Cargando…

Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing

Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by mo...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Sanshu, Breaker, Ronald R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597705/
https://www.ncbi.nlm.nih.gov/pubmed/23376932
http://dx.doi.org/10.1093/nar/gkt057
_version_ 1782262680625610752
author Li, Sanshu
Breaker, Ronald R.
author_facet Li, Sanshu
Breaker, Ronald R.
author_sort Li, Sanshu
collection PubMed
description Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5′ splice site, which greatly increases use of this 5′ splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches.
format Online
Article
Text
id pubmed-3597705
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-35977052013-03-15 Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing Li, Sanshu Breaker, Ronald R. Nucleic Acids Res Gene Regulation, Chromatin and Epigenetics Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5′ splice site, which greatly increases use of this 5′ splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches. Oxford University Press 2013-03 2013-02-01 /pmc/articles/PMC3597705/ /pubmed/23376932 http://dx.doi.org/10.1093/nar/gkt057 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Gene Regulation, Chromatin and Epigenetics
Li, Sanshu
Breaker, Ronald R.
Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title_full Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title_fullStr Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title_full_unstemmed Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title_short Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
title_sort eukaryotic tpp riboswitch regulation of alternative splicing involving long-distance base pairing
topic Gene Regulation, Chromatin and Epigenetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597705/
https://www.ncbi.nlm.nih.gov/pubmed/23376932
http://dx.doi.org/10.1093/nar/gkt057
work_keys_str_mv AT lisanshu eukaryotictppriboswitchregulationofalternativesplicinginvolvinglongdistancebasepairing
AT breakerronaldr eukaryotictppriboswitchregulationofalternativesplicinginvolvinglongdistancebasepairing