| Full text | |
| Author(s): |
Pereira de Almeida, Joao Paulo
[1]
;
Vencio, Ricardo Z. N.
[2]
;
Lorenzetti, Alan P. R.
[1]
;
ten-Caten, Felipe
[1]
;
Gomes-Filho, Jose Vicente
[1]
;
Koide, Tie
[1]
Total Authors: 6
|
| Affiliation: | [1] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, BR-14049900 Sao Paulo - Brazil
[2] Univ Sao Paulo, Dept Computat & Math, Fac Filosofia Ciencias & Letras Ribeirao Preto, BR-14049900 Sao Paulo - Brazil
Total Affiliations: 2
|
| Document type: | Journal article |
| Source: | GENES; v. 10, n. 4 APR 2019. |
| Web of Science Citations: | 0 |
| Abstract | |
Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3 ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin-antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that similar to 10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that similar to 19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea. (AU) | |
| FAPESP's process: | 15/12012-9 - Transcription Start Site (TSS) identification in extremophilic archaeon Halobacterium salinarum NRC-1 and its association with intraRNAs production |
| Grantee: | Felipe ten Caten |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| 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: | 13/21522-5 - Functional characterization of non-coding RNAs associated with IS1341 transposons in Halobacterium salinarum |
| Grantee: | José Vicente Gomes Filho |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| 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 |
| FAPESP's process: | 11/14455-4 - RNA-seq: segmentation and modeling of the signal |
| Grantee: | Felipe ten Caten |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |