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- Aurell, Erik, 1961-, et al.
(author)
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The bulk and the tail of minimal absent words in genome sequences
- 2016
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In: Physical Biology. - : Institute of Physics (IOP). - 1478-3967 .- 1478-3975. ; 13:2
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Journal article (peer-reviewed)abstract
- Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.
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| 2. |
- Maes, Alexandre, et al.
(author)
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Landscape of RNA polyadenylation in E. coli
- 2016
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In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962.
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Journal article (peer-reviewed)abstract
- Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.
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