Exploring the relationship between intron retention and chromatin accessibility in plants

BMC Genomics
Fahad UllahAsa Ben-Hur

Abstract

Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular. In this study we use publicly available DNase I-seq data in arabidopsis and rice to investigate the relationship...Continue Reading

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Datasets Mentioned

BETA
E
53322
41302
38480

Methods Mentioned

BETA
RNA-seq
I-seq
methylation profiling
bisulfite-seq

Software Mentioned

STAR
R package
R
trimmer
Trim Galore !
bismark
clustalw2
SpliceGrapher
FastQC
Bowtie

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