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Exploring the relationship between intron retention and chromatin accessibility in plants
Fahad Ullah1, Michael Hamilton1, Anireddy S N Reddy2
1Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA.
BMC Genomics
|January 7, 2018
Summary
Plant intron retention (IR) is linked to open chromatin structures. This study reveals that IR events occur in accessible chromatin regions, suggesting a role for chromatin structure in regulating this key splicing process.
Area of Science:
- Plant molecular biology
- Genomics
- Epigenetics
Background:
- Intron retention (IR) is a prevalent alternative splicing form in plants, crucial for gene product diversity.
- Splicing is co-transcriptional and influenced by transcription speed, which is affected by chromatin structure.
- The role of chromatin structure in regulating plant IR remains largely unknown.
Purpose of the Study:
- To investigate the relationship between intron retention and chromatin structure in plants.
- To explore the potential regulatory mechanisms involving chromatin accessibility and DNA-binding proteins in IR.
Main Methods:
- Analysis of publicly available DNase I-seq data in Arabidopsis and rice.
- Genome-wide identification of DNase I Hypersensitive Sites (DHSs).
- Exhaustive search for DNA-binding protein footprints associated with IR events.
Main Results:
- IR events are significantly enriched within DHSs in both Arabidopsis and rice.
- Open chromatin in retained introns supports a kinetic model of co-transcriptional splicing.
- Hundreds of conserved, footprinted sequence elements indicate regulation by DNA-binding proteins.
Conclusions:
- An association between intron retention and chromatin accessibility in plants is established.
- A mechanistic hypothesis linking chromatin structure, transcription kinetics, and IR is proposed.
- Conserved regulatory elements suggest functional importance of DNA-binding proteins in IR.
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