Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii - PubMed (original) (raw)

Comparative Study

Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii

Yingjia Shen et al. Genetics. 2008 May.

Abstract

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 3'-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 3'-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 approximately 1% of these genes having poly(A) sites residing in predicted coding sequences, introns, and 5'-UTRs. These potentially contribute to transcriptome diversity and gene expression regulation.

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Figures

Figure 1.—

Single-nucleotide profiles of the 3′-UTR for different species. (A) Chlamydomonas; (B) Arabidopsis; (C) human. The poly(A) site is at position −1. The upstream sequence (300 nt) of the poly(A) site is in “−” designation, and the downstream (100 nt) sequence is in “+” designation.

Figure 2.—

Distribution of the length of the 3′-UTR in Chlamydomonas. The average length is 595 nt.

Figure 3.—

The 20 top-ranked signals in the designated poly(A) signal regions. (A) Pentamers from −150 to −25 in FUEs. (B) Pentamers from −25 to −5 in NUEs. (C) Heptamers from −5 to +5 in CEs. (D) Hexamers from +5 to +30 in DEs. The poly(A) site is at position −1. The upstream sequence of the poly(A) site is in “−” designation, and the downstream sequence is in “+” designation.

Figure 4.—

Correlation of UGUAA and gene expression level. The higher the expression level is (more EST copies), the better the chance is of having UGUAA in their NUE as a poly(A) signal.

Figure 5.—

Distribution of UGUAA and AAUAAA signals in different species. (A) Chlamydomonas; (B) Arabidopsis; (C) human. The region of −100 to +100 surrounding the poly(A) site is shown. The poly(A) site is at position −1.

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Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii - PubMed (original) (raw)