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Long non-coding RNA regulation of gene expression during differentiation

Pflügers Archiv - European Journal of Physiology volume 468, pages 971–981 (2016)Cite this article

Abstract

Transcriptome analysis of mammalian genomes has revealed widespread transcription, much of which does not encode protein. Long non-coding RNAs (lncRNAs) are a subset of the non-coding transcriptome that are emerging as critical regulators of various cellular processes. Differentiation of stem and progenitor cells requires a careful execution of specific genetic programs, and recent studies have revealed that lncRNA expression contributes to specification of cell identity. LncRNAs participate in regulating differentiation at multiple levels of gene expression through various mechanisms of action. In this review, functional roles of lncRNAs in regulating cellular differentiation of blood, muscle, skin, cardiomyocytes, adipocytes, and neurons are discussed.

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Fig. 1

Abbreviations

lncRNA:

long non-coding RNA

ORF:

open reading frame

eRNA:

enhancer RNA

RBP:

RNA binding protein

RNP:

ribonucleic protein complex

ceRNA:

competing endogenous RNA

miRNA:

microRNA

ESC:

embryonic stem cell

iPSC:

induce pluripotent stem cell

TF:

transcription factor

RIP:

RNA immunoprecipitation assay

FISH:

fluorescence in situ hybridization assay

PMA:

protein microarray

RIA-seq:

RNA interactome followed by high-throughput sequencing

ChIRP:

chromatin isolation by RNA purification

CHART:

capture hybridization analysis of RNA targets

UV-RIP:

UV-crosslinking RNA immunoprecipitation

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  1. Program in Epithelial Biology, Stanford University, 269 Campus Drive, Room 2150, Stanford, CA, 94305, USA

    Vanessa Lopez-Pajares

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Lopez-Pajares, V. Long non-coding RNA regulation of gene expression during differentiation. Pflugers Arch - Eur J Physiol 468, 971–981 (2016). https://doi.org/10.1007/s00424-016-1809-6

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Keywords

  • LncRNAs
  • Differentiation
  • Stem cells
  • Gene expression
  • Transcription factors