| Full text | |
| Author(s): |
Zaramela, Livia S.
[1]
;
Vencio, Ricardo Z. N.
[2]
;
ten-Caten, Felipe
[1]
;
Baliga, Nitin S.
[3]
;
Koide, Tie
[1]
Total Authors: 5
|
| Affiliation: | [1] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, BR-14049 Ribeirao Preto - Brazil
[2] Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, BR-14049 Ribeirao Preto - Brazil
[3] Inst Syst Biol, Seattle, WA - USA
Total Affiliations: 3
|
| Document type: | Journal article |
| Source: | PLoS One; v. 9, n. 9 SEP 19 2014. |
| Web of Science Citations: | 8 |
| Abstract | |
A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (similar to 7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life. (AU) | |
| 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) |
| FAPESP's process: | 11/07487-7 - Identification and characterization of Lsm-binding non-coding RNAs in the extremophile Halobacterium salinarum |
| Grantee: | Lívia Soares Zaramela |
| Support Opportunities: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 09/09532-0 - Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model |
| Grantee: | Tie Koide |
| Support Opportunities: | Research Grants - Young Investigators Grants |