title: Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.
abstract: The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.
authors: a Department of Biochemistry and Immunology ; Ribeirão Preto Medical School ; University of São Paulo ; Ribeirão Preto , Brazil.
authors: José Vicente
authors: JV
authors: Gomes-Filho
authors: Livia Soares
authors: LS
authors: Zaramela
authors: Valéria Cristina da Silva
authors: VC
authors: Italiani
authors: Nitin S
authors: NS
authors: Baliga
authors: Ricardo Z N
authors: RZ
authors: Vêncio
authors: Tie
authors: T
authors: Koide
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling; D019766:Genes, Archaeal; D019617:Halobacterium salinarum / Q000235:genetics* / Q000254:growth & development; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D019895:Transposases / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D018626:Retroelements; D019895:Transposases
keywords: HgcC RNA family; IS1341; IS1341-type; IS200/605; RNA-seq; non-coding RNA; overlaping transcripts; sense overlaping transcripts; tetraloop; transposons