In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

Tanaka, Mizuki; Sakai, Yoshifumi; Shintani, Takahiro; Gomi, Katsuya

doi:10.1093/dnares/dsr011

Cited by 14 publications

(10 citation statements)

References 47 publications

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“…Interestingly, AATGAA always ranks second for all strand-specific data sets in S. pombe. This motif ranks as the highest NUE motif in Aspergillus oryzae (Tanaka et al 2011), emphasizing the evolutionary conservation of the PAS sequence motifs across some organisms. However, the mutation of AATAAA to AATGAA can lead to loss of PAS function in humans (Bennett et al 2001).…”

Section: Discussionmentioning

confidence: 87%

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

Schlackow

Marguerat

Proudfoot

et al. 2013

RNA

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Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3 ′ UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3 ′ RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).

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Section: Discussionmentioning

confidence: 87%

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

Schlackow

Marguerat

Proudfoot

et al. 2013

RNA

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“…In the 3′UTR regions, there is predominance of AT/AT (gymnosperms) and AAT/ATT (both taxa), which are not the target for methylation [62]. An increased content in A + T nucleotides in the 3′UTR fraction has been reported before in vertebrates [63], mammals [64], yeast [65] and Arabidopsis [4], which seems to be related to the UTR processing signal composition.…”

Section: Discussionmentioning

confidence: 91%

Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera

et al. 2014

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BackgroundSimple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).ResultsOur analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.ConclusionsOur analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.

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“…Analysis of genes in humans and rats have shown that the 3′ region of genes can be dynamically altered by TEs during evolution, which suggests that TEs can provide alternative polyadenylation sites when inserted downstream of endogenous genes [ 40 ]. However, the only analysis of polyadenylation sites in fungi has been performed in Aspergillus oryzae [ 41 ]. Therefore, because of the current lack of knowledge about the 3′ gene regulatory regions of fungi, additional studies are necessary to measure the possible involvement of TEs in the evolution of the 3′ ends of genes.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases

Santana¹,

Silva

Mizubuti

et al. 2014

BMC Microbiol

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BackgroundSclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of several species. Transposons from the Tc1-Mariner superfamily are thought to be ubiquitous components of fungal genomes and are generally found in low copy numbers with large numbers of deleterious mutations in their transposase coding sequence.ResultsThis study shows that the genome of S. sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3′ regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation.ConclusionsFourteen novel Tc1-Mariner families were characterized. Some families had evidence of introns, which might or might not be excised depending on the family or element in question, and this finding demonstrates a possible strategy for overcoming possible mutations that generate premature stop codons in a RNA sequence. Tc1-Mariner elements likely play an important role in the structure and evolution of the S. sclerotiorum genome.

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In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

Cited by 14 publications

References 47 publications

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera

Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases

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