Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis.
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.
Gene Expression, Microarrays Laboratory, IRCCS-Bambino Gesù Children's Hospital, P.za S.Onofrio 4, 00165 Rome, Italy; E-Mails:  letizia.dasacco@opbg.net  (L.D.S.);  antonellabalda@libero.it  (A.B.).
Letizia
L
Da Sacco
Antonella
A
Baldassarre
Andrea
A
Masotti
D000818:Animals; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA
D002843:Chromatin; D062085:RNA, Long Noncoding