Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

Autor(es)

Zaramela, Livia S. ^[1] ; Vencio, Ricardo Z. N. ^[2] ; ten-Caten, Felipe ^[1] ; Baliga, Nitin S. ^[3] ; Koide, Tie ^[1]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 9, n. 9 SEP 19 2014.
• Citações Web of Science: 8

Resumo

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)

• Processo FAPESP: 11/14455-4 - RNA-seq: segmentação e modelagem do sinal
• Beneficiário: Felipe ten Caten
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 11/07487-7 - Identificação e caracterização de RNAs não codificantes ligantes a Lsm no extremófilo Halobacterium salinarum
• Beneficiário: Lívia Soares Zaramela
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 09/09532-0 - Biologia sistêmica do extremófilo Halobacterium salinarum: contribuição dos RNAs não-codificantes ao modelo global de regulação gênica
• Beneficiário: Tie Koide
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores