Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans.
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 articleSubject
3' Untranslated RegionsAlternative Splicing
Animals
Caenorhabditis elegans
Cluster Analysis
Exons
Gene Expression Profiling
Gene Expression Regulation, Developmental
Operon
RNA Isoforms
RNA, Messenger
Trans-Splicing
Transcriptome
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https://hdl.handle.net/10161/10402Published Version (Please cite this version)
10.1101/gr.133587.111Publication 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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Show full item recordScholars@Duke
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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