An exploration of 3′-end processing signals and their tissue distribution in Oryza sativa

Dong, Hua; Deng, Ye; Chen, Jack; Wang, Sheng; Peng, Syd S.; Dai, Chengen; Fang, Yongqi; Shao, Jing; Lou, Yiting; Li, Debao

doi:10.1016/j.gene.2006.10.015

Cited by 18 publications

(11 citation statements)

References 24 publications

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“…As shown in Figure 1, the 39-UTR of Chlamydomonas is notably rich in G nucleotides, except the À25 to À5 region where U and A are dominant, while the downstream 15 to 130 region has a high C content but the transition to high C starts before the poly(A) site. This profile is distinctly different from the profiles of two land plant species, Arabidopsis ( Figure 1B; Loke et al 2005) and rice (Dong et al 2007;Shen et al 2008), as well as yeast (Graber et al 1999) and human ( Figure 1C; Tian et al 2005), which are all AU rich in their 39-UTR. It is known that the Chlamydomonas genome is uniquely GC rich (64%; Merchant et al 2007), which would contribute, in part, to the G richness in the 39-UTR.…”

Section: Resultsmentioning

confidence: 57%

Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii

et al. 2008

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To understand nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii, we generated a data set of 16,952 in silico-verified poly(A) sites from EST sequencing traces based on Chlamydomonas Genome Assembly v.3.1. Analysis of this data set revealed a unique and complex polyadenylation signal profile that is setting Chlamydomonas apart from other organisms. In contrast to the high-AU content in the 39-UTRs of other organisms, Chlamydomonas shows a high-guanylate content that transits to high-cytidylate around the poly(A) site. The average length of the 39-UTR is 595 nucleotides (nt), significantly longer than that of Arabidopsis and rice. The dominant poly(A) signal, UGUAA, was found in 52% of the near-upstream elements, and its occurrence may be positively correlated with higher gene expression levels. The UGUAA signal also exists in Arabidopsis and in some mammalian genes but mainly in the far-upstream elements, suggesting a shift in function. The C-rich region after poly(A) sites with unique signal elements is a characteristic downstream element that is lacking in higher plants. We also found a high level of alternative polyadenylation in the Chlamydomonas genome, with a range of up to 33% of the 4057 genes analyzed having at least two unique poly(A) sites and $1% of these genes having poly(A) sites residing in predicted coding sequences, introns, and 59-UTRs. These potentially contribute to transcriptome diversity and gene expression regulation.

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Section: Resultsmentioning

confidence: 57%

Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii

et al. 2008

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“…With the rice genome sequences being made available, it is now feasible to perform large-scale analysis on rice poly(A) signals. Recently, two groups performed analyses on rice poly(A) signals based on 12 969 and 9911 rice poly(A) sites (26,27), respectively. However, these analyses failed to address some important issues.…”

Section: Introductionmentioning

confidence: 99%

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

Shen

Haas

et al. 2008

Nucleic Acids Research

157

200

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The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3′-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5′-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites.

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“…Importantly, the nucleotide distribution profile of the 3′ UTR in A. oryzae was similar to that in plants, 7,8,39 yeast, 4 and mammals, 24 although the U-rich region was expanded towards the coding region of A. oryzae . On the basis of the nucleotide profile observed, the 3′ UTR plus 100 nt sequence downstream of the poly(A) site was divided into six signal element regions, designated regions I–VI, to identify the sequence elements for 3′-end-processing (Fig.…”

Section: Resultsmentioning

confidence: 74%

In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

et al. 2011

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To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them.

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An exploration of 3′-end processing signals and their tissue distribution in Oryza sativa

Cited by 18 publications

References 24 publications

Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii

Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

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