Ago2 immunoprecipitation identifies predicted MicroRNAs in human embryonic stem cells and neural precursors

Loyal Goff, Jonathan Davila, Mavis R. Swerdel, Jennifer C. Moore, Rick I. Cohen, Hao Wu, Yi E. Sun, Ronald P. Hart

Research output: Contribution to journalArticle

Abstract

Background: MicroRNAs are required for maintenance of pluripotency as well as differentiation, but since more microRNAs have been computationally predicted in genome than have been found, there are likely to be undiscovered microRNAs expressed early in stem cell differentiation. Methodology/Principal Findings: SOLiD ultra-deep sequencing identified >107 unique small RNAs from human embryonic stem cells (hESC) and neural-restricted precursors that were fit to a model of microRNA biogenesis to computationally predict 818 new microRNA genes. These predicted genomic loci are associated with chromatin patterns of modified histones that are predictive of regulated gene expression. 146 of the predicted microRNAs were enriched in Ago2-containing complexes along with 609 known microRNAs, demonstrating association with a functional RISC complex. This Ago2 IP-selected subset was consistently expressed in four independent hESC lines and exhibited complex patterns of regulation over development similar to previously-known microRNAs, including pluripotency-specific expression in both hESC and iPS cells. More than 30% of the Ago2 IP-enriched predicted microRNAs are new members of existing families since they share seed sequences with known microRNAs. Conclusions/Significance: Extending the classic definition of microRNAs, this large number of new microRNA genes, the majority of which are less conserved than their canonical counterparts, likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes, the presence of chromatin marks indicative of regulated gene expression, and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation.

Original languageEnglish (US)
Article numbere7192
JournalPLoS One
Volume4
Issue number9
DOIs
StatePublished - Sep 28 2009
Externally publishedYes

Fingerprint

embryonic stem cells
Stem cells
MicroRNAs
microRNA
Immunoprecipitation
Genes
Gene expression
cell differentiation
Human Embryonic Stem Cells
Chromatin
chromatin
Cell Differentiation
Gene Expression
High-Throughput Nucleotide Sequencing
gene expression
Reduced instruction set computing
histones
Histones
Seed
stem cells

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Ago2 immunoprecipitation identifies predicted MicroRNAs in human embryonic stem cells and neural precursors. / Goff, Loyal; Davila, Jonathan; Swerdel, Mavis R.; Moore, Jennifer C.; Cohen, Rick I.; Wu, Hao; Sun, Yi E.; Hart, Ronald P.

In: PLoS One, Vol. 4, No. 9, e7192, 28.09.2009.

Research output: Contribution to journalArticle

Goff, Loyal ; Davila, Jonathan ; Swerdel, Mavis R. ; Moore, Jennifer C. ; Cohen, Rick I. ; Wu, Hao ; Sun, Yi E. ; Hart, Ronald P. / Ago2 immunoprecipitation identifies predicted MicroRNAs in human embryonic stem cells and neural precursors. In: PLoS One. 2009 ; Vol. 4, No. 9.
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abstract = "Background: MicroRNAs are required for maintenance of pluripotency as well as differentiation, but since more microRNAs have been computationally predicted in genome than have been found, there are likely to be undiscovered microRNAs expressed early in stem cell differentiation. Methodology/Principal Findings: SOLiD ultra-deep sequencing identified >107 unique small RNAs from human embryonic stem cells (hESC) and neural-restricted precursors that were fit to a model of microRNA biogenesis to computationally predict 818 new microRNA genes. These predicted genomic loci are associated with chromatin patterns of modified histones that are predictive of regulated gene expression. 146 of the predicted microRNAs were enriched in Ago2-containing complexes along with 609 known microRNAs, demonstrating association with a functional RISC complex. This Ago2 IP-selected subset was consistently expressed in four independent hESC lines and exhibited complex patterns of regulation over development similar to previously-known microRNAs, including pluripotency-specific expression in both hESC and iPS cells. More than 30{\%} of the Ago2 IP-enriched predicted microRNAs are new members of existing families since they share seed sequences with known microRNAs. Conclusions/Significance: Extending the classic definition of microRNAs, this large number of new microRNA genes, the majority of which are less conserved than their canonical counterparts, likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes, the presence of chromatin marks indicative of regulated gene expression, and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation.",
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