Abstract
Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA’s transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5′UTR of divergently transcribed mRNAs.
Highlights
The generally accepted classification of non-coding regulatory RNAs is primarily based on their genomic positioning relatively to the target gene subjected to regulation
The mode of ncRNA’s biogenesis—from IGRs by means of transcription from specified promoter or from coding genomic region and adjacent loci mediated by RNAse E—implies the involvement of different molecular mechanisms in the regulation of their abundance. ncRNA excised from mRNA precursor follows the pathways implicated in the control of parental RNA synthesis, additional level of regulation may be imposed by accessibility of distinct structural motifs to RNAses
Mapping of additional transcription start sites (TSSs) in upstream regions of annotated ncRNAs contributes to our knowledge regarding the diversity of specious RNA produced from the same intergenic region, and enforces us to reconsider functional attribution of certain ncRNAs
Summary
The generally accepted classification of non-coding regulatory RNAs (ncRNAs) is primarily based on their genomic positioning relatively to the target gene subjected to regulation. The amount of corresponding ncRNAs depends on the growth conditions Both short and long RNAs are consistently activated in stationary phase along with the transcription of the adjacent tfaS gene demonstrating cooperative behavior (Supplementary Figure S1A, data set of Thomason et al, 2015). 5′-end of Ffs-born intracellular fragment (Alikina et al, 2018; Supplementary Table S1) is shifted down by 11 nt relatively to TSS refined according to the data of Thomason et al (2015) It means that additional stem-loop structure expected to form in 5′extended transcript (Figure 3B) may exert functional role for nibbling out short RNA. Undeservedly rejected divergently transcribed ncRNAs may regain their place in E. coli genome annotation
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