Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog

Riboregulators regulate translation by having two elements, a cis-repressive sequence upstream of RBS in mRNA, and a non-coding RNA device, called trans-activating RNA. The cis-repressive sequence will binds to the 5'UTR, including the RBS by Watson-Crick base pairing, the sequestration of RBS represses translation. While trans-activating RNA will form complementary bases to cis-repressive sequence and exposing RBS for ribosomal binding and allow translation.

Proposed Categories: /RNA/non_coding/post_transcriptional/Riboregulator

A RNA apatamer is any RNA molecule that can fold into a tertiary confirmation that binds with strong affinity and high specificity to small molecules through non-Watson-Crick base pairing.

A riboswitch is a segment on mRNA that has the ability to detect small molecules or temperature, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domain for binding of small molecules and a regulatory domain for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo confirmation changes that can lead to different outcomes like translation inhibition or mRNA degradation.

RNA-OUT is a small non-coding RNA that works at RNA level . RNA-OUT will bind to 5'UTR, which include RBS, of mRNA and prevents ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a non-coding RNA that is antisense to RNA-OUT and the binding of RNA-IN and RNA-OUT will prevent RNA-OUT from binding to mRNA, thus allowing ribosome to bind to mRNA and initiate translation.

asRNAs are single stranded RNAs that usually form base pair extensively with the target sense RNA / DNA. RNAs belonging to this class are capable of blocking translation, interfering with transcription, or modulating RNA stability. A review by Thomason and Storz(2010) provided detailed descriptions to their properties and functions.

Reference:

Thomason MK, Storz G.,Bacterial antisense RNAs: how many are there, and what are they doing?, Annual Review of Genetics Vol 44:167±188(2010)

siRNAs work in the RNA interference (RNAi) pathway. siRNAs are usually produced by "dicing" exogenous, long double stranded RNA into 21-nucleotides small fragments. The siRNAs will then bind to Argonaute in RNA-induced silencing complex (RISC) and one strand is discarded. The remaining strand then guides the RISC to RNA targets with complementary base pairs and in most cases degrades the latter, result in inhibition of gene expression.

miRNAs, like siRNA, work through the RNA interference (RNAi) pathway They are usually 19-25nt single stranded RNA that have an endogenous origin. They started as hairpin transcripts and processed by Drosha in non-random manner and are then processed by Dicer. Following binding to RISC, they regulate normal biological processes by degrading or inhibiting mRNAs that it has complementarity to.

sgRNAs work in the CRISPR/Cas system. They are constructed by fusing functional domains of CRISPR RNA (crRNA) and trans-acting crRNA (taRNA) together through RNA linkers. They associate with Cas9 proteiens or their derivatives and guide them to DNA with complementarity with the targeting sequence of crRNA.

A ribozyme is a RNA molecule with intrinsic catalytic activity, that can catalyse conversion of substrate into a product.

RNA aptazymes, as the name suggests, are RNAs that carry properties from both aptamers and ribozymes. They are capable of sensing small molecules. Upon activation by a ligand, they can trigger ribozyme-mediated cleavage.

These ncRNAs have multiple interaction domains concatenated into a single molecule so as to facilitate co-localization of functional modules.

The pT181-RNAI is a special class of regulatory RNAs derived from elements in Staphylococcus aureus pathogenicity plasmid pT181. A specific 5’ UTR region would normally form an anti-termination loop. Upon interacting with a pT181-RNAI, a premature terminator loop 5’ to the CDS will form and result in early termination before the mRNA can be completely transcribed.

This class of ncRNAs can help to stabilize or destabilize a RNA molecule, typically by giving rise to hairpin structures that block or facilitate access of ribonucleases to the RNA itself.

This category contains ncRNA with dual or more functions resulting from combining 2 or multiple natures / functions of existing ncRNAs.

This category deals with segments of ncRNAs that serve as recognizable targets by other ncRNAs.

ncRNAs not belonging to the any of the above categories are listed here.