Integrating multi-omics data to investigate pseudogene expression in Mycolicibacterium smegmatis

•Multi-dimensional -omics data can be used to study various functional aspects of the genome.•Using -omic data, expression signals in the pseudogene regions in M. smegmatis were investigated•Further analysis showed sequencing errors in many potentially important pseudogenic regions. Large-scale -omi...

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Bibliographic Details
Published in:Gene 2020-09, Vol.755, p.144908-144908, Article 144908
Main Authors: Balasubramanian, Rami, Hegde, Shubhada R.
Format: Article
Language:English
Subjects:
Gene annotation
Gene expression
Pseudogene
Ribo-Seq
RNA-Seq
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Summary:•Multi-dimensional -omics data can be used to study various functional aspects of the genome.•Using -omic data, expression signals in the pseudogene regions in M. smegmatis were investigated•Further analysis showed sequencing errors in many potentially important pseudogenic regions. Large-scale -omics data now allows for investigating genome-wide functional elements. Using RNA-Seq data, we tested the expression of 134 pseudogenes which do not show duplicated protein coding genes in the M. smegmatis genome. We observe significant expression and translation of 28 pseudogenes. Further examination using RNA-Seq reads suggested the sequencing errors in many pseudogenes. These include some of the functionally relevant genes such as recN and manB. We propose that the analysis of transcriptional and translational landscape using multi-dimensional -omics data could shed light on the current annotations of the bacterial pseudogenes.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2020.144908