Literature DB >> 34963059

Integrative approaches in genome structure analysis.

Lorenzo Boninsegna1, Asli Yildirim1, Yuxiang Zhan2, Frank Alber3.   

Abstract

New technological advances in integrated imaging, sequencing-based assays, and computational analysis have revolutionized our view of genomes in terms of their structure and dynamics in space and time. These advances promise a deeper understanding of genome functions and mechanistic insights into how the nucleus is spatially organized and functions. These wide arrays of complementary data provide an opportunity to produce quantitative integrative models of nuclear organization. In this article, we highlight recent key developments and discuss the outlook for these fields.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  genome function; genome structure modeling; genomics experiments; nuclear architecture; super-resolution imaging

Mesh:

Year:  2021        PMID: 34963059      PMCID: PMC8959402          DOI: 10.1016/j.str.2021.12.003

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  84 in total

1.  Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes.

Authors:  Marion Cremer; Florian Grasser; Christian Lanctôt; Stefan Müller; Michaela Neusser; Roman Zinner; Irina Solovei; Thomas Cremer
Journal:  Methods Mol Biol       Date:  2008

2.  Producing genome structure populations with the dynamic and automated PGS software.

Authors:  Nan Hua; Harianto Tjong; Hanjun Shin; Ke Gong; Xianghong Jasmine Zhou; Frank Alber
Journal:  Nat Protoc       Date:  2018-04-05       Impact factor: 13.491

3.  Transferable model for chromosome architecture.

Authors:  Michele Di Pierro; Bin Zhang; Erez Lieberman Aiden; Peter G Wolynes; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-29       Impact factor: 11.205

4.  Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.

Authors:  Elizabeth H Finn; Gianluca Pegoraro; Hugo B Brandão; Anne-Laure Valton; Marlies E Oomen; Job Dekker; Leonid Mirny; Tom Misteli
Journal:  Cell       Date:  2019-02-21       Impact factor: 41.582

Review 5.  How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization.

Authors:  Jyotsana J Parmar; Maxime Woringer; Christophe Zimmer
Journal:  Annu Rev Biophys       Date:  2019-03-05       Impact factor: 12.981

6.  The 4D nucleome project.

Authors:  Job Dekker; Andrew S Belmont; Mitchell Guttman; Victor O Leshyk; John T Lis; Stavros Lomvardas; Leonid A Mirny; Clodagh C O'Shea; Peter J Park; Bing Ren; Joan C Ritland Politz; Jay Shendure; Sheng Zhong
Journal:  Nature       Date:  2017-09-13       Impact factor: 49.962

7.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

Authors:  Adrian L Sanborn; Suhas S P Rao; Su-Chen Huang; Neva C Durand; Miriam H Huntley; Andrew I Jewett; Ivan D Bochkov; Dharmaraj Chinnappan; Ashok Cutkosky; Jian Li; Kristopher P Geeting; Andreas Gnirke; Alexandre Melnikov; Doug McKenna; Elena K Stamenova; Eric S Lander; Erez Lieberman Aiden
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-23       Impact factor: 11.205

8.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

9.  Multiscale and integrative single-cell Hi-C analysis with Higashi.

Authors:  Ruochi Zhang; Tianming Zhou; Jian Ma
Journal:  Nat Biotechnol       Date:  2021-10-11       Impact factor: 54.908

10.  Multiscale modeling of genome organization with maximum entropy optimization.

Authors:  Xingcheng Lin; Yifeng Qi; Andrew P Latham; Bin Zhang
Journal:  J Chem Phys       Date:  2021-07-07       Impact factor: 3.488

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  2 in total

1.  Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.

Authors:  Lorenzo Boninsegna; Asli Yildirim; Guido Polles; Yuxiang Zhan; Sofia A Quinodoz; Elizabeth H Finn; Mitchell Guttman; Xianghong Jasmine Zhou; Frank Alber
Journal:  Nat Methods       Date:  2022-07-11       Impact factor: 47.990

Review 2.  Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants.

Authors:  Wujuan Zhong; Weifang Liu; Jiawen Chen; Quan Sun; Ming Hu; Yun Li
Journal:  Front Cell Dev Biol       Date:  2022-08-19
  2 in total

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