Cargando…

Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants

There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review prov...

Descripción completa

Detalles Bibliográficos
Autores principales: Yu, Dongliang, Ma, Xiaoxia, Zuo, Ziwei, Wang, Huizhong, Meng, Yijun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960741/
https://www.ncbi.nlm.nih.gov/pubmed/29868116
http://dx.doi.org/10.3389/fgene.2018.00168
_version_ 1783324631805984768
author Yu, Dongliang
Ma, Xiaoxia
Zuo, Ziwei
Wang, Huizhong
Meng, Yijun
author_facet Yu, Dongliang
Ma, Xiaoxia
Zuo, Ziwei
Wang, Huizhong
Meng, Yijun
author_sort Yu, Dongliang
collection PubMed
description There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review provides a detailed description of these transcription boundary-associated RNAs (TBARs), including their classification. Based on their genomic distribution, TBARs are divided into two major groups: promoter-associated RNAs (PARs) and terminus-associated RNAs (TARs). Depending on the sequence length, each group is further classified into long RNA species (>200 nt) and small RNA species (<200 nt). According to these rules of TBAR classification, divergent ncRNAs with confusing nomenclatures, such as promoter upstream transcripts (PROMPTs), upstream antisense RNAs (uaRNAs), stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), upstream non-coding transcripts (UNTs), transcription start site-associated RNAs (TSSaRNAs), transcription initiation RNAs (tiRNAs), and transcription termination site-associated RNAs (TTSaRNAs), were assigned to specific classes. Although the biogenesis pathways of PARs and TARs have not yet been clearly elucidated, previous studies indicate that some of the PARs have originated either through divergent transcription or via RNA polymerase pausing. Intriguing findings regarding the functional implications of the TBARs such as the long-range “gene looping” model, which explains their role in the transcriptional regulation of protein-coding genes, are also discussed. Altogether, this review provides a comprehensive overview of the current research status of TBARs, which will promote further investigations in this research area.
format Online
Article
Text
id pubmed-5960741
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-59607412018-06-04 Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants Yu, Dongliang Ma, Xiaoxia Zuo, Ziwei Wang, Huizhong Meng, Yijun Front Genet Genetics There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review provides a detailed description of these transcription boundary-associated RNAs (TBARs), including their classification. Based on their genomic distribution, TBARs are divided into two major groups: promoter-associated RNAs (PARs) and terminus-associated RNAs (TARs). Depending on the sequence length, each group is further classified into long RNA species (>200 nt) and small RNA species (<200 nt). According to these rules of TBAR classification, divergent ncRNAs with confusing nomenclatures, such as promoter upstream transcripts (PROMPTs), upstream antisense RNAs (uaRNAs), stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), upstream non-coding transcripts (UNTs), transcription start site-associated RNAs (TSSaRNAs), transcription initiation RNAs (tiRNAs), and transcription termination site-associated RNAs (TTSaRNAs), were assigned to specific classes. Although the biogenesis pathways of PARs and TARs have not yet been clearly elucidated, previous studies indicate that some of the PARs have originated either through divergent transcription or via RNA polymerase pausing. Intriguing findings regarding the functional implications of the TBARs such as the long-range “gene looping” model, which explains their role in the transcriptional regulation of protein-coding genes, are also discussed. Altogether, this review provides a comprehensive overview of the current research status of TBARs, which will promote further investigations in this research area. Frontiers Media S.A. 2018-05-14 /pmc/articles/PMC5960741/ /pubmed/29868116 http://dx.doi.org/10.3389/fgene.2018.00168 Text en Copyright © 2018 Yu, Ma, Zuo, Wang and Meng. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Yu, Dongliang
Ma, Xiaoxia
Zuo, Ziwei
Wang, Huizhong
Meng, Yijun
Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title_full Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title_fullStr Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title_full_unstemmed Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title_short Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants
title_sort classification of transcription boundary-associated rnas (tbars) in animals and plants
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960741/
https://www.ncbi.nlm.nih.gov/pubmed/29868116
http://dx.doi.org/10.3389/fgene.2018.00168
work_keys_str_mv AT yudongliang classificationoftranscriptionboundaryassociatedrnastbarsinanimalsandplants
AT maxiaoxia classificationoftranscriptionboundaryassociatedrnastbarsinanimalsandplants
AT zuoziwei classificationoftranscriptionboundaryassociatedrnastbarsinanimalsandplants
AT wanghuizhong classificationoftranscriptionboundaryassociatedrnastbarsinanimalsandplants
AT mengyijun classificationoftranscriptionboundaryassociatedrnastbarsinanimalsandplants