Journal article
Robust 4C-seq data analysis to screen for regulatory DNA interactions
Nature Methods, Vol.9(10), pp.969-+
Oct/2012
Abstract
Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.
Details
- Title
- Robust 4C-seq data analysis to screen for regulatory DNA interactions
- Creators
- de Werken, Harmen J. G. van de Werken (null)Gilad Landan (null) - The Weizmann Institute of ScienceSjoerd J. B. Holwerda (null)Michael Hoichman (null) - The Weizmann Institute of SciencePetra Klous (null)Ran Chachik (null)Erik Splinter (null)Christian Valdes-Quezada (null)Yuva Oz (null)Britta A. M. Bouwman (null)Marjon J. A. M. Verstegen (null)Wit, Elzo de Wit (null)Amos Tanay (null) - 972WIS_INST___83Laat, Wouter de Laat (null)
- Resource Type
- Journal article
- Publication Details
- Nature Methods, Vol.9(10), pp.969-+; Oct/2012
- Number of pages
- 8
- Language
- English
- DOI
- https://doi.org/10.1038/NMETH.2173
- Grant note
- Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project; Dutch Scientific Organization (NWO) [91204082, 935170621]; European Research Council [209700]; InteGeR FP7 Marie Curie Initial Training Networks [PITN-GA-2007-214902]; Israeli Science FoundationWe would like to thank R. Palstra, E. Yaffe and other members of our labs for help and input, G. Geeven for testing the 4C-seq pipeline and H.T. Timmers (Netherlands Proteomics Centre and University Medical Center Utrecht) and J.P.P. Meijerink (Erasmus Medical Center-Sophia Children's Hospital) for providing cells. This work was supported by grants from the Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project to W.d.L. and A.T., grants from the Dutch Scientific Organization (NWO) (91204082 and 935170621), a European Research Council Starting Grant (209700, '4C') and InteGeR FP7 Marie Curie Initial Training Networks contract (no. PITN-GA-2007-214902) to W.d.L., and the Israeli Science Foundation integrated technologies grant to A.T._ALMAME_DELIMITER_
- Record Identifier
- 993267372103596
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