The relationships among GC content, nucleosome occupancy, and exon size
نویسندگان
چکیده
1Cold Spring Harbor Laboratory, Williams 5, Cold Spring Harbor, NY 11724 2Ontario Institute for Cancer Research, 101 College St. Suite 800, Toronto, ON, M5G0A3, Canada 3Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON MSS 1AB, Canada 4US Department of Agriculture/Agricultural Research Service North Atlantic Area, Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853
منابع مشابه
DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.
DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon-intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occ...
متن کاملDifferential GC content between exons and introns establishes distinct strategies of splice-site recognition.
During evolution segments of homeothermic genomes underwent a GC content increase. Our analyses reveal that two exon-intron architectures have evolved from an ancestral state of low GC content exons flanked by short introns with a lower GC content. One group underwent a GC content elevation that abolished the differential exon-intron GC content, with introns remaining short. The other group ret...
متن کاملDNA Sequence Complexity Reveals Structure Beyond GC Content in Nucleosome Occupancy
We introduce methods that rapidly evaluate a battery of informationtheoretic and algorithmic complexity measures on DNA sequences in application to potential binding sites for nucleosomes. The first application of this new tool demonstrates structure beyond GC content on DNA sequences in the context of nucleosome binding. We tested the measures on well-studied genomic sequences of size 20K and ...
متن کاملWhen epigenetics meets alternative splicing: the roles of DNA methylation and GC architecture.
The process of pre-mRNA splicing has been studied for more than 30 years, yet it is far from being fully understood. Accumulating evidence suggests that many splicing events occur cotranscriptionally and that the mRNA precursor remains associated with the chromatin until all of the introns have been removed. Cotranscriptional splicing adds many more factors that might take part in the complex a...
متن کاملThe organization of nucleosomes around splice sites
The occupancy of nucleosomes along chromosome is a key factor for gene regulation. However, except promoter regions, genome-wide properties and functions of nucleosome organization remain unclear in mammalian genomes. Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined a...
متن کامل