure Valton1, Job Dekker2.   

Abstract

Topologically Associating Domains (TADs) are conserved during evolution and play roles in guiding and constraining long-range regulation of gene expression. Disruption of TAD boundaries results in aberrant gene expression by exposing genes to inappropriate regulatory elements. Recent studies have shown that TAD disruption is often found in cancer cells and contributes to oncogenesis through two mechanisms. One mechanism locally disrupts domains by deleting or mutating a TAD boundary leading to fusion of the two adjacent TADs. The other mechanism involves genomic rearrangements that break up TADs and creates new ones without directly affecting TAD boundaries. Understanding the mechanisms by which TADs form and control long-range chromatin interactions will therefore not only provide insights into the mechanism of gene regulation in general, but will also reveal how genomic rearrangements and mutations in cancer genomes can lead to misregulation of oncogenes and tumor suppressors.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2016        PMID: 27111891      PMCID: PMC4880504          DOI: 10.1016/j.gde.2016.03.008

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  48 in total

1.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

2.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

Authors:  Josée Dostie; Todd A Richmond; Ramy A Arnaout; Rebecca R Selzer; William L Lee; Tracey A Honan; Eric D Rubio; Anton Krumm; Justin Lamb; Chad Nusbaum; Roland D Green; Job Dekker
Journal:  Genome Res       Date:  2006-09-05       Impact factor: 9.043

3.  Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.

Authors:  Jessica Zuin; Jesse R Dixon; Michael I J A van der Reijden; Zhen Ye; Petros Kolovos; Rutger W W Brouwer; Mariëtte P C van de Corput; Harmen J G van de Werken; Tobias A Knoch; Wilfred F J van IJcken; Frank G Grosveld; Bing Ren; Kerstin S Wendt
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-13       Impact factor: 11.205

4.  A switch between topological domains underlies HoxD genes collinearity in mouse limbs.

Authors:  Guillaume Andrey; Thomas Montavon; Bénédicte Mascrez; Federico Gonzalez; Daan Noordermeer; Marion Leleu; Didier Trono; François Spitz; Denis Duboule
Journal:  Science       Date:  2013-06-07       Impact factor: 47.728

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.  Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Authors:  Denes Hnisz; Abraham S Weintraub; Daniel S Day; Anne-Laure Valton; Rasmus O Bak; Charles H Li; Johanna Goldmann; Bryan R Lajoie; Zi Peng Fan; Alla A Sigova; Jessica Reddy; Diego Borges-Rivera; Tong Ihn Lee; Rudolf Jaenisch; Matthew H Porteus; Job Dekker; Richard A Young
Journal:  Science       Date:  2016-03-03       Impact factor: 47.728

7.  CTCF Binding Polarity Determines Chromatin Looping.

Authors:  Elzo de Wit; Erica S M Vos; Sjoerd J B Holwerda; Christian Valdes-Quezada; Marjon J A M Verstegen; Hans Teunissen; Erik Splinter; Patrick J Wijchers; Peter H L Krijger; Wouter de Laat
Journal:  Mol Cell       Date:  2015-10-29       Impact factor: 17.970

Review 8.  Structural and functional diversity of Topologically Associating Domains.

Authors:  Job Dekker; Edith Heard
Journal:  FEBS Lett       Date:  2015-09-05       Impact factor: 4.124

9.  Formation of Chromosomal Domains by Loop Extrusion.

Authors:  Geoffrey Fudenberg; Maxim Imakaev; Carolyn Lu; Anton Goloborodko; Nezar Abdennur; Leonid A Mirny
Journal:  Cell Rep       Date:  2016-05-19       Impact factor: 9.423

10.  Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients.

Authors:  B A Walker; C P Wardell; A Brioli; E Boyle; M F Kaiser; D B Begum; N B Dahir; D C Johnson; F M Ross; F E Davies; G J Morgan
Journal:  Blood Cancer J       Date:  2014-03-14       Impact factor: 11.037

View more
  76 in total

1.  Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.

Authors:  Alan Perez-Rathke; Samira Mali; Lin Du; Jie Liang
Journal:  IEEE EMBS Int Conf Biomed Health Inform       Date:  2019-09-12

Review 2.  Models of polymer physics for the architecture of the cell nucleus.

Authors:  Andrea Esposito; Carlo Annunziatella; Simona Bianco; Andrea M Chiariello; Luca Fiorillo; Mario Nicodemi
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2018-12-19

Review 3.  Understanding 3D genome organization by multidisciplinary methods.

Authors:  Ivana Jerkovic; Giacomo Cavalli
Journal:  Nat Rev Mol Cell Biol       Date:  2021-05-05       Impact factor: 94.444

Review 4.  Controlling gene expression by DNA mechanics: emerging insights and challenges.

Authors:  David Levens; Laura Baranello; Fedor Kouzine
Journal:  Biophys Rev       Date:  2016-11-14

Review 5.  Controlling gene expression by DNA mechanics: emerging insights and challenges.

Authors:  David Levens; Laura Baranello; Fedor Kouzine
Journal:  Biophys Rev       Date:  2016-08-20

6.  multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments.

Authors:  John C Stansfield; Kellen G Cresswell; Mikhail G Dozmorov
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

Review 7.  Blank spots on the map: some current questions on nuclear organization and genome architecture.

Authors:  Carmen Adriaens; Leonid A Serebryannyy; Marina Feric; Andria Schibler; Karen J Meaburn; Nard Kubben; Pawel Trzaskoma; Sigal Shachar; Sandra Vidak; Elizabeth H Finn; Varun Sood; Gianluca Pegoraro; Tom Misteli
Journal:  Histochem Cell Biol       Date:  2018-09-20       Impact factor: 4.304

8.  Long-range chromatin interactions in pathogenic gene expression control.

Authors:  Nahyun Kong; Inkyung Jung
Journal:  Transcription       Date:  2020-11-05

Review 9.  Predicting chromatin architecture from models of polymer physics.

Authors:  Simona Bianco; Andrea M Chiariello; Carlo Annunziatella; Andrea Esposito; Mario Nicodemi
Journal:  Chromosome Res       Date:  2017-01-09       Impact factor: 5.239

10.  Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

Authors:  Houda Belaghzal; Job Dekker; Johan H Gibcus
Journal:  Methods       Date:  2017-04-18       Impact factor: 3.608

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.