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Genetics. 2019 Jul;212(3):931-951. doi: 10.1534/genetics.119.302223. Epub 2019 May 9.

ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities.

Author information

1
Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287.
2
Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona.
3
Barrett, The Honors College, Arizona State University, Tempe, Arizona 85281.
4
Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287 mangone@asu.edu.

Abstract

MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3'UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.

KEYWORDS:

ALG-1; Caenorhabditis elegans; alternative splicing; asd-2; body muscle; hrp-2; intestine; miRNA; smu-2; transcriptome

PMID:
31073019
PMCID:
PMC6614907
[Available on 2020-07-01]
DOI:
10.1534/genetics.119.302223

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