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...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3832601?pdf=render |
| _version_ | 1818873859054501888 |
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| author | Xiu-Qing Li Donglei Du |
| author_facet | Xiu-Qing Li Donglei Du |
| author_sort | Xiu-Qing Li |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T13:01:24Z |
| format | Article |
| id | doaj.art-3ed86decebaa4505a58552fd87a70ee7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T13:01:24Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-3ed86decebaa4505a58552fd87a70ee72022-12-21T20:20:14ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01811e7951110.1371/journal.pone.0079511RNA polyadenylation sites on the genomes of microorganisms, animals, and plants.Xiu-Qing LiDonglei DuPre-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.http://europepmc.org/articles/PMC3832601?pdf=render |
| spellingShingle | Xiu-Qing Li Donglei Du RNA polyadenylation sites on the genomes of microorganisms, animals, and plants. PLoS ONE |
| title | 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_short | RNA polyadenylation sites on the genomes of microorganisms, animals, and plants. |
| title_sort | rna polyadenylation sites on the genomes of microorganisms animals and plants |
| url | http://europepmc.org/articles/PMC3832601?pdf=render |
| work_keys_str_mv | AT xiuqingli rnapolyadenylationsitesonthegenomesofmicroorganismsanimalsandplants AT dongleidu rnapolyadenylationsitesonthegenomesofmicroorganismsanimalsandplants |