Volume 1859, Issue 1, January 2016

SPECIALISSUE
Clues to long noncoding RNA
taxonomy
EDITED BY Tetsuro Hirose, Institute for Genetic Medicine, Hokkaido University andShinichi Nakagawa, Nakagawa RNA Biology laboratory, RIKEN

This special issue aims to assemble available
knowledge on long noncoding RNAs (lncRNAs) andprovide future research directions for discovering
the molecular functions of this emerging family ofmolecules. The genomes of eukaryotes, particularly
mammalian species including human and mouse,possess large chunks of nonprotein-coding regions.
Only 2% of the human genome is dedicated tocoding for proteins; the remainder is constituted ofnoncoding regions, which are for the most partfunctionally unannotated. At the beginning of the
postgenomic era, transcriptome genome-wide
analyses in various organisms unexpectedly
revealed that large portions of the mammalian
genome produce numerous transcripts that lackprotein-coding potential. Among these RNAs,
noncoding transcripts longer than 200 nt arearbitrary referred to as "lncRNAs". As in the case ofproteins, ncRNAs are extremely diverse and havespecific characteristics that determine theirfunctions. However, lncRNAs have been collectively
and passively defined as RNA molecules without
polypeptide-coding capacity, with no consideration
for their functions. However, it is now broadly
accepted that a certain subset of lncRNAs possess

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specific regulatory functions that control a wide
range of physiological events. In light of this, it is thetime to establish a new classification, which wetentatively call “lncRNA taxonomy”, which classifies
lncRNAs into functional groups according to thetype(s) of function-conferring RNA element(s) theypossess. This approach should make it possible topredict the functions of unannotated lncRNAs andimprove our understanding of their biologicalsignificance. In this special issue, we haveassembled as much information as possible toprovide “clues to lncRNA taxonomy”, including clues
about their genomic organization, expression,processing, structure, chemical modifications, andinteracting factors, as well as their molecular andphysiological functions and putative involvement invarious diseases.

Clues to long noncoding RNA
taxonomy
Volume 1859, Issue 1, January 2016

Contents:
Clues to long noncoding RNATaxonomy
Edited by Tetsuro Hirose and Shinichi
Nakagawa

piRNA biogenesis in the germline:from transcription of piRNA
genomic sources to piRNAmaturation
Siomi Mikiko C.

Discovery and functional analysis
of lncRNAs: methodologies toinvestigate an uncharacterizedtranscriptome
Carninci Piero

Pervasive lncRNA binding bychromatin modifying complexes the challenges ahead
Betancur Juan G.

The specificity of long noncoding
RNA expression
Dinger Marcel E.

Long noncoding RNAs: Lessons
from Genomic imprinting
Kanduri Chandrasekhar

Bioinformatics tools for lncRNA
research
Asai Kiyoshi

Dynamic interplay and function ofmultiple noncoding genes
governing X chromosome
inactivation
Ogawa Yuya

Methods for distinguishing between
protein-coding and long noncoding
RNAs and the elusive biological
purpose of translation of longnoncoding RNAs
Ulitsky Igor
Towards structural classification oflong non-coding RNAs
Sanbonmatsu Karissa
The ins and outs of lncRNA
structure: how, why and whatcomes next?
Bond Charles S
The Emerging Epitranscriptomics
of Long Noncoding RNAs
Preiss Thomas

Insight into lncRNA biology using
hybridization capture analyses
Simon Matthew D.
Long noncoding RNAs: Re-writing
dogmas of RNA processing andstability
Wilusz Jeremy E.
Architectural RNAs (arcRNAs): aclass of long noncoding RNAs thatfunction as the scaffold of nuclear
bodiesHirose Tetsuro
The long non-coding RNA world inyeasts
Yamashita Akira

RISC assembly: coordination
between small RNAs andArgonaute proteinsTomari Yukihide

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Circular RNAs: Identification,
Biogenesis and Function P.A. Del
Hansen Thomas B.
lncRNAs and microRNAs with arole in cancer development
Esteller Manel
Lessons from reverse-geneticstudies of lncRNAs
Nakagawa ShinichiStressing out over long noncoding
RNALee Stephen
MALAT1 long non-coding RNA incancer
Yoshimoto Rei
Expanding the p53 regulatory
network: lncRNAs take up thechallenge
Huarte Maite
Long noncoding RNAs in Diseasesof Aging
Gorospe Myriam