Functional Classification and Experimental Dissection of Long Noncoding RNAs

Florian Kopp, Joshua T. Mendell

Research output: Contribution to journalReview article

334 Citations (Scopus)

Abstract

Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease. Identifying functional noncoding transcripts within a complex transcriptome remains a challenge. This review explores examples of known functional lncRNAs and then presents a framework for unlocking biological insights from new lncRNAs of interest.

Original languageEnglish (US)
Pages (from-to)393-407
Number of pages15
JournalCell
Volume172
Issue number3
DOIs
StatePublished - Jan 25 2018

Fingerprint

Long Noncoding RNA
Dissection
Transcriptome
Physiology
Transcription
Gene expression
Genes
Genome
Gene Expression

Keywords

  • lncRNA
  • noncoding RNA

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Functional Classification and Experimental Dissection of Long Noncoding RNAs. / Kopp, Florian; Mendell, Joshua T.

In: Cell, Vol. 172, No. 3, 25.01.2018, p. 393-407.

Research output: Contribution to journalReview article

@article{514e7829fcc44eb187b47125850fe3cd,
title = "Functional Classification and Experimental Dissection of Long Noncoding RNAs",
abstract = "Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease. Identifying functional noncoding transcripts within a complex transcriptome remains a challenge. This review explores examples of known functional lncRNAs and then presents a framework for unlocking biological insights from new lncRNAs of interest.",
keywords = "lncRNA, noncoding RNA",
author = "Florian Kopp and Mendell, {Joshua T.}",
year = "2018",
month = "1",
day = "25",
doi = "10.1016/j.cell.2018.01.011",
language = "English (US)",
volume = "172",
pages = "393--407",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "3",

}

TY - JOUR

T1 - Functional Classification and Experimental Dissection of Long Noncoding RNAs

AU - Kopp, Florian

AU - Mendell, Joshua T.

PY - 2018/1/25

Y1 - 2018/1/25

N2 - Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease. Identifying functional noncoding transcripts within a complex transcriptome remains a challenge. This review explores examples of known functional lncRNAs and then presents a framework for unlocking biological insights from new lncRNAs of interest.

AB - Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease. Identifying functional noncoding transcripts within a complex transcriptome remains a challenge. This review explores examples of known functional lncRNAs and then presents a framework for unlocking biological insights from new lncRNAs of interest.

KW - lncRNA

KW - noncoding RNA

UR - http://www.scopus.com/inward/record.url?scp=85041930461&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85041930461&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2018.01.011

DO - 10.1016/j.cell.2018.01.011

M3 - Review article

C2 - 29373828

AN - SCOPUS:85041930461

VL - 172

SP - 393

EP - 407

JO - Cell

JF - Cell

SN - 0092-8674

IS - 3

ER -