Limits...
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.

Show MeSH

Related in: MedlinePlus

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR011F5: 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.

Mentions: Based on the information presented in this study, we proposed putative 3′-end-processing signals in A. oryzae (Fig. 5). The putative 3′-end-processing signals in A. oryzae were similar to those in yeast and plants but some differences were observed between them. First, A-rich sequences upstream of the poly(A) site were less well conserved in all three species than in mammals, and the predominant hexanucleotide in this region of A. oryzae differed from that of yeast and plants. The canonical hexanucleotide AAUAAA signal in mammals is also the most frequently occurring signal in this 3′ UTR of yeast and plants, whereas it is found only in ∼13% and 7–10% of yeast and plant genes, respectively. In contrast, the most over-represented hexanucleotide in A. oryzae was AAUGAA, although this sequence accounted for only 6% of all transcripts, similar to yeast and plant AAUAAA sequences. Second, in the upstream of the A-rich region, while most dominant sequence motifs are well defined in yeast and plants (UAUAUA in yeast and UGUA in plants), no conserved sequence motif was observed in A. oryzae, except for the U-rich elements described earlier.Figure 5.


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)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR011F5: 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.
Mentions: Based on the information presented in this study, we proposed putative 3′-end-processing signals in A. oryzae (Fig. 5). The putative 3′-end-processing signals in A. oryzae were similar to those in yeast and plants but some differences were observed between them. First, A-rich sequences upstream of the poly(A) site were less well conserved in all three species than in mammals, and the predominant hexanucleotide in this region of A. oryzae differed from that of yeast and plants. The canonical hexanucleotide AAUAAA signal in mammals is also the most frequently occurring signal in this 3′ UTR of yeast and plants, whereas it is found only in ∼13% and 7–10% of yeast and plant genes, respectively. In contrast, the most over-represented hexanucleotide in A. oryzae was AAUGAA, although this sequence accounted for only 6% of all transcripts, similar to yeast and plant AAUAAA sequences. Second, in the upstream of the A-rich region, while most dominant sequence motifs are well defined in yeast and plants (UAUAUA in yeast and UGUA in plants), no conserved sequence motif was observed in A. oryzae, except for the U-rich elements described earlier.Figure 5.

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