Strategies to Annotate and Characterize Long Noncoding RNAs

Advantages and Pitfalls

Huifen Cao, Claes R Wahlestedt, Philipp Kapranov

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.

Original languageEnglish (US)
JournalTrends in Genetics
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

Long Noncoding RNA
Explosions
Noise
Guidelines
RNA

Keywords

  • challenges to lncRNA annotation
  • functional annotation of lncRNAs
  • integrative approach to lncRNA annotation
  • lncRNAs
  • methods to analyze lncRNA function
  • unique features of lncRNAs

ASJC Scopus subject areas

  • Genetics

Cite this

Strategies to Annotate and Characterize Long Noncoding RNAs : Advantages and Pitfalls. / Cao, Huifen; Wahlestedt, Claes R; Kapranov, Philipp.

In: Trends in Genetics, 01.01.2018.

Research output: Contribution to journalArticle

@article{3bea48c98662491aa1834cd411f90aa3,
title = "Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls",
abstract = "The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.",
keywords = "challenges to lncRNA annotation, functional annotation of lncRNAs, integrative approach to lncRNA annotation, lncRNAs, methods to analyze lncRNA function, unique features of lncRNAs",
author = "Huifen Cao and Wahlestedt, {Claes R} and Philipp Kapranov",
year = "2018",
month = "1",
day = "1",
doi = "10.1016/j.tig.2018.06.002",
language = "English (US)",
journal = "Trends in Genetics",
issn = "0168-9525",
publisher = "Elsevier Limited",

}

TY - JOUR

T1 - Strategies to Annotate and Characterize Long Noncoding RNAs

T2 - Advantages and Pitfalls

AU - Cao, Huifen

AU - Wahlestedt, Claes R

AU - Kapranov, Philipp

PY - 2018/1/1

Y1 - 2018/1/1

N2 - The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.

AB - The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.

KW - challenges to lncRNA annotation

KW - functional annotation of lncRNAs

KW - integrative approach to lncRNA annotation

KW - lncRNAs

KW - methods to analyze lncRNA function

KW - unique features of lncRNAs

UR - http://www.scopus.com/inward/record.url?scp=85049734555&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85049734555&partnerID=8YFLogxK

U2 - 10.1016/j.tig.2018.06.002

DO - 10.1016/j.tig.2018.06.002

M3 - Article

JO - Trends in Genetics

JF - Trends in Genetics

SN - 0168-9525

ER -