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Cited by 139RNA Research and SplicingRNA regulation and diseaseCancer-related molecular mechanisms research

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

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Dittmar, Kimberly A., Jiang, Peng, Park, Juw Won, Amirikian, Karine, Wan, Ji, Shen, Shihao, Xing, Yi, Carstens, Russell P.·2012·Molecular and Cellular Biology
DOI 10.1128/mcb.06536-11PMC PMC3318588
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Abstract

Tissue-specific alternative splicing is achieved through the coordinated assembly of RNA binding proteins at specific sites to enhance or silence splicing at nearby splice sites. We used high-throughput sequencing (RNA-Seq) to investigate the complete spectrum of alternative splicing events that are regulated by the epithelium-specific splicing regulatory proteins ESRP1 and ESRP2. We also combined this analysis with direct RNA sequencing (DRS) to reveal ESRP-mediated regulation of alternative polyadenylation. To define binding motifs that mediate direct regulation of splicing and polyadenylation by ESRP, SELEX-Seq analysis was performed, coupling traditional SELEX with high-throughput sequencing. Identification and scoring of high-affinity ESRP1 binding motifs within ESRP target genes allowed the generation of RNA maps that define the position-dependent activity of the ESRPs in regulating cassette exons and alternative 3' ends. These extensive analyses provide a comprehensive picture of the functions of the ESRPs in an epithelial posttranscriptional gene expression program.

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  • The in vivo ESRP2-binding site determination with FLAG-ESRP2 eCLIP is accurate, as the identified UG-containing motifs match those identified in vitro by SELEX-seq and RNA bind-n-seq.

    “Similar UG-containing sequence motifs for ESRP proteins have been identified in vitro by SELEX-seq (Dittmar et al. 2012) and RNA bind-n-seq (Nostrand et al. 2020), confirming the accuracy of our in vivo ESRP2-binding site determination with FLAG-ESRP2 eCLIP.”

    From ESRP2–microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation (2025) · cites this paper as Dittmar et al. 2012

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Authors
Dittmar, K. A., Jiang, P., Park, J. W., Amirikian, K., Wan, J., Shen, S., Xing, Y., & Carstens, R. P.
Affiliations
  • University of Pennsylvania (US)
  • University of Iowa (US)
  • Renal Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
ORCID
Venue
Molecular and Cellular Biology
Publisher
Informa UK Limited
Published
2012-04-01
Volume
32
Issue
8
Pages
1468-1482
ISSN
  • 0270-7306 (ISSN-L)
  • 1098-5549
DOI
10.1128/mcb.06536-11
PMC
PMC3318588
OpenAlex
W2136041152
Cited by
139
References
4
Citations by year
2026: 1 · 2025: 3 · 2024: 13 · 2023: 7 · 2022: 6 · 2021: 4 · 2020: 10 · 2019: 11 · 2018: 10 · 2017: 11 · 2016: 17 · 2015: 5 · 2014: 19 · 2013: 14 · 2012: 8
FWCI
5.92
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Molecular and Cellular Biology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Institute of Clinical and Translational Sciences
  • Edward Mallinckrodt, Jr. Foundation
  • National Institutes of Health
  • National Heart, Lung, and Blood Institute (T32HL007638)
  • National Institute of General Medical Sciences (R01GM088342, R01GM088809)
  • National Institute of Diabetes and Digestive and Kidney Diseases (P30DK054759)
  • National Center for Research Resources (UL1RR024979)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Keywords
ESRP1, ESRP2, alternative splicing, alternative polyadenylation, RNA-binding proteins, post-transcriptional regulation, direct RNA sequencing, cassette exons, tissue-specific gene expression, epithelial cells
MeSH terms
Base Sequence, Binding Sites, Epithelium, Humans, Organ Specificity, Genome, Human, RNA-Binding Proteins, Alternative Splicing, Sequence Analysis, RNA, RNA Splice Sites, Genome-Wide Association Study, Nucleotide Motifs

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