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Title: A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

Abstract

Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentally-dynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclear-localized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. We conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

Authors:
 [1];  [2];  [2];  [3];  [1];  [2]
  1. Univ. of California, Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. New York Blood Center, New York, NY (United States). Red Cell Physiology Laboratory
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1256072
Alternate Identifier(s):
OSTI ID: 1379053
Grant/Contract Number:  
AC02-05CH1123; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 44; Journal Issue: 2; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Pimentel, Harold, Parra, Marilyn, Gee, Sherry L., Mohandas, Narla, Pachter, Lior, and Conboy, John G. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. United States: N. p., 2015. Web. doi:10.1093/nar/gkv1168.
Pimentel, Harold, Parra, Marilyn, Gee, Sherry L., Mohandas, Narla, Pachter, Lior, & Conboy, John G. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. United States. doi:10.1093/nar/gkv1168.
Pimentel, Harold, Parra, Marilyn, Gee, Sherry L., Mohandas, Narla, Pachter, Lior, and Conboy, John G. Tue . "A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis". United States. doi:10.1093/nar/gkv1168. https://www.osti.gov/servlets/purl/1256072.
@article{osti_1256072,
title = {A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis},
author = {Pimentel, Harold and Parra, Marilyn and Gee, Sherry L. and Mohandas, Narla and Pachter, Lior and Conboy, John G.},
abstractNote = {Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentally-dynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclear-localized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. We conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.},
doi = {10.1093/nar/gkv1168},
journal = {Nucleic Acids Research},
number = 2,
volume = 44,
place = {United States},
year = {2015},
month = {11}
}

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