ArticleBMC genomics2009
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts.Molecular cell · 2017Article
- A cautionary note on the use of chromosome conformation capture in plants.Plant methods · 2017Article
- MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3.Cell death & disease · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigher eukaryotes control the expression of their genes by mechanisms that we are just beginning to understand. A complex layer of control is the dynamic spatial organization of the nucleus.
resultsWe present a bioinformatics solution (3PD) to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays. 3C assays take a snapshot of chromosomal contacts by a fixation step and quantify them by PCR. Our contribution is to rapidly design an optimal primer set for the crucial PCR step. Our primer design reduces the level of experimental error as primers are highly similar in terms of physical properties and amplicon length. All 3C primers are compatible with multiplex PCR reactions. Primer uniqueness is checked genome-wide with a suitable index structure.
conclusionsIn summary, our software 3PD facilitates genome-wide primer design for 3C experiments in a matter of seconds. Our software is available as a web server at: http://www.pristionchus.org/3CPrimerDesign/.
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