Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.
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.
['Gomes-Filho|José Vicente|JV|', 'Zaramela|Livia Soares|LS|', 'Italiani|Valéria Cristina da Silva|VC|', 'Baliga|Nitin S|NS|', 'Vêncio|Ricardo Z N|RZ|', 'Koide|Tie|T|']
D001483:Base Sequence D020869:Gene Expression Profiling D019766:Genes, Archaeal D019617:Halobacterium salinarum D008969:Molecular Sequence Data D059372:Nucleotide Motifs D012333:RNA, Messenger D022661:RNA, Untranslated D018626:Retroelements D019895:Transposases
sense overlaping transcripts overlaping transcripts IS1341-type non-coding RNA tetraloop HgcC RNA family IS1341 IS200/605 RNA-seq transposons