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

Tanaka M, Sakai Y, Yamada O, Shintani T, Gomi K - DNA Res. (2011)

Bottom Line: 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 most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts.Although these putative 3'-end-processing signals are similar to those in yeast and plants, some notable differences exist between them.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioindustrial Genomics, Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.

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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Distribution of 3′ UTR lengths determined for 1065 unique EST sequences. The average length is 241 nt.
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DSR011F2: Distribution of 3′ UTR lengths determined for 1065 unique EST sequences. The average length is 241 nt.

Mentions: In eukaryotes, 3′ UTR regulates mRNA stability and translational efficiency through sequence elements for 3′ UTR-binding proteins and microRNAs or through its length.26–31 In A. nidulans, stability of transcripts involved in nitrogen metabolism was dependent on their 3′ UTRs.32,33 Therefore, the 3′ UTRs may play an important role in gene expression regulation in filamentous fungi. However, no comprehensive information exists about 3′ UTRs in filamentous fungi. Hence, we analysed the distribution of 3′ UTR lengths in A. oryzae and determined their average and median lengths to compare with those in yeast and plants, which were also determined by analysis of EST sequencing data. In A. oryzae, 3′ UTR lengths were predominantly distributed in the range of 51 to 350 nt (Fig. 2). The average 3′ UTR length in A. oryzae was 241 nt, while the median 3′ UTR length was 203 nt. The average 3′ UTR length in Saccharomyces cerevisiae is 144 nt (median 3′ UTR length is 121 nt)5 and that in plants is 289 nt (Oryza sativa) and 223 nt (Arabidopsis thaliana).8 These results suggested that 3′ UTR length in A. oryzae is greater than that in yeast but similar to that in plants.Figure 2.


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

Tanaka M, Sakai Y, Yamada O, Shintani T, Gomi K - DNA Res. (2011)

Distribution of 3′ UTR lengths determined for 1065 unique EST sequences. The average length is 241 nt.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3111234&req=5

DSR011F2: Distribution of 3′ UTR lengths determined for 1065 unique EST sequences. The average length is 241 nt.
Mentions: In eukaryotes, 3′ UTR regulates mRNA stability and translational efficiency through sequence elements for 3′ UTR-binding proteins and microRNAs or through its length.26–31 In A. nidulans, stability of transcripts involved in nitrogen metabolism was dependent on their 3′ UTRs.32,33 Therefore, the 3′ UTRs may play an important role in gene expression regulation in filamentous fungi. However, no comprehensive information exists about 3′ UTRs in filamentous fungi. Hence, we analysed the distribution of 3′ UTR lengths in A. oryzae and determined their average and median lengths to compare with those in yeast and plants, which were also determined by analysis of EST sequencing data. In A. oryzae, 3′ UTR lengths were predominantly distributed in the range of 51 to 350 nt (Fig. 2). The average 3′ UTR length in A. oryzae was 241 nt, while the median 3′ UTR length was 203 nt. The average 3′ UTR length in Saccharomyces cerevisiae is 144 nt (median 3′ UTR length is 121 nt)5 and that in plants is 289 nt (Oryza sativa) and 223 nt (Arabidopsis thaliana).8 These results suggested that 3′ UTR length in A. oryzae is greater than that in yeast but similar to that in plants.Figure 2.

Bottom Line: 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 most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts.Although these putative 3'-end-processing signals are similar to those in yeast and plants, some notable differences exist between them.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioindustrial Genomics, Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.

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.

Show MeSH
Related in: MedlinePlus