Exploring the relationship between intron retention and chromatin accessibility in plants View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Fahad Ullah, Michael Hamilton, Anireddy S.N. Reddy, Asa Ben-Hur

ABSTRACT

BACKGROUND: 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. RESULTS: In this study we use publicly available DNase I-seq data in arabidopsis and rice to investigate the relationship between IR and chromatin structure. We find that IR events are highly enriched in DHSs in both species. This implies that chromatin is more open in retained introns, which is consistent with a kinetic model of the process whereby higher speeds of transcription in those regions give less time for the spliceosomal machinery to recognize and splice out those introns co-transcriptionally. The more open chromatin in IR can also be the result of regulation mediated by DNA-binding proteins. To test this, we performed an exhaustive search for footprints left by DNA-binding proteins that are associated with IR. We identified several hundred short sequence elements that exhibit footprints in their DNase I-seq coverage, the telltale sign for binding events of a regulatory protein, protecting its binding site from cleavage by DNase I. A highly significant fraction of those sequence elements are conserved between arabidopsis and rice, a strong indication of their functional importance. CONCLUSIONS: In this study we have established an association between IR and chromatin accessibility, and presented a mechanistic hypothesis that explains the observed association from the perspective of the co-transcriptional nature of splicing. Furthermore, we identified conserved sequence elements for DNA-binding proteins that affect splicing. More... »

PAGES

21

References to SciGraph publications

  • 2014-12. Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis in BMC GENOMICS
  • 2013-08. DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements in NATURE GENETICS
  • 1994. Pre-mRNA Splicing in Plants in PRE-MRNA PROCESSING
  • 2012-12. Epigenetic features are significantly associated with alternative splicing in BMC GENOMICS
  • 2012-01. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data in GENOME BIOLOGY
  • 2003-01. Controlling the double helix in NATURE
  • 2015-12. Efficient Test and Visualization of Multi-Set Intersections in SCIENTIFIC REPORTS
  • 2009-04. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting in NATURE METHODS
  • 2010-12. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii in BMC GENOMICS
  • 2013-04. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions in GENOME BIOLOGY
  • 2007. Searching for splicing motifs. in ALTERNATIVE SPLICING IN THE POSTGENOMIC ERA
  • 2008. Splice Site Requirements and Switches in Plants in NUCLEAR PRE-MRNA PROCESSING IN PLANTS
  • 2007-12. A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana in BMC BIOINFORMATICS
  • 2011-03. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns in NATURE GENETICS
  • 2010-09. AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling in PROTOPLASMA
  • 2012-09. The accessible chromatin landscape of the human genome in NATURE
  • 2011-10. Functional consequences of developmentally regulated alternative splicing in NATURE REVIEWS GENETICS
  • 2007-07. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project in NATURE
  • 2009-03. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome in GENOME BIOLOGY
  • 2017-12. Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants in GENOME BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12864-017-4393-z

    DOI

    http://dx.doi.org/10.1186/s12864-017-4393-z

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1100194333

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29304739


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