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piRNAQuest: searching the piRNAome for silencers

BACKGROUND: PIWI-interacting RNA (piRNA) is a novel and emerging class of small non-coding RNA (sncRNA). Ranging in length from 26-32 nucleotides, this sncRNA is a potent player in guiding the vital regulatory processes within a cellular system. Inspite of having such a wide role within cellular sys...

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Detalles Bibliográficos
Autores principales: Sarkar, Arijita, Maji, Ranjan Kumar, Saha, Sudipto, Ghosh, Zhumur
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227290/
https://www.ncbi.nlm.nih.gov/pubmed/24997126
http://dx.doi.org/10.1186/1471-2164-15-555
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author Sarkar, Arijita
Maji, Ranjan Kumar
Saha, Sudipto
Ghosh, Zhumur
author_facet Sarkar, Arijita
Maji, Ranjan Kumar
Saha, Sudipto
Ghosh, Zhumur
author_sort Sarkar, Arijita
collection PubMed
description BACKGROUND: PIWI-interacting RNA (piRNA) is a novel and emerging class of small non-coding RNA (sncRNA). Ranging in length from 26-32 nucleotides, this sncRNA is a potent player in guiding the vital regulatory processes within a cellular system. Inspite of having such a wide role within cellular systems, piRNAs are not well organized and classified, so that a researcher can pool out the biologically relevant information concerning this class. DESCRIPTION: Here we present piRNAQuest- a unified and comprehensive database of 41749 human, 890078 mouse and 66758 rat piRNAs obtained from NCBI and different small RNA sequence experiments. This database provides piRNA annotation based on their localization in gene, intron, intergenic, CDS, 5(/)UTR, 3(/)UTR and repetitive regions which has not been done so far. We have also annotated piRNA clusters and have elucidated characteristic motifs within them. We have looked for the presence of piRNAs and piRNA clusters in pseudogenes, which are known to regulate the expression of protein coding transcripts by generating small RNAs. All these will help researchers progress towards solving the unanswered queries on piRNA biogenesis and their mode of action. Further, expression profile for piRNA in different tissues and from different developmental stages has been provided. In addition, we have provided several tools like 'homology search’, 'dynamic cluster search’ and 'pattern search’. Overall, piRNAQuest will serve as a useful resource for exploring human, mouse and rat piRNAome. The database is freely accessible and available at http://bicresources.jcbose.ac.in/zhumur/pirnaquest/. CONCLUSION: piRNAs play a remarkable role in stem cell self-renewal and various vital processes of developmental biology. Although researchers are mining different features on piRNAs, the exact regulatory mechanism is still fuzzy. Thus, understanding the true potential of these small regulatory molecules with respect to their origin, localization and mode of biogenesis is crucial. piRNAQuest will provide us with a better insight on piRNA origin and function which will help to explore the true potential of these sncRNAs.
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spelling pubmed-42272902014-11-12 piRNAQuest: searching the piRNAome for silencers Sarkar, Arijita Maji, Ranjan Kumar Saha, Sudipto Ghosh, Zhumur BMC Genomics Database BACKGROUND: PIWI-interacting RNA (piRNA) is a novel and emerging class of small non-coding RNA (sncRNA). Ranging in length from 26-32 nucleotides, this sncRNA is a potent player in guiding the vital regulatory processes within a cellular system. Inspite of having such a wide role within cellular systems, piRNAs are not well organized and classified, so that a researcher can pool out the biologically relevant information concerning this class. DESCRIPTION: Here we present piRNAQuest- a unified and comprehensive database of 41749 human, 890078 mouse and 66758 rat piRNAs obtained from NCBI and different small RNA sequence experiments. This database provides piRNA annotation based on their localization in gene, intron, intergenic, CDS, 5(/)UTR, 3(/)UTR and repetitive regions which has not been done so far. We have also annotated piRNA clusters and have elucidated characteristic motifs within them. We have looked for the presence of piRNAs and piRNA clusters in pseudogenes, which are known to regulate the expression of protein coding transcripts by generating small RNAs. All these will help researchers progress towards solving the unanswered queries on piRNA biogenesis and their mode of action. Further, expression profile for piRNA in different tissues and from different developmental stages has been provided. In addition, we have provided several tools like 'homology search’, 'dynamic cluster search’ and 'pattern search’. Overall, piRNAQuest will serve as a useful resource for exploring human, mouse and rat piRNAome. The database is freely accessible and available at http://bicresources.jcbose.ac.in/zhumur/pirnaquest/. CONCLUSION: piRNAs play a remarkable role in stem cell self-renewal and various vital processes of developmental biology. Although researchers are mining different features on piRNAs, the exact regulatory mechanism is still fuzzy. Thus, understanding the true potential of these small regulatory molecules with respect to their origin, localization and mode of biogenesis is crucial. piRNAQuest will provide us with a better insight on piRNA origin and function which will help to explore the true potential of these sncRNAs. BioMed Central 2014-07-04 /pmc/articles/PMC4227290/ /pubmed/24997126 http://dx.doi.org/10.1186/1471-2164-15-555 Text en Copyright © 2014 Sarkar et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Database
Sarkar, Arijita
Maji, Ranjan Kumar
Saha, Sudipto
Ghosh, Zhumur
piRNAQuest: searching the piRNAome for silencers
title piRNAQuest: searching the piRNAome for silencers
title_full piRNAQuest: searching the piRNAome for silencers
title_fullStr piRNAQuest: searching the piRNAome for silencers
title_full_unstemmed piRNAQuest: searching the piRNAome for silencers
title_short piRNAQuest: searching the piRNAome for silencers
title_sort pirnaquest: searching the pirnaome for silencers
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227290/
https://www.ncbi.nlm.nih.gov/pubmed/24997126
http://dx.doi.org/10.1186/1471-2164-15-555
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