RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants

Pre–messenger RNA (mRNA) 3′-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A)] sites among major kingdoms. We suspect that the preci...

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Main Authors:	Li, Xiu-Qing, Du, Donglei
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832601/

id	pubmed-3832601
recordtype	oai_dc
spelling	pubmed-38326012013-11-20 RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants Li, Xiu-Qing Du, Donglei Research Article Pre–messenger RNA (mRNA) 3′-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A)] sites among major kingdoms. We suspect that the precise poly(A) sites are very selective, and we therefore mapped mRNA poly(A) sites on complete and nearly complete genomes using mRNA sequences available in the National Center for Biotechnology Information (NCBI) Nucleotide database. In this paper, we describe the mRNA nucleotide [i.e., the poly(A) tail attachment position] that is directly in attachment with the poly(A) tail and the pre-mRNA nucleotide [i.e., the poly(A) tail starting position] that corresponds to the first adenosine of the poly(A) tail in the 29 most-mapped species (2 fungi, 2 protists, 18 animals, and 7 plants). The most representative pre-mRNA dinucleotides covering these two positions were UA, CA, and GA in 17, 10, and 2 of the species, respectively. The pre-mRNA nucleotide at the poly(A) tail starting position was typically an adenosine [i.e., A-type poly(A) sites], sometimes a uridine, and occasionally a cytidine or guanosine. The order was U>C>G at the attachment position but A>>U>C≥G at the starting position. However, in comparison with the mRNA nucleotide composition (base composition), the poly(A) tail attachment position selected C over U in plants and both C and G over U in animals, in both A-type and non-A-type poly(A) sites. Animals, dicot plants, and monocot plants had clear differences in C/G ratios at the poly(A) tail attachment position of the non-A-type poly(A) sites. This study of poly(A) site evolution indicated that the two positions within poly(A) sites had distinct nucleotide compositions and were different among kingdoms. Public Library of Science 2013-11-18 /pmc/articles/PMC3832601/ /pubmed/24260238 http://dx.doi.org/10.1371/journal.pone.0079511 Text en © 2013 Li, Du http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Li, Xiu-Qing Du, Donglei
spellingShingle	Li, Xiu-Qing Du, Donglei RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
author_facet	Li, Xiu-Qing Du, Donglei
author_sort	Li, Xiu-Qing
title	RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
title_short	RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
title_full	RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
title_fullStr	RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
title_full_unstemmed	RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants
title_sort	rna polyadenylation sites on the genomes of microorganisms, animals, and plants
description	Pre–messenger RNA (mRNA) 3′-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A)] sites among major kingdoms. We suspect that the precise poly(A) sites are very selective, and we therefore mapped mRNA poly(A) sites on complete and nearly complete genomes using mRNA sequences available in the National Center for Biotechnology Information (NCBI) Nucleotide database. In this paper, we describe the mRNA nucleotide [i.e., the poly(A) tail attachment position] that is directly in attachment with the poly(A) tail and the pre-mRNA nucleotide [i.e., the poly(A) tail starting position] that corresponds to the first adenosine of the poly(A) tail in the 29 most-mapped species (2 fungi, 2 protists, 18 animals, and 7 plants). The most representative pre-mRNA dinucleotides covering these two positions were UA, CA, and GA in 17, 10, and 2 of the species, respectively. The pre-mRNA nucleotide at the poly(A) tail starting position was typically an adenosine [i.e., A-type poly(A) sites], sometimes a uridine, and occasionally a cytidine or guanosine. The order was U>C>G at the attachment position but A>>U>C≥G at the starting position. However, in comparison with the mRNA nucleotide composition (base composition), the poly(A) tail attachment position selected C over U in plants and both C and G over U in animals, in both A-type and non-A-type poly(A) sites. Animals, dicot plants, and monocot plants had clear differences in C/G ratios at the poly(A) tail attachment position of the non-A-type poly(A) sites. This study of poly(A) site evolution indicated that the two positions within poly(A) sites had distinct nucleotide compositions and were different among kingdoms.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832601/
_version_	1612028130545893376

RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants

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