Transcriptome-scale, condition-specific regulation of mrna isoform stability via the 3'UTR

This Project Grant award from the National Institutes of Health's National Institute of General Medical Sciences provides $227,480.44 to President and Fellows of Harvard College, doing business as Harvard Medical School, to conduct research from May 1, 2021 through September 30, 2022.

The research will comprehensively examine condition-specific mRNA isoforms and their properties, as well as cellular factors involved in regulating isoform half-lives on a genome-wide scale under various conditions. Specifically, the research will obtain a catalog of isoform half-lives for different growth conditions and examine isoforms for sequence and structural elements that influence stability. The relevance of any cis-features identified will be directly tested in the context of defective trans-factors such as mRNA degradation machinery components or putative RNA-binding proteins. This work aims to advance the understanding of molecular mechanisms underlying regulated mRNA decay and reveal isoform-dependent regulation of stability by major degradation pathways and RNA-binding proteins in response to environmental triggers. The funding supports this research within the Biomedical Research and Research Training program.

Abstract

Altering environmental conditions leads to reprograming of eukaryotic gene expression. One important cellular process that helps adapt gene expression levels to environmental triggers is the regulation of mrna stability. Mrnas are degraded by specialized cellular machineries, which have been studied in great detail. However, little data exists to explain what cellular signals determine mrna longevity in response to changing conditions. Alternative polyadenylation allows an individual gene to give rise to multiple distinct mrna 3' isoforms. Distinct 3' isoforms from the same gene can have different half-lives, and the steady-state distribution of mrna 3' isoforms can vary under different growth conditions. IT is plausible that a diverse array of isoforms is needed for cells to respond to environmental conditions. In part, different isoforms could allow for prompt modulation of gene expression via regulation of mrna stability. Until now, there have been no genome-wide studies addressing the importance of different isoform profiles for mrna stabilities under different conditions. This work will comprehensively examine condition-specific isoforms, isoform properties, and cellular factors involved in the regulation of isoform half-lives. In particular, a catalog of isoform half-lives for different growth conditions will be obtained using techniques optimized and/or developed in the struhl laboratory for studying 3' isoforms. The isoforms will be subsequently examined for sequence and structural elements. The relevance of any CIS-features identified will be directly tested in the context of defective trans-factors, such as degradation machinery components or putative RNA-binding proteins. The proposed work will advance our understanding of the molecular mechanisms that underlie regulated mrna decay by investigating isoform half-lives and sequence/structural elements under various conditions on a genome-wide scale. The work is expected to reveal 3' isoform-dependent regulation of mrna stability by the major degradation pathways and/or RNA-binding proteins in response to environmental triggers. Building on the investigator's background in nuclear proteostasis, training and expertise in genomics and bioinformatics will be gained. The project will be conducted in a world-renowned transcription group with deep experience in this field, providing a strong foundation for the applicant's future independent research as a principal investigator in the field of gene expression.