Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells

Lioudmila V. Sharova, Alexei A. Sharov, Timur Nedorezov, Yulan Piao, Nabeebi Shaik, Minoru Ko

Research output: Contribution to journalArticle

267 Citations (Scopus)

Abstract

Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3′-untranslated region (UTR) and CpG di-nucleotides in the 5′-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.

Original languageEnglish
Pages (from-to)45-58
Number of pages14
JournalDNA Research
Volume16
Issue number1
DOIs
Publication statusPublished - 2009 Feb
Externally publishedYes

Fingerprint

RNA Stability
Microarray Analysis
Oligonucleotide Array Sequence Analysis
Half-Life
Databases
Messenger RNA
Genes
3' Untranslated Regions
AU Rich Elements
5' Untranslated Regions
Regulator Genes
Embryonic Stem Cells
Cytoskeleton
Open Reading Frames
Extracellular Matrix
Mouse Embryonic Stem Cells
Mammals
Exons
Transcription Factors
Nucleotides

Keywords

  • AU-rich elements (ARE)
  • Cell differentiation
  • Embryonic stem cells
  • Exon junction
  • Leukemia inhibitory factor (LIF)
  • Microarray
  • Mouse strain
  • MRNA decay
  • MRNA degradation
  • Retinoic acid (RA)
  • Transcript

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. / Sharova, Lioudmila V.; Sharov, Alexei A.; Nedorezov, Timur; Piao, Yulan; Shaik, Nabeebi; Ko, Minoru.

In: DNA Research, Vol. 16, No. 1, 02.2009, p. 45-58.

Research output: Contribution to journalArticle

Sharova, Lioudmila V. ; Sharov, Alexei A. ; Nedorezov, Timur ; Piao, Yulan ; Shaik, Nabeebi ; Ko, Minoru. / Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. In: DNA Research. 2009 ; Vol. 16, No. 1. pp. 45-58.
@article{9886b915607342eaa2b6104cbbfdf7b8,
title = "Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells",
abstract = "Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3′-untranslated region (UTR) and CpG di-nucleotides in the 5′-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.",
keywords = "AU-rich elements (ARE), Cell differentiation, Embryonic stem cells, Exon junction, Leukemia inhibitory factor (LIF), Microarray, Mouse strain, MRNA decay, MRNA degradation, Retinoic acid (RA), Transcript",
author = "Sharova, {Lioudmila V.} and Sharov, {Alexei A.} and Timur Nedorezov and Yulan Piao and Nabeebi Shaik and Minoru Ko",
year = "2009",
month = "2",
doi = "10.1093/dnares/dsn030",
language = "English",
volume = "16",
pages = "45--58",
journal = "DNA Research",
issn = "1340-2838",
publisher = "Oxford University Press",
number = "1",

}

TY - JOUR

T1 - Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells

AU - Sharova, Lioudmila V.

AU - Sharov, Alexei A.

AU - Nedorezov, Timur

AU - Piao, Yulan

AU - Shaik, Nabeebi

AU - Ko, Minoru

PY - 2009/2

Y1 - 2009/2

N2 - Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3′-untranslated region (UTR) and CpG di-nucleotides in the 5′-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.

AB - Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3′-untranslated region (UTR) and CpG di-nucleotides in the 5′-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.

KW - AU-rich elements (ARE)

KW - Cell differentiation

KW - Embryonic stem cells

KW - Exon junction

KW - Leukemia inhibitory factor (LIF)

KW - Microarray

KW - Mouse strain

KW - MRNA decay

KW - MRNA degradation

KW - Retinoic acid (RA)

KW - Transcript

UR - http://www.scopus.com/inward/record.url?scp=65249141709&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=65249141709&partnerID=8YFLogxK

U2 - 10.1093/dnares/dsn030

DO - 10.1093/dnares/dsn030

M3 - Article

VL - 16

SP - 45

EP - 58

JO - DNA Research

JF - DNA Research

SN - 1340-2838

IS - 1

ER -