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Gene regulation of mammalian long non-coding RNA

Abstract

RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development. In this review, the newly discovered transcription mechanisms, characteristics, and functions of lncRNA are discussed.

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Abbreviations

ANRIL:

Antisense non-coding RNA in the INK4 locus

ATM:

Ataxia telangiectasia mutated

BACE:

B-site APP cleaving enzyme-1

BACE-AS:

B-site APP cleaving enzyme-1- antisense transcript

CARL:

Cardiac apoptosis-related lncRNA

CTCF:

CCCTC-binding factor

DNMT3:

DNA methyltransferase 3

DNA-PK:

DNA-dependent protein kinase

DSIF:

DRB sensitivity-inducing factor

eRNA:

Enhancer RNA

HSF1:

Heat shock factor 1

HSP70:

Heat shock protein 70

HOTAIR:

Hox transcript antisense RNA

HEK293:

Human embryonic kidney 293

LncRNA:

Long non-coding RNA

MALAT1:

Metastasis-associated lung adenocarcinoma transcription 1

mES:

Mouse embryonic stem

MIAT:

Myocardial infarction associated transcript

MYH7:

Myosin heavy gene 7

NAT:

Natural antisense transcript

NELF:

Negative elongation factor

NcRNA:

Non-coding RNA

PABPN1:

Poly(A)-binding protein nuclear 1

pTEFb:

Positive transcription elongation factor b

Pol II:

RNA polymerase II

SNP:

Single nucleotide polymorphism

TSS:

Transcription start site

TTS:

Transcription termination site

TRIM28:

Tripartite motif containing 28

XIST:

X inactivate-specific transcript

XUT:

XRN1 (5′ → 3′ exonuclease)-sensitive unstable transcript

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Acknowledgements

I appreciate my colleagues in the School of Applied Biosciences at Kyungpook National University, D. Taatjes at the University of Colorado, J. Roberts at Cornell University, G. Hu at National Institute of Environmental Health Sciences (NIEHS), and B. Chen and M. Story at the University of Texas Southwestern Medical Center for their support. I thank D. Bunch and R. Baker for their loving encouragement. I also thank Enago for the help with editing manuscript.

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Correspondence to Heeyoun Bunch.

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Funding

This study was supported by Grants from the Industry-Academic Cooperation Foundation at Kyungpook National University (KNU) to H.B.

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There is no conflict of interest for the enclosed review article.

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Communicated by S. Hohmann.

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Bunch, H. Gene regulation of mammalian long non-coding RNA. Mol Genet Genomics 293, 1–15 (2018). https://doi.org/10.1007/s00438-017-1370-9

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Keywords

  • Long non-coding RNA
  • Transcriptional mechanism
  • Gene expression regulation