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Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans.

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2.6 Mb
Date
2012-10
Authors
Maxwell, Colin S
Antoshechkin, Igor
Kurhanewicz, Nicole
Belsky, Jason A
Baugh, L Ryan
Repository Usage Stats
191
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259
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Abstract
Nutrient availability profoundly influences gene expression. Many animal genes encode multiple transcript isoforms, yet the effect of nutrient availability on transcript isoform expression has not been studied in genome-wide fashion. When Caenorhabditis elegans larvae hatch without food, they arrest development in the first larval stage (L1 arrest). Starved larvae can survive L1 arrest for weeks, but growth and post-embryonic development are rapidly initiated in response to feeding. We used RNA-seq to characterize the transcriptome during L1 arrest and over time after feeding. Twenty-seven percent of detectable protein-coding genes were differentially expressed during recovery from L1 arrest, with the majority of changes initiating within the first hour, demonstrating widespread, acute effects of nutrient availability on gene expression. We used two independent approaches to track expression of individual exons and mRNA isoforms, and we connected changes in expression to functional consequences by mining a variety of databases. These two approaches identified an overlapping set of genes with alternative isoform expression, and they converged on common functional patterns. Genes affecting mRNA splicing and translation are regulated by alternative isoform expression, revealing post-transcriptional consequences of nutrient availability on gene regulation. We also found that phosphorylation sites are often alternatively expressed, revealing a common mode by which alternative isoform expression modifies protein function and signal transduction. Our results detail rich changes in C. elegans gene expression as larvae initiate growth and post-embryonic development, and they provide an excellent resource for ongoing investigation of transcriptional regulation and developmental physiology.
Type
Journal article
Subject
3' Untranslated Regions
Alternative Splicing
Animals
Caenorhabditis elegans
Cluster Analysis
Exons
Gene Expression Profiling
Gene Expression Regulation, Developmental
Operon
RNA Isoforms
RNA, Messenger
Trans-Splicing
Transcriptome
Permalink
https://hdl.handle.net/10161/10402
Published Version (Please cite this version)
10.1101/gr.133587.111
Publication Info
Maxwell, Colin S; Antoshechkin, Igor; Kurhanewicz, Nicole; Belsky, Jason A; & Baugh, L Ryan (2012). Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. Genome Res, 22(10). pp. 1920-1929. 10.1101/gr.133587.111. Retrieved from https://hdl.handle.net/10161/10402.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Baugh

L. Ryan Baugh

Professor of Biology
The Baugh Lab is interested in phenotypic plasticity and physiological adaptation to variable environmental conditions. We are using the roundworm C. elegans to understand how animals adapt to starvation using primarily genetic and genomic approaches. We are studying how development is governed by nutrient availability, how animals survive starvation, and the long-term consequences of starvation including adult disease and transgenerational epigenetic inheritance.
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