Literature DB >> 28905911

The 4D nucleome project.

Job Dekker1, Andrew S Belmont2, Mitchell Guttman3, Victor O Leshyk4, John T Lis5, Stavros Lomvardas6, Leonid A Mirny7, Clodagh C O'Shea8, Peter J Park9, Bing Ren10, Joan C Ritland Politz11, Jay Shendure12, Sheng Zhong4.   

Abstract

The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.

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Year:  2017        PMID: 28905911      PMCID: PMC5617335          DOI: 10.1038/nature23884

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  98 in total

1.  Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.

Authors:  Emily M Darrow; Miriam H Huntley; Olga Dudchenko; Elena K Stamenova; Neva C Durand; Zhuo Sun; Su-Chen Huang; Adrian L Sanborn; Ido Machol; Muhammad Shamim; Andrew P Seberg; Eric S Lander; Brian P Chadwick; Erez Lieberman Aiden
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-18       Impact factor: 11.205

2.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

Authors:  Marieke Simonis; Petra Klous; Erik Splinter; Yuri Moshkin; Rob Willemsen; Elzo de Wit; Bas van Steensel; Wouter de Laat
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

Review 3.  Biogenesis and function of nuclear bodies.

Authors:  Yuntao S Mao; Bin Zhang; David L Spector
Journal:  Trends Genet       Date:  2011-06-15       Impact factor: 11.639

4.  The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.

Authors:  Jesse M Engreitz; Amy Pandya-Jones; Patrick McDonel; Alexander Shishkin; Klara Sirokman; Christine Surka; Sabah Kadri; Jeffrey Xing; Alon Goren; Eric S Lander; Kathrin Plath; Mitchell Guttman
Journal:  Science       Date:  2013-07-04       Impact factor: 47.728

5.  The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

Authors:  Hendrik G Stunnenberg; Martin Hirst
Journal:  Cell       Date:  2016-11-17       Impact factor: 41.582

6.  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

7.  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

8.  Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.

Authors:  Sami Hocine; Pascal Raymond; Daniel Zenklusen; Jeffrey A Chao; Robert H Singer
Journal:  Nat Methods       Date:  2012-12-23       Impact factor: 28.547

9.  FISH-ing for captured contacts: towards reconciling FISH and 3C.

Authors:  Geoffrey Fudenberg; Maxim Imakaev
Journal:  Nat Methods       Date:  2017-06-12       Impact factor: 28.547

10.  Nucleolar tethering mediates pairing between the IgH and Myc loci.

Authors:  Daniel E Strongin; Mark Groudine; Joan C Ritland Politz
Journal:  Nucleus       Date:  2014 Sep-Oct       Impact factor: 4.197

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  187 in total

Review 1.  Epigenetics and the dynamics of chromatin during adenovirus infections.

Authors:  Kelsey L Lynch; Linda R Gooding; Charlie Garnett-Benson; David A Ornelles; Daphne C Avgousti
Journal:  FEBS Lett       Date:  2019-12-15       Impact factor: 4.124

2.  Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

Authors:  Furqan M Fazal; Shuo Han; Kevin R Parker; Pornchai Kaewsapsak; Jin Xu; Alistair N Boettiger; Howard Y Chang; Alice Y Ting
Journal:  Cell       Date:  2019-06-20       Impact factor: 41.582

3.  Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system.

Authors:  Wenqing Qiu; Zhijiao Xu; Min Zhang; Dandan Zhang; Hui Fan; Taotao Li; Qianfeng Wang; Peiru Liu; Zaihua Zhu; Duo Du; Minjia Tan; Bo Wen; Yun Liu
Journal:  Nucleic Acids Res       Date:  2019-05-21       Impact factor: 16.971

Review 4.  Nucleosome structure and dynamics are coming of age.

Authors:  Keda Zhou; Guillaume Gaullier; Karolin Luger
Journal:  Nat Struct Mol Biol       Date:  2018-12-10       Impact factor: 15.369

Review 5.  Functional Assays to Screen and Dissect Genomic Hits: Doubling Down on the National Investment in Genomic Research.

Authors:  Kiran Musunuru; Daniel Bernstein; F Sessions Cole; Mustafa K Khokha; Frank S Lee; Shin Lin; Thomas V McDonald; Ivan P Moskowitz; Thomas Quertermous; Vijay G Sankaran; David A Schwartz; Edwin K Silverman; Xiaobo Zhou; Ahmed A K Hasan; Xiao-Zhong James Luo
Journal:  Circ Genom Precis Med       Date:  2018-04

Review 6.  Blood disease-causing and -suppressing transcriptional enhancers: general principles and GATA2 mechanisms.

Authors:  Emery H Bresnick; Kirby D Johnson
Journal:  Blood Adv       Date:  2019-07-09

Review 7.  Mapping chromatin modifications at the single cell level.

Authors:  Connor H Ludwig; Lacramioara Bintu
Journal:  Development       Date:  2019-06-27       Impact factor: 6.868

8.  Visual Pattern-Driven Exploration of Big Data.

Authors:  Michael Behrisch; Tobias Schreck; Robert Krüger; Nils Gehlenborg; Fritz Lekschas; Hanspeter Pfister
Journal:  2018 Int Symp Big Data Vis Immers Analyt (BDVA) (2018)       Date:  2018-11-15

9.  Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains.

Authors:  Kelvin See; Yemin Lan; Joshua Rhoades; Rajan Jain; Cheryl L Smith; Jonathan A Epstein
Journal:  Development       Date:  2019-02-05       Impact factor: 6.868

10.  Tibanna: software for scalable execution of portable pipelines on the cloud.

Authors:  Soohyun Lee; Jeremy Johnson; Carl Vitzthum; Koray Kırlı; Burak H Alver; Peter J Park
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

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