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Exploring the relationship between intron retention and DNase I hypersensitivity in plants Fahad Ullah1, A.S.N. Reddy2, and Asa Ben-Hur1 1Computer Science Department, Colorado State University 2Department of Biology and Program in Molecular Plant Biology, Colorado State University
INTRODUCTION • •
• •
RESULTS
Alternative Splicing (AS) is a regulated phenomenon responsible for generating multiple transcripts from a single gene. Intron Retention is the most common form of AS in plants [1].
METHODS
DNase I-seq data profile across IR and IE events
DNase I digests DNA at regions of open chromatin. These regions are known as DNase I Hypersensitive Sites (DHSs). • These sites can be identified using a method called DNase I-Seq.
Data Source Arabidopsis [2] Arabidopsis [3] Rice [4]
DHS Content IR IE 9.39% 3.37% 8.87% 3.42% 18.23% 4.61%
• • • •
RNA-Seq and DNase I-Seq data in Arabidopsis [3,4] and rice [5]. IR and IE events extracted from the RNA-Seq data. Adjusted for the profile coverage of DNase I-Seq data across genes. Experiment pipeline: associating DHSs with IR/IE and footprint analysis
DHS content is the fraction of intron retention (IR) / intron excision (IE) events with an overlapping DNase I hypersensitive site(s). The significance of the overlap of DHSs with IR events is verified by the hypergeometric test.
Transcription speed and nucleosome occupancy affects splicing [2].
• IR events are enriched for DNase I hypersensitive sites.
• DNase I-seq data profile indicates more flexible chromatin in IR. • Evidence for protein footprints near the occurrences of k-mers associated with IR and IE. Future Work • Extend this work to other forms of AS.
Identification of denovo footprints using continuous HMMs
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Hypergeometric p-value 5.50E-11 1.54E-47 8.90E-67
• Chromatin state can affect splicing since splicing is cotranscriptional.
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Reddy, A.S.N., Roger, M.F. , Hamilton M., Ben-Hur A. et al. (2012) Frontiers in Plant Sciences. 3, 18. Almeida, S.F. et al. (2014) Seminars in Cell and Developmental Biology. 32, 2-10. Sullivan A.M., Arsovski A.A. et al. (2014) Cell Reports 8(6), 2015-30. Zhang W, Zhang T et al. (2012) Plant Cell 24(7). Zhang W., Wu Y et al. (2012) Genome Research 22(1).
ACKNOWLEDGMENTS This project was funded by the US Department of Energy (DOE) Plant Feedstocks Genomics for Bioenergy program.
