| 1. |
- 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. |
- Innocenti, Nicolas, 1986-, et al.
(author)
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An observation of circular RNAs in bacterial RNA-seq data.
- 2015
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Other publication (other academic/artistic)abstract
- Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from Enterococcus faecalis and Escherichia coli in a way similar to previous studies performed on eukaryotes. We report observations of circRNAs in RNA-seq data that are reproducible across multiple experiments performed with different protocols or growth conditions.
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| 3. |
- Innocenti, Nicolas, 1986-, et al.
(author)
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Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bateria using tagRNA-seq
- 2015
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In: RNA Biology. - : Taylor & Francis. - 1547-6286 .- 1555-8584.
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Journal article (peer-reviewed)abstract
- Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tag is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.
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| 4. |
- Innocenti, Nicolas, 1986-, et al.
(author)
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Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends
- 2013
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In: Journal of Statistical Mechanics. - : Institute of Physics (IOP). - 1742-5468. ; 2013:10, s. P10013-
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Journal article (peer-reviewed)abstract
- High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows us to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when sequencing RNA fragments from one end, as is the case on most platforms, an oscillation in the read count is observed at the other end. We further show that these oscillations can be well described by Kolmogorov's 1941 broken stick model. We investigate how the model can be used to improve predictions of gene ends (3' transcript ends), but conclude that with present data the improvement is only marginal. The results highlight subtle effects in high-throughput transcriptomics experiments which do not have a biological origin, but which may still be used to obtain biological information.
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| 5. |
- Innocenti, Nicolas, 1986-, et al.
(author)
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Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
- 2015
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In: RNA. - : RNA Society. - 1355-8382 .- 1469-9001.
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Journal article (peer-reviewed)abstract
- Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA-and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small-and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
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| 6. |
- 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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