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ncRNA–Protein Interactions in Development and Disease from the Perspective of High-Throughput Studies

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Abstract

Genome-scale studies have provided strong support to the prevalent transcription of nonprotein-coding RNAs (ncRNAs) in various organisms. The immense functional potential embedded in long intergenic ncRNAs (>200 nucleotides) have especially aroused excitement in the scientific community. ncRNA–protein complexes are now known to participate in an astonishing array of processes in transcriptional and posttranscriptional gene regulations; the mechanisms reviewed here may just be a minor fraction of the vast unknowns. These ncRNA-mediated cellular activities contribute to an expansive spectrum of developmental processes such as embryogenesis and organogenesis, and the misregulation of these leads to tumor growth and diseases. The characterization of ncRNAs is progressing at a very fast pace, so much aided by innovations in genome-wide high-throughput technologies (e.g., mass spectrometry, deep sequencing, large scale RNAi screen), and the development of computational tools for data processing. We here present an up-to-date view of the expanding field of ncRNAs in epigenetic regulation, and the development of genome-wide high-throughput methodologies that facilitates our understanding of ncRNAs in a systematic manner.

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Abbreviations

CD:

Chromodomain

CHART:

Capture hybridization analysis of RNA targets

ChIP-seq:

Chromatin immunoprecipitation followed by sequencing

ChIRP:

Chromatin isolation by RNA Purification

CLIP:

Cross-linking and immunoprecipitation

CRP:

Chromatin-remodeling proteins

CUTS:

Cryptic unstable transcripts

eRNAs:

Enhancer derived RNAs

ESCs:

Embryonic stem cell

HOTAIR:

Hox antisense intergenic RNA

lncRNAs:

Long intergenic noncoding RNAs

LSD/co-rest:

Lysine-specific demethylase corepressor for element1 silencing transcription factor

mRNA:

Messenger RNA

Nats:

Natural antisense transcripts

ncRNAs:

Noncoding RNAs

NoDS:

ncRNA with nuclear detention sequence

PAR-CLIP:

Photo-activable ribonucleoside-enhanced CLIP

PASRs:

Promoter-associated short RNAs

PRC2:

Polycome repressive complex 2

PROMPTS:

Promoter upstream transcripts

RBP:

RNA-binding proteins

RIP:

Ribonucleoprotein immunoprecipitation for RNA

RIP-seq:

RIP sequencing

RNAcompete

RNAPII:

RNA polymerase II

SELEX:

Systematic evolution of ligands by exponential enrichment

TASRs:

Terminator-associated short RNAs

TF:

Transcription factor

tiRNAs:

Transcription initiation-associated RNAs

TSSa-RNAs:

Transcription start site-associated RNAs

uaRNAs:

Upstream antisense RNAs

UNTS:

Upstream noncoding transcripts

Xuts:

Xrn1 sensitive unstable transcripts

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Acknowledgment

This work was supported by Ontario Research Fund—Global Leader (Round 2) to JG and ZZ. YL is co-funded by NSERC Canada Graduate Scholarship and Ontario Graduate Scholarship.

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Authors and Affiliations

  1. Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

    Dorothy Yanling Zhao B.Sc., M.Sc., Ph.D. Candidate

  2. Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

    Yue Li B.Sc., M.Sc., Ph.D. Candidate

  3. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada, M5S 3E1

    Jack Greenblatt

  4. Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, 6th Floor, Toronto, ON, Canada, M5S 3E1

    Zhaolei Zhang B.Sc., Ph.D.

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  1. Dorothy Yanling Zhao B.Sc., M.Sc., Ph.D. Candidate
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  2. Yue Li B.Sc., M.Sc., Ph.D. Candidate
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  3. Jack Greenblatt
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  4. Zhaolei Zhang B.Sc., Ph.D.
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Corresponding author

Correspondence to Zhaolei Zhang B.Sc., Ph.D. .

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Editors and Affiliations

  1. Banting & Best Dept. Medical Research, University of Toronto Donnelly Ctr Cell. & Biomolecular Res., Toronto, Ontario, Canada

    Andrew Emili

  2. University of Toronto Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada

    Jack Greenblatt

  3. Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada

    Shoshana Wodak

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Zhao, D.Y., Li, Y., Greenblatt, J., Zhang, Z. (2014). ncRNA–Protein Interactions in Development and Disease from the Perspective of High-Throughput Studies. In: Emili, A., Greenblatt, J., Wodak, S. (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7931-4_5

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