title: The Landscape of long noncoding RNA classification.
abstract: Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long noncoding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the noncoding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual unambiguous classification framework results in a number of challenges in the annotation and interpretation of noncoding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel the function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then, we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets.
authors: St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801 USA; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
authors: Georges
authors: G
authors: St Laurent
authors: Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136 USA. Electronic address: cwahlestedt@med.miami.edu.
authors: Claes
authors: C
authors: Wahlestedt
authors: Institute of Genomics, School of Biomedical Sciences, Huaqiao Univerisity, 668 Jimei Road, Xiamen, China 361021; St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801 USA. Electronic address: philippk08@hotmail.com.
authors: Philipp
authors: P
authors: Kapranov
mesh_terms: D000818:Animals; D006801:Humans; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000145:classification* / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding
keywords: annotation of long non-coding RNAs; classification of long non-coding RNAs; function of long non-coding RNAs; lincRNA; lncRNA; long non-coding RNA; systems biology; transcriptome; vlincRNA