RegTransBase is a database of regulatory sequences and regulatory interactions on the transcriptional and posttranscriptional levels in prokaryotic genomes. RegTransBase contains experimental data and predicted sites published in scientific journals. We also plan to include our own unpublished predictions in the nearest future.

Each article in RegTransBase was annotated independently. Each annotation includes a list of sequence and regulatory elements as well as a number of experiments (with a short description).

There are five main classes of sequence elements in RegTransBase: site, gene, transcript, operon and locus.

Site. Any sequence fragment can be defined as a site, independently of its real function.
Gene. For a protein-coding gene it is its CDS. For RNAs (rRNA, tRNA etc.) "gene" is a region from the promoter to the terminator (where they are known)
Transcript. It is a single transcription unit starting at a promoter and ending at a terminator.
Operon. This element includes one or more overlapping transcriptional units.
Locus. Locus is a sequence region that can include elements of any class mentioned above, located in a continous fragment.

Sequence elements can be linked positionally (like genes that are inside of the operon) or logically (like sites that regulate expression of one gene). To depict such links, we set "parent-to-child" relations where "child" is a "subelement". The types of elements form a hierarchy locus->operon->transcript->gene-> site, so that a lower-level element can be a subelement of any higher-level element. RegTransBase, see table below for summary.

		ELEMENTS
		Site	Gene	Transcript	Operon	Locus
S U B E L E M E N T S	Site	+	+	+	+	+
	Gene	-	+	+	+	+
	Transcript	-	-	+	+	+
	Operon	-	-	-	+	+
	Locus	-	-	-	-	+

There are three additional classes of sequence elements but they are rarely used: regulon, RNA secondary structure and helix.

Regulon. Regulon is a set of all sequence elements regulated by one transcriptional regulator. An element of any class can by its subelement.
RNA secondary structure. As follows from its name, this element describes the secondary structures of terminators, regulatory regions of mRNA etc. It also can be used for any other RNA. This element can be a subelement of any class mentioned above.
Helix. RNA double helix is a basic unit of the RNA secondary structure. This element corresponds to a single continous stem in a RNA structure, so it can be a subelement of RNA secondary structure.

We use regulatory elements to describe regulatory interactions controlling expression of bacterial genes and operons. There are two classes of regulatory elements in RegTransBase: regulators and effectors.

Regulator. Regulator is a protein or RNA molecule directly binding the regulated gene.

Effector. Effector is a molecule (or a physical effect, like heat shock) affecting gene expression that is not a regulator. It can be a small molecule (like a metal ion) or a protein (an indirect regulator, like sensor kinase) or even a macromolecular complex (RNA polymerase, if it stabilizes binding of a sigma factor with a promoter region).

Usually, an experiment includes experimental results describing regulation of a gene or an operon studied with one technique. However, some exceptions exists such as site predictions or array experiments where multiple genes are studied in a single experiment.
Annotation of each experiment includes formal description of the aim of the experiment, the list of experimental techniques used in the experiment and the list of regulatory elements studied. A short textual description is also provided.

We collect the following types of experimental data:

• Experiments investigating the activation or repression of a gene's (or operon's) transcription by an identified direct regulator.
• Regulation of the gene's (or operon's) expression on the posttranscriptional level.
• Promoter or terminator mapping.
• Characterization of an operons' structure (cotranscription, complementation etc.).
• Experimental evidence for the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA).
• Mapping of a binding site of a regulatory protein.
• Characterization of a regulatory mutation if the regulated gene was identified.
• Prediction of binding sites of a regulatory protein (including alternative sigma factors).
• Experiments investigating the RNA secondary structure of terminators and mRNA regulatory regions.

 

We are not interested in the following types of experimental data:

• Experiments investigating regulation of the gene (or operon) transcription where the regulator was not identified.
• Regulation of the protein function on the posttranslational level.
• Regulation of the gene (or operon) expression by a regulator not binding DNA (RNA) directly (e.g. a sensor kinase).
• Study of the protein function (except direct transcriptional regulators).
• Experiments on cloning and sequencing.
• Study of regulatory mutations if the regulated gene was not identified.
• Mapping of translation starts.
• Mutations affecting well-known regulatory proteins.
• Experiments on regulation of unknown gene, even if the regulator was identified (for instance, regulation of a biochemical fuction).
• Prediction of promoters (except promoters of alternative sigma factors) or terminating stem-loops by sequence analysis.