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Literature DB >> 25431936

Interpreting 4C-Seq data: how far can we go?

Ramya Raviram¹, Pedro P Rocha, Richard Bonneau, Jane A Skok.

Abstract

Entities: Chemical Disease Species

Keywords: 4C-Seq; chromosomal interactions; chromosome conformation capture; resolution

Mesh：

Year: 2014 PMID： 25431936 PMCID： PMC4406053 DOI： 10.2217/epi.14.47

Source DB: PubMed Journal: Epigenomics ISSN： 1750-192X Impact factor: 4.778

× No keyword cloud information.

17 in total

1. The pluripotent genome in three dimensions is shaped around pluripotency factors.

Authors: Elzo de Wit; Britta A M Bouwman; Yun Zhu; Petra Klous; Erik Splinter; Marjon J A M Verstegen; Peter H L Krijger; Nicola Festuccia; Elphège P Nora; Maaike Welling; Edith Heard; Niels Geijsen; Raymond A Poot; Ian Chambers; Wouter de Laat
Journal: Nature Date: 2013-07-24 Impact factor: 49.962

Review 2. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Authors: Job Dekker; Marc A Marti-Renom; Leonid A Mirny
Journal: Nat Rev Genet Date: 2013-05-09 Impact factor: 53.242

3. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Authors: Erik Splinter; Elzo de Wit; Elphège P Nora; Petra Klous; Harmen J G van de Werken; Yun Zhu; Lucas J T Kaaij; Wilfred van Ijcken; Joost Gribnau; Edith Heard; Wouter de Laat
Journal: Genes Dev Date: 2011-06-20 Impact factor: 11.361

4. 4C technology: protocols and data analysis.

Authors: Harmen J G van de Werken; Paula J P de Vree; Erik Splinter; Sjoerd J B Holwerda; Petra Klous; Elzo de Wit; Wouter de Laat
Journal: Methods Enzymol Date: 2012 Impact factor: 1.600

5. Robust 4C-seq data analysis to screen for regulatory DNA interactions.

Authors: Harmen J G van de Werken; Gilad Landan; Sjoerd J B Holwerda; Michael Hoichman; Petra Klous; Ran Chachik; Erik Splinter; Christian Valdes-Quezada; Yuva Oz; Britta A M Bouwman; Marjon J A M Verstegen; Elzo de Wit; Amos Tanay; Wouter de Laat
Journal: Nat Methods Date: 2012-09-09 Impact factor: 28.547

6. Close proximity to Igh is a contributing factor to AID-mediated translocations.

Authors: Pedro P Rocha; Mariann Micsinai; JungHyun Rachel Kim; Susannah L Hewitt; Patricia P Souza; Thomas Trimarchi; Francesco Strino; Fabio Parisi; Yuval Kluger; Jane A Skok
Journal: Mol Cell Date: 2012-08-02 Impact factor: 17.970

7. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.

Authors: Matthew Denholtz; Giancarlo Bonora; Constantinos Chronis; Erik Splinter; Wouter de Laat; Jason Ernst; Matteo Pellegrini; Kathrin Plath
Journal: Cell Stem Cell Date: 2013-09-12 Impact factor: 24.633

8. RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation.

Authors: Amélie Collins; Susannah L Hewitt; Julie Chaumeil; Maclean Sellars; Mariann Micsinai; Jeanne Allinne; Fabio Parisi; Elphège P Nora; Dan J Bolland; Anne E Corcoran; Yuval Kluger; Remy Bosselut; Wilfried Ellmeier; Mark M W Chong; Dan R Littman; Jane A Skok
Journal: Immunity Date: 2011-03-25 Impact factor: 31.745

9. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

Authors: Jasna Medvedovic; Anja Ebert; Hiromi Tagoh; Ido M Tamir; Tanja A Schwickert; Maria Novatchkova; Qiong Sun; Pim J Huis In 't Veld; Chunguang Guo; Hye Suk Yoon; Yves Denizot; Sjoerd J B Holwerda; Wouter de Laat; Michel Cogné; Yang Shi; Frederick W Alt; Meinrad Busslinger
Journal: Immunity Date: 2013-08-22 Impact factor: 31.745

10. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.

Authors: Supat Thongjuea; Ralph Stadhouders; Frank G Grosveld; Eric Soler; Boris Lenhard
Journal: Nucleic Acids Res Date: 2013-05-13 Impact factor: 16.971

5 in total

Interpreting 4C-Seq data: how far can we go?

1. The pluripotent genome in three dimensions is shaped around pluripotency factors.

Review 2. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

3. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

4. 4C technology: protocols and data analysis.

5. Robust 4C-seq data analysis to screen for regulatory DNA interactions.

6. Close proximity to Igh is a contributing factor to AID-mediated translocations.

7. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.

8. RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation.

9. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

10. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.

1. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

2. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Review 3. Computational Methods for Assessing Chromatin Hierarchy.

Review 4. Functional genomic approaches to elucidate the role of enhancers during development.

5. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.