Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling). LncRNAs may have different roles: gene activators (signaling), repressors (decoy), cis and trans gene expression regulators (guides) and chromatin modificators (scaffolds) without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.

Original languageEnglish
Pages (from-to)97-114
Number of pages18
JournalInternational Journal of Molecular Sciences
Volume13
Issue number1
DOIs
Publication statusPublished - 2012

Fingerprint

Long Noncoding RNA
functional analysis
Functional analysis
Bioinformatics
Computational Biology
RNA
annotations
resources
chromatin
gene expression
Gene expression
decoys
Chromatin
sequencing
genome
Genes
regulators
genes
Human Genome Project
Gene Expression

Keywords

  • Bioinformatics
  • Genomics
  • LncRNAs
  • Non-coding RNAs
  • Systems biology

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Spectroscopy
  • Inorganic Chemistry
  • Catalysis
  • Molecular Biology
  • Computer Science Applications
  • Medicine(all)

Cite this

@article{4f0f6c47fb204b4eb9ffac7e60a10a92,
title = "Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis",
abstract = "The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling). LncRNAs may have different roles: gene activators (signaling), repressors (decoy), cis and trans gene expression regulators (guides) and chromatin modificators (scaffolds) without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.",
keywords = "Bioinformatics, Genomics, LncRNAs, Non-coding RNAs, Systems biology",
author = "{da Sacco}, Letizia and Antonella Baldassarre and Andrea Masotti",
year = "2012",
doi = "10.3390/ijms13010097",
language = "English",
volume = "13",
pages = "97--114",
journal = "International Journal of Molecular Sciences",
issn = "1661-6596",
publisher = "MDPI AG",
number = "1",

}

TY - JOUR

T1 - Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis

AU - da Sacco, Letizia

AU - Baldassarre, Antonella

AU - Masotti, Andrea

PY - 2012

Y1 - 2012

N2 - The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling). LncRNAs may have different roles: gene activators (signaling), repressors (decoy), cis and trans gene expression regulators (guides) and chromatin modificators (scaffolds) without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.

AB - The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling). LncRNAs may have different roles: gene activators (signaling), repressors (decoy), cis and trans gene expression regulators (guides) and chromatin modificators (scaffolds) without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.

KW - Bioinformatics

KW - Genomics

KW - LncRNAs

KW - Non-coding RNAs

KW - Systems biology

UR - http://www.scopus.com/inward/record.url?scp=84856255316&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84856255316&partnerID=8YFLogxK

U2 - 10.3390/ijms13010097

DO - 10.3390/ijms13010097

M3 - Article

VL - 13

SP - 97

EP - 114

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 1

ER -