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

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

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

DSR011F3: 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.

Mentions: To determine 3′ end processing elements in A. oryzae, we first measured the single nucleotide frequencies for all positions within the 3′ UTR and 100 nt sequence downstream of the poly(A) site (set at position 0). As shown in Fig. 3A, this region was notably U-rich, while AU accounted for 62% of nucleotides in this region (U = 34%; A = 28%). Meanwhile, AU content of the coding region in A. oryzae was 48% (http://www.kazusa.or.jp/codon/), suggesting that a high AU content is characteristic of this region. The 3′ UTR was markedly U-rich, but a A-rich region was observed upstream of the poly(A) site—particularly, the −29 to −14 nt region had a high A content with >30%. In addition, a high U content was also observed in the +1 to +20 nt region immediately downstream of the poly(A) site, but A and U content in the downstream +20 to +100 nt region was almost equal. This AU-rich element (ARE) located in the region immediately downstream of the U-rich region flanking the poly(A) site was also found in yeast and plants, but it has not been defined as the 3′-end-processing element in those organisms.4,7,8 Moreover, the poly(A) site (position 0) had an extremely high A content (78%), and as described in the Materials and methods section, the first adenine of the poly(A) tail was designated as the poly(A) site nucleotide. High C nucleotide usage was observed at position −1 immediately before the poly(A) site compared with other positions (position −3, 20%; position −2, 21%; position −1, 37%; and position 0, 7%; Fig. 3B). The content of pyrimidine nucleotides (C and U) at position −1 was 68%, suggesting that CA or UA dinucleotides form the optimal cleavage site in A. oryzae, similar to that observed in plants.Figure 3.


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)

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

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

DSR011F3: 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.
Mentions: To determine 3′ end processing elements in A. oryzae, we first measured the single nucleotide frequencies for all positions within the 3′ UTR and 100 nt sequence downstream of the poly(A) site (set at position 0). As shown in Fig. 3A, this region was notably U-rich, while AU accounted for 62% of nucleotides in this region (U = 34%; A = 28%). Meanwhile, AU content of the coding region in A. oryzae was 48% (http://www.kazusa.or.jp/codon/), suggesting that a high AU content is characteristic of this region. The 3′ UTR was markedly U-rich, but a A-rich region was observed upstream of the poly(A) site—particularly, the −29 to −14 nt region had a high A content with >30%. In addition, a high U content was also observed in the +1 to +20 nt region immediately downstream of the poly(A) site, but A and U content in the downstream +20 to +100 nt region was almost equal. This AU-rich element (ARE) located in the region immediately downstream of the U-rich region flanking the poly(A) site was also found in yeast and plants, but it has not been defined as the 3′-end-processing element in those organisms.4,7,8 Moreover, the poly(A) site (position 0) had an extremely high A content (78%), and as described in the Materials and methods section, the first adenine of the poly(A) tail was designated as the poly(A) site nucleotide. High C nucleotide usage was observed at position −1 immediately before the poly(A) site compared with other positions (position −3, 20%; position −2, 21%; position −1, 37%; and position 0, 7%; Fig. 3B). The content of pyrimidine nucleotides (C and U) at position −1 was 68%, suggesting that CA or UA dinucleotides form the optimal cleavage site in A. oryzae, similar to that observed in plants.Figure 3.

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