RegulonDB ( ) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. However, accessing and navigating such a wealth of data is not straightforward. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions.
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