Young intragenic miRNAs are less coexpressed with host genes than old ones: Implications of miRNA-host gene coevolution

C. He, Z. Li, P. Chen, H. Huang, L. D. Hurst, J. Chen

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50 of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms. © 2012 The Author(s).
Original languageEnglish
Pages (from-to)4002-4012
Number of pages11
JournalNucleic Acids Research
Volume40
Issue number9
DOIs
Publication statusPublished - 2012

Fingerprint

MicroRNAs
Genes
Human Genome
Regulator Genes
Transcriptome
Chromatin
Genome
Gene Expression

Cite this

Young intragenic miRNAs are less coexpressed with host genes than old ones: Implications of miRNA-host gene coevolution. / He, C.; Li, Z.; Chen, P.; Huang, H.; Hurst, L. D.; Chen, J.

In: Nucleic Acids Research, Vol. 40, No. 9, 2012, p. 4002-4012.

Research output: Contribution to journalArticle

@article{77b919bc4fc2424c89dce8776fadf0e7,
title = "Young intragenic miRNAs are less coexpressed with host genes than old ones: Implications of miRNA-host gene coevolution",
abstract = "MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50 of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms. {\circledC} 2012 The Author(s).",
author = "C. He and Z. Li and P. Chen and H. Huang and Hurst, {L. D.} and J. Chen",
year = "2012",
doi = "10.1093/nar/gkr1312",
language = "English",
volume = "40",
pages = "4002--4012",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford Univerity Press",
number = "9",

}

TY - JOUR

T1 - Young intragenic miRNAs are less coexpressed with host genes than old ones: Implications of miRNA-host gene coevolution

AU - He, C.

AU - Li, Z.

AU - Chen, P.

AU - Huang, H.

AU - Hurst, L. D.

AU - Chen, J.

PY - 2012

Y1 - 2012

N2 - MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50 of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms. © 2012 The Author(s).

AB - MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50 of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms. © 2012 The Author(s).

UR - http://www.scopus.com/inward/record.url?scp=84861357388&partnerID=8YFLogxK

UR - http://dx.doi.org/10.1093/nar/gkr1312

U2 - 10.1093/nar/gkr1312

DO - 10.1093/nar/gkr1312

M3 - Article

VL - 40

SP - 4002

EP - 4012

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 9

ER -