RNA-Based Regulation

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4 Terms

1
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Riboswitch

involves an mRNA binding a small molecule

binding of this molecule alters the translation or transcriptional termination (acting as an attenuator) of that same mRNA.

utilize alternate folding structures that can form in the 5’ UTR of the mRNA

one form of folding can cover the ribosome binding side (SD) or form an attentuator to decrease gene expression.

acts in cis

primarily found in bacteria but some eukaryotic examples

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antisense RNA (sRNA)

described primarily in bacteria

2 genes: gene 1 produces the structural gene’s mRNA (OmpF), which is the target of regulation. gene 2 produces a short RNA (sRNA) that is complementary to gene 1 mRNA

base-pairing of the sRNA (RNA 2) to the target mRNA (RNA 1) turns off gene 1’s translation by covering the ribosome binding site (SD) or the start codon (AUG).

acts in trans

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RNA silencing / RNA interference (RNAi)

acts in trans

key RNA-based regulatory mechanism in eukaryotes

double-stranded RNA is recognized and used to degrade or block transcription or translation of other RNAs that share the same sequence

Process:

  1. initiating dsRNA recognized by Dicer enzyme, cutting it into small pieces approx. 22 nucleotides long

  2. these small pieces rebound by a protein complex called RISC. RISC uses the small RNA p piece as a guide to find matching sequences in other RNAs.

  3. outcome depends on degree of complementarity:

    1. if there is a perf match to the mRNA (typical of siRNA), RISC will cut up and degrade the target mRNA

    2. if near-perf match (typical of miRNA), RISC will block the translation of the mRNA.

  4. for siRNA, a related protein complex called RITS can find matching sequences in the DNA (often recognizing transcribing mRNA) and induce methylation, leading to the silencing of the gene at the transcriptional level

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RNAi uses in the cell

  • viral defense, particularly noted in plants

  • normal silencing and heterochromatin formation in repetitive DNA like retrotransposons and satellite repeats at centromeres, involving siRNA-like piRNAs

  • regulation of other target genes, particularly mRNAs encoding transcription factors.