Table 1.

Bacterial regulatory RNAs nomenclature and mode of action.

Bacterial regulatory RNAs
Mode of action Nomenclature		Abbreviations	Description
cis-acting RNAs		caRNA	The descriptor “cis-acting RNA” is used to describe regulatory RNAs that act (Ruiz de los Mozos et al., 2013), or are located at the untranslated regions (UTRs) of mRNA molecules (Gossringer and Hartmann, 2012).
	UnTranslatedRegion	UTR	UTRs are cis-acting RNAs located on untranslated regions of a coding transcript. They can activate/inhibit translation by releasing/hindering the RBS, respectively. They can also participate in the mRNA transcript stabilization (Gossringer and Hartmann, 2012). The base pairing between 5′- and 3′-UTRs can also control mRNA translation (Ruiz de los Mozos et al., 2013).
	5′ UnTranslatedRegion	5′ UTR	5′ UTRs are RNAs that act on the 5′-end of the mRNA transcript. They modulate the expression of the downstream genes by controlling the access of the ribosome to the translation initiation region (TIR). This class of UTRs includes Riboswitches, non-transcribed RNA, and independent transcripts. They play an important role in bacterial metabolism control. The modulation of the expression of the 5′ UTR-downstream genes occurs through a metabolite-induced alteration of the RNA secondary structure, such as tRNAs (Loh et al., 2009).
	3′ UnTranslatedRegion	3′ UTR	3′ UTRs are RNAs that act on the 3′-end of the mRNA transcript. They constitute the region of the mRNA that immediately follows the translation termination codon (TTC; Chao et al., 2012).
trans-acting RNAs (traRNAs)
	cis-encoded (antisense)RNA	asRNA	asRNAs are cis-encoded RNAs that act on the mRNA molecule encoded by the opposite DNA strand. They present a perfect base-pairing with their mRNA target (Thomason and Storz, 2010). We also distinguish toxin–antitoxin systems (Lee and Hong, 2011) and asRNAs encoded by the streptococcal pIP501 plasmid (Brantl and Wagner, 1996), or long asRNAs described in eukaryotes (Vadaie and Morris, 2013).
	5′ antisense RNA	5′ asRNA	5′ asRNAs are asRNAs that act on the 5′-end of the sense mRNA target. They activate or inhibit the translation of the mRNA transcript (Thomason and Storz, 2010). 5′ asRNAs can also act by transcription attenuation, which is frequently found on plasmids (Thomason and Storz, 2010).
	3′ antisense RNA	3′ asRNA	3′ asRNAs are asRNAs that act on the 3′-end of the sense mRNA target. The role of the 3′ asRNAs is not yet well-deciphered. However, it was suggested that they participate in the transcript stabilization (Opdyke et al., 2004; Padalon-Brauch et al., 2008).
	trans-encoded RNA	treRNA	treRNAs are RNAs that target distant and/or different RNAs, eliminate invading cognate DNA, or form ribonucleo-protein complexes (Storz et al., 2011). We can also distinguish in this class: housekeeping RNAs such as 6S RNA, RNase P RNA (Brantl, 2009), overlapping ncRNA (Kumar et al., 2010), and operon RNAs (Kreikemeyer et al., 2001).
	cia-dependent small RNA	csRNA	csRNAs are treRNAs that are transcribed from the promoters associated to CiaRH two-component system. They present a complementarity to the Shine-Dalgarno sequence and the translation initiation codon (AUG; Marx et al., 2010).
	microRNA-size sRNA	msRNA	msRNAs are a very small RNAs (15 to 26 nts) that are first described in Streptococcus mutans. The role of these microRNA-like sRNAs in bacterial gene regulation is not yet understood (Lee and Hong, 2011; Kang et al., 2013).
	CRISPR RNA	crRNA	As a part of the CRISPR (clustered regularly interspaced short palindromic repeat) system, the crRNAs act as treRNAs targeting and processing foreign DNA (Karvelis et al., 2013).
	trans-activating CRISPR RNA	tracrRNA	In the CRISPR/Cas system, tracrRNAs are in charge of the activation of the pre-crRNAs (Karvelis et al., 2013).