| Summary: | Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, <i>Halobacterium</i> <i>salinarum</i> NRC-1 and <i>Haloferax</i> <i>volcanii</i> DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of <i>H. salinarum</i> genes and 3515 TPS in 49% of <i>H. volcanii</i> chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene <i>ftsZ2,</i> whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS<i>200</i>/IS<i>605</i>. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.
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