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MicroRNA Cancer Regulation pp 169–187Cite as

Coordinated Networks of microRNAs and Transcription Factors with Evolutionary Perspectives

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 774))

Abstract

MicroRNAs (miRNAs) and transcription factors (TFs) are two major classes of trans-regulators in gene regulatory networks. Coordination between miRNAs and TFs has been demonstrated by individual studies on developmental processes and the pathogenesis of various cancers. Systematic computational approaches have an advantage in elucidating global network features of the miRNA-TF coordinated regulation. miRNAs and TFs have distinct molecular and evolutionary properties. In particular, miRNA genes have a rapid turnover of birth-and-death processes during evolution, and their effects are widespread but modest. Therefore, miRNAs and TFs are considered to have different contributions to their coordination. The miRNA-TF coordinated feedforward circuits are considered to cause significant increases in redundancy but drastically reduce the target gene repertoire, which poses the question, to what extent is miRNA-TF coordination beneficial? Evolutionary analyses provide wide perspectives on the features of miRNA-TF coordinated regulatory networks at a systems level.

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Abbreviations

miRNA:

microRNA

TF:

transcription factor

TFBS:

transcription factor binding site

PSSM:

position-specific scoring matrix

PWM:

position-weight matrix

pri-miRNA:

primary miRNA

pre-miRNA:

precursor miRNA

RISC:

RNA-induced silencing complex

UTR:

untranslated region

HITS-CLIP:

high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation

PAR-CLIP:

photoactivatable-ribonucleoside-enhanced crosslinking and immuno­precipitation

TE:

transposable element

MITE:

miniature inverted-repeat transposable element

Myr:

million years

GO:

Gene Ontology

FFL:

feedforward loop

FFC:

feedforward circuit

Y1H:

yeast one-hybrid

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Acknowledgment

This work was supported by Grant-in-Aid for Scientific Research (MEXT) KAKENHI 23570273.

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Authors and Affiliations

  1. Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan

    Hisakazu Iwama M.D., D. Med. Sci.

  2. Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan

    Hisakazu Iwama M.D., D. Med. Sci.

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  1. Hisakazu Iwama M.D., D. Med. Sci.
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Correspondence to Hisakazu Iwama M.D., D. Med. Sci. .

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Editors and Affiliations

  1. Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Ulf Schmitz

  2. Dept. of Systems Biology and Bioinformat, Universität Rostock Institut of Computer Science, Rostock, Germany

    Olaf Wolkenhauer

  3. Rostock, Germany

    Julio Vera

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Iwama, H. (2013). Coordinated Networks of microRNAs and Transcription Factors with Evolutionary Perspectives. In: Schmitz, U., Wolkenhauer, O., Vera, J. (eds) MicroRNA Cancer Regulation. Advances in Experimental Medicine and Biology, vol 774. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5590-1_10

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