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Cited by 10RNA Research and SplicingRNA and protein synthesis mechanismsGene Regulatory Network Analysis

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A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms

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Jiang, Wen, Guo, Zhanyong, Lages, Nuno, Zheng, W. Jim, Feliers, Denis, Zhang, Fangyuan, Wang, Degeng·2018·Scientific Reports
DOI 10.1038/s41598-018-24039-1PMC PMC5893539

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Abstract

To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured transcription rate (TR), mRNA abundance (RA) and translation activity (TA). This revealed multiple insights. First, the three parameters displayed systematic statistical differences. Sequentially more genes exhibited extreme (low or high) expression values from TR to RA, and then to TA; that is, cellular coordination of multiple transcriptome regulatory mechanisms leads to sequentially enhanced gene expression selectivity as the genetic information flow from the genome to the proteome. Second, contribution of the stabilization-by-translation regulatory mechanism to the cellular coordination process was assessed. The data enabled an estimation of mRNA stability, revealing a moderate but significant positive correlation between mRNA stability and translation activity. Third, the proportion of mRNA occupied by un-translated regions (UTR) exhibited a negative relationship with the level of this correlation, and was thus a major determinant of the mode of regulation of the mRNA. High-UTR-proportion mRNAs tend to defy the stabilization-by-translation regulatory mechanism, staying out of the polysome but remaining stable; mRNAs with little UTRs largely followed this regulation. In summary, we quantitatively delineated the relationship among multiple transcriptome regulation parameters, i.e ., cellular coordination of corresponding regulatory mechanisms.

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Metadata

Authors
Jiang, W., Guo, Z., Lages, N., Zheng, W. J., Feliers, D., Zhang, F., & Wang, D.
Affiliations
  • Texas Tech University (US)
  • Henan Agricultural University (CN)
  • University of Lisbon (PT)
  • The University of Texas Health Science Center at Houston (US)
Corresponding author
Wang, Degeng
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2018-04-10
Volume
8
Issue
1
Pages
5742-5742
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-018-24039-1
PMC
PMC5893539
OpenAlex
W2952358358
Cited by
10
References
4
Citations by year
2025: 2 · 2024: 1 · 2023: 1 · 2022: 1 · 2020: 4 · 2018: 1
FWCI
0.44
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ThinkTech (Texas Tech University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Cancer Prevention and Research Institute of Texas (RP170668)
  • Texas Tech University
  • National Institute of General Medical Sciences (R15GM122006)
  • U.S. National Library of Medicine (R01LM010212)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
transcriptome regulation, transcription rate, mRNA levels, translation practice, mRNA stability
MeSH terms
Animals, Gene Expression Regulation, Humans, Models, Biological, RNA, Messenger, Protein Biosynthesis, Computational Biology, Untranslated Regions, RNA Stability, Cell Line, Tumor, Transcriptome

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