InTAD: chromosome conformation guided analysis of enhancer target genes
نویسندگان
چکیده
منابع مشابه
The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.
Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATα cells use HMR. The recombination enhancer (RE) located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating-type-specific and possibly ...
متن کاملCapturing chromosome conformation.
We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in ...
متن کاملSnapShot: Chromosome Conformation Capture
Examples Determine interaction between a known promoter and enhancer Determine comprehensively higher-order chromosome structure in a defi ned region All genes and genomic elements associated with a known LCR All intraand interchromosomal associations Determine the role of specifi c transcription factors in the interaction between a known promoter and enhancer Map chromatin interaction network ...
متن کاملChromosome Conformation Capture (3C) (PROT05)
An alternative protocol (PROT31) for 3C has been adopted by the author's lab. Much of it is identical to this version. The major differences are in the amounts of DNA used at different steps. We reliably get the same results as with this version, but also a greater yield of 3C material. Yields from this version are ample for real-time PCR analysis, but greater yields are required if the 3C mate...
متن کاملThe statistical-mechanics of chromosome conformation capture
Since Jacob and Monod's characterization of the role of DNA elements in gene control, it has been recognized that the linear organization of genome structure is important for the regulation of gene transcription and hence the manifestation of phenotypes. Similarly, it has long been hypothesized that the spatial organization (in three dimensions evolving through time), as part of the epigenome, ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2019
ISSN: 1471-2105
DOI: 10.1186/s12859-019-2655-2