| Full text | |
| Author(s): |
Ibrahim, Amr Galal Abd El-Raheem
[1]
;
Vencio, Ricardo Z. N.
[1]
;
Lorenzetti, Alan P. R.
[2]
;
Koide, Tie
[2]
Total Authors: 4
|
| Affiliation: | [1] Univ Sao Paulo, Dept Computat & Math, Fac Filosofia Ciencias & Letras Ribeirao Preto, BR-14040900 Ribeirao Preto - Brazil
[2] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, BR-14040900 Ribeirao Preto - Brazil
Total Affiliations: 2
|
| Document type: | Journal article |
| Source: | GENES; v. 12, n. 7 JUL 2021. |
| Web of Science Citations: | 0 |
| Abstract | |
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, Halobacterium salinarum NRC-1 and Haloferax volcanii 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 H. salinarum genes and 3515 TPS in 49% of H. volcanii 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 ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface. (AU) | |
| FAPESP's process: | 15/21038-1 - The antisense transcriptome of the halophilic archaeon Halobacterium salinarum |
| Grantee: | Tie Koide |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 17/03052-2 - Non-coding RNAs derived from insertion sequences in the halophilic archaeon Halobacterium salinarum NRC-1 |
| Grantee: | Alan Péricles Rodrigues Lorenzetti |
| Support Opportunities: | Scholarships in Brazil - Doctorate |