The Landscape of long noncoding RNA classification

Abstract

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long non-coding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the non-coding 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 un-ambiguous classification framework results in a number of challenges in the annotation and interpretation of non-coding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel 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.

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

“…2,5,7,8,[10][11][12][13][14][15][16][17] However, the data on tandemly organized DNA repeats transcription in the amphibian and avian taxa is fragmentary and insufficiently represented in the literature. 18,19 Meanwhile, the amphibians and birds are promising model organisms to investigate the phenomena of satellite DNA transcription.…”

Accumulation of GAS5 in exosomes is a marker of apoptosis induction

“…Certain molecules have been reported to be similar to protein-coding genes with respect to splicing and polyadenylation. As a result of relatively high functional diversity, confusing and overlapping terminology has been used to name and classify lncRNAs (7). Various attributes, including transcript length, association with annotated protein-coding gene or other DNA elements/repeats, association with a biochemical pathway or stability, or sequence and structure conservation have been used for classification.…”

Long Non-Coding RNA in Non-Small Cell Lung Cancers

“…The most prevalent classiication method is based on the genomic location and context. According to this method, lncRNAs can be deined as: (1) sense lncRNAs; (2) antisense lncRNAs that are transcribed from the sense or antisense strands, respectively, overlapping one or more exons of protein-coding gene on the same or opposite strand; (3) bidirectional lncRNAs, whose transcription and neighbouring coding transcript on the opposite strand is initiated in close genomic proximity; (4) intronic lncRNA that are transcribed entirely from introns of protein-coding genes; (5) intergenic lncRNA that lies within the genomic interval between two genes [20,23,24]. Functions of lncRNAs may difer from each category.…”