In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data - PubMed (original) (raw)

In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data

Mizuki Tanaka et al. DNA Res. 2011 Jun.

Abstract

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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Figures

Figure 1.

Figure 1.

Profile of the A. oryzae poly(A) data set. (A) Frequency distribution of EST contigs based on the EST copy number. The EST copy number of each contig contained in the A. oryzae poly(A) data set was obtained from the A. oryzae EST database (

http://nribf2.nrib.go.jp/EST2/index.html

). Data on the total EST contigs were obtained from the study by Akao et al. (B) Gene expression levels determined by DNA microarray analysis. The fluorescence intensity of each gene was normalized to that of the histone H4 gene.

Figure 2.

Figure 2.

Distribution of 3′ UTR lengths determined for 1065 unique EST sequences. The average length is 241 nt.

Figure 3.

Figure 3.

Single nucleotide frequencies in the 3′ UTR and 100 nt sequence downstream of the poly(A) site. (A) Single nucleotide profile in the 3′ UTR and 100 nt sequence downstream of the poly(A) site. The poly(A) site is at position 0. The upstream sequence of the poly(A) site is designated minus and the downstream sequence is designated plus. (B) Sequence logo generated from the actual frequency of occurrence of each of the four nucleotides around the cleavage site. (C) Six regions of the 3′ UTR and 100 nt sequence downstream of the poly(A) site formed according to the single nucleotide profile. The cleavage and polyadenylation site is located between regions IV and V.

Figure 4.

Figure 4.

Representative hexanucleotide signals in the poly(A) signal region (from −40 to −1 nt).

Figure 5.

Figure 5.

A schematic representation of the alignment of 3′-end-processing signals in A. oryzae, yeast, and plants. The arrow indicates the cleavage and polyadenylation site.

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