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Transcription Start Site (TSS) identification in extremophilic archaeon Halobacterium salinarum NRC-1 and its association with intraRNAs production

Grant number: 15/12012-9
Support Opportunities:Scholarships in Brazil - Doctorate (Direct)
Effective date (Start): October 01, 2015
Effective date (End): July 31, 2016
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Tie Koide
Grantee:Felipe ten Caten
Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil


With the development of large scale gene expression quantification technologies it is growing the number of evidences indicating that much of the genome of different organisms has some level of gene expression. The universe of RNA in cells has been expanded, showing that independent transcripts can be detected on the opposite strand of the coding regions, overlap to 5' and 3' ends of genes, in intergenic regions, or may extend over several base pairs, generating transcripts with dual function, acting as non-conding and coding RNAs. This phenomenon was called pervasive transcription. Among the numerous transcripts generated through the pervasive transcription a very interesting group are the intraRNAs, or transcripts overlapping coding regions wich can perform distinct functions of its cognate genes. Using differential RNA seq experiments (dRNA-seq) in the reference condition of growing of the extremophilic archaeon Halobacterium salinarum NRC-1, we detected 1633 Transcription Start Sites (TSSs) along whole genome this microorganism. 161 are located in the inner portion of protein-coding genes and are possibly related to production intraRNAs. Furthermore, the presence of conserved protein domains related to some of these internal TSSs provides evidence that the existence of intraRNAs overlapping these regions could produce functional proteins. To expand the previously obtained information additional dRNA-seq experiments will be performed along the growth curve for H. salinarum NRC-1, since many genes could be detected under specific growth conditions. With this new information we can also detect genes produced from different transcription starts and check whether the identified intraRNAs exhibit differential expression according to the growth condition of microorganism. (AU)

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
PEREIRA DE ALMEIDA, JOAO PAULO; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; TEN-CATEN, FELIPE; GOMES-FILHO, JOSE VICENTE; KOIDE, TIE. The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. GENES, v. 10, n. 4, . (15/12012-9, 15/21038-1, 13/21522-5, 17/03052-2, 11/14455-4)
TEN-CATEN, FELIPE; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN PERICLES R.; ZARAMELA, LIVIA SOARES; SANTANA, ANA CAROLINA; KOIDE, TIE. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA BIOLOGY, v. 15, n. 8, p. 1119-1132, . (11/14455-4, 15/21038-1, 17/03052-2, 11/07487-7, 15/12012-9)

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