RNA Mediated Gene Regulation Lecture

RNA Mediated Gene Regulation

RNA Structure

  • RNA molecules are polyribonucleotides composed of base units:

    • Uracil (U)

    • Adenine (A)

    • Guanine (G)

    • Cytosine (C)

  • RNA bases perform hydrogen bonding in specific pairs:

    • U:A pairs

    • G:C pairs

  • These base pairs can interact in two ways:

    • Intramolecular: within the same RNA molecule

    • Intermolecular: between different RNA molecules

  • RNA has complex secondary structures, including:

    • Hairpin structures: known as stem-loop formations

  • RNA bases are subject to chemical modifications affecting interactions.

Small RNA Regulators

Riboswitches

  • A riboswitch is a stem-loop structure that forms at the 5'-end of bacterial mRNA.

  • Modifies translation efficiency by blocking the Shine-Dalgarno sequence, inhibiting ribosome binding.

  • An effector molecule binds to the riboswitch, stabilizing its structure, exhibiting a negative feedback mechanism in gene regulation.

Anti-sense RNAs (sRNA)

  • Prokaryotic cells can possess non-coding regulatory genes that produce antisense RNA.

  • This antisense RNA is the reverse complement of an mRNA sequence.

  • The sRNA binds to an mRNA from a structural gene, obstructing translation.

CRISPR

  • Prokaryotes utilize a specific defense mechanism against foreign DNA through CRISPR.

  • Mechanism involves an array of sequences that generate small crRNA molecules, which guide Cas proteins to degrade specific DNA sequences.

    • Cas proteins are responsible for cleaving foreign DNA.

    • DNA fragments from the foreign DNA are integrated into the bacterial chromosome at the CRISPR array.

    • RNAs transcribed from this CRISPR array direct Cas proteins to degrade other foreign DNAs bearing those specific sequences.

Micro RNAs (miRNAs)

  • miRNAs are small, double-stranded RNA molecules created by cleaving hairpin RNA with the enzyme Dicer.

  • In eukaryotes, miRNAs are transcribed complementary to sequences on other genes.

  • miRNAs form a RISC complex by combining with Argonaut proteins.

    • This complex binds to target mRNA and inhibits translation.

    • miRNAs generally exhibit an imperfect sequence match with target mRNA.

    • When binding occurs near the 5'-end of an mRNA, it does not typically result in mRNA cleavage.

  • Binding of miRNAs to the 3'-end may trigger "Slicer independent" degradation, achieved by recruiting de-capping and de-tailing enzymes.

Long Non-coding RNA (lncRNA)

  • Eukaryotes transcribe long non-coding RNAs (lncRNAs) that undergo capping and polyadenylation but do not translate into proteins.

  • These lncRNAs function as decoys, competing with mRNAs for binding with miRNAs, diminishing the effectiveness of mRNA.

Small Interfering RNAs (siRNAs)

  • Eukaryotes have a defensive small RNA system for RNA interference (RNAi).

  • Utilizes double-stranded siRNA molecules formed by Dicer cleaving double-stranded RNA originating from retroviruses or transposons.

  • siRNA associates with Ago proteins to construct a RISC complex.

    • This complex cleaves complementary mRNA derived from viral or transposon DNA, resulting in degradation.

    • Furthermore, siRNA can induce transcription silencing of specific genes by recruiting histone methyltransferase enzymes to nucleosomes.

Epigenetics

  • Refers to modifications of DNA and histones that lead to heritable changes in gene expression without changes to DNA sequences.

  • These modifications respond to environmental conditions and can be reversible in future generations.

  • DNA methylation inhibits transcription, frequently occurring on a cytosine (C) within a CpG pair, often clustered in regions termed CpG islands located near gene promoters.

    • Maintenance of DNA methylation: Executed by DNA methyltransferase enzymes that methylate daughter DNA at the same locations as methylated parental CpGs.

Example: DNA Methylation in Bees

  • DNA methylation influences the developmental fate of female bees.

    • Larvae receiving a diet rich in royal jelly, which inhibits methylase enzymes, can develop into queens.

    • In contrast, other female larvae that undergo standard DNA methylation are differentiated into worker bees.

Example: Developmental Regulation in Eukaryotes

  • Cells gradually differentiate by selectively expressing certain genes and silencing others.

  • Inappropriate genes are turned off long-term via DNA and histone methylation.

  • Genomic imprinting: A phenomenon where alleles are differentially silenced based on the parent of origin.