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

Epigenomics

Volumn 6, Issue 5, 2014, Pages 455-457

  Raviram, Ramya ^a   Rocha, Pedro P ^a   Bonneau, Richard ^b,c,d   Skok, Jane A ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c NEW YORK UNIVERSITY   (United States)

^d Simons Center for Data Analysis   (United States)

Author keywords

4C Seq; chromosomal interactions; chromosome conformation capture; resolution

Indexed keywords

4C SEQ METHOD; ARTIFACT; CHROMOSOME STRUCTURE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCUS; GENETIC PROCEDURES; HUMAN; NOTE; POLYMERASE CHAIN REACTION; X CHROMOSOME INACTIVATION; BIOLOGY; CHEMISTRY; CHROMOSOME; CONFORMATION; GENETICS; GENOMICS; METABOLISM; PROCEDURES;

CHROMOSOMES; COMPUTATIONAL BIOLOGY; GENOMICS; NUCLEIC ACID CONFORMATION;

EID: 84913616870     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.14.47     Document Type: Note

References (17)

1. Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2(4), 292-301 (2001).
2. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 295(5558), 1306-1311 (2002).
3. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14(6), 390-403 (2013).
4. Splinter E, De Wit E, Nora EP et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev. 25(13), 1371-1383 (2011).
5. Ghavi-Helm Y, Klein FA, Pakozdi T et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512 (7512) 96-100 (2014).
6. Van De Werken HJ, Landan G, Holwerda SJ et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9(10), 969-972 (2012).
7. Medvedovic J, Ebert A, Tagoh H et al. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire. Immunity 39(2), 229-244 (2013).
8. Rocha PP, Micsinai M, Kim JR et al. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol. Cell 47(6), 873-885 (2012).
9. Simonis M, Klous P, Homminga I et al. High-resolution identifcation of balanced and complex chromosomal rearrangements by 4C technology. Nat. Methods 6(11), 837-842 (2009).
10. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science 334(6053), 222-225 (2011).
11. Van De Werken HJ, De Vree PJ, Splinter E et al. 4C technology: protocols and data analysis. Methods Enzymol. 513, 89-112 (2012).
12. Denholtz M, Bonora G, Chronis C et al. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell 13(5), 602-616 (2013).
13. Williams RL Jr, Starmer J, Mugford JW et al. fourSig: a method for determining chromosomal interactions in 4C-Seq data. Nucleic Acids Res. 42(8), e68 (2014).
14. De Wit E, Bouwman BA, Zhu Y et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501(7466), 227-231 (2013).
15. Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 41(13), e132 (2013).
16. Collins A, Hewitt SL, Chaumeil J et al. RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation. Immunity 34(3), 303-314 (2011).
17. Hewitt SL, Farmer D, Marszalek K et al. Association between the Igk and Igh immunoglobulin loci mediated by the 3' Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells. Nat. Immunol. 9(4), 396-404 (2008).