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Biology 430 > small RNAs > Flashcards

small RNAs Flashcards

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1
Q

miRNAs

A

microRNAs

  • 20-24 nt
  • produced from larger precursor transcript (70-100) nt that have a hairpin structure
  • hairpin cleaved by Dicer endonuclease enzyme to generate miRNAs
  • located in various locations: intergenic, introns
  • hundreds identified in eukaryotes – Illumina sequencing
  • plant completely complementary
  • animals not completely complementary
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2
Q

miRNA biogenesis

A

initial transcript forms stem-loop structure (pri-miRNA)

  • stem cleaved from rest of transcript (still have loop) (pre-miRNA)
  • loop cleaved
  • mature single stranded miRNA
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3
Q

miRNA functions

A
  1. post translational gene silencing/ transcript cleavage
    - incorporated into RISC complex where acts as guide to target and degrade Complementary mRNA by cleavage
    - down regulates gene expression
  2. blocking translation
    can be involved in translational repression: form RISC that prevents binding of mRNA to ribosomes
    - down regulates gene expression (complete or partial)
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4
Q

Draw miRNA mechanism

A

DRAW

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5
Q

miRNA expression patterns

A

can be expressed in tissue specific manner and can be developmentally regulated

  • miRNAs regulate many developmental processes, as well as other functions
  • can have many targets or one target
  • binding sites can have phenotypic effects (sheap muscle ex)
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6
Q

families of small RNAs

A

classified into families based on sequences

  • expand by gene duplication, contract by deletion
  • some have early origins = roles in development
  • recent origin= wider variety of roles
  • some new miRNAs are derived from transposons and repeat sequences
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7
Q

evolution of miRNAs in animals

A
  • lineage specific miRNAs
    • many evolutionary recent miRNAs
  • expression patterns in conserved miRNAs can vary
    • not strictly conserved even between 2 closely related species
  • expression can change rapidly in evolutionary time
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8
Q

acquiring a new miRNA

A
  • initially expressed at low levels in specific spatio-temporal domain
    • many targets deleterious
  • later most targets are neutral or advantageous and expressed at higher levels
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9
Q

siRNAs

A

small interfering RNAS

  • post transcriptional gene silencing
  • no dedicated genes for siRNAs
  • produced from double stranded RNAs
  • some originate form TE and heterochromatin regions
  • some help prevent expression of TEs
  • FULLY complementary to targets
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10
Q

siRNA mechanism

A

DRAW

- DICER, AGO, RISC

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11
Q

siRNA silencing of retrotransposons

A

Dicer, Ago, risc binds TE mrRNA

- results in post transcriptional silencing of TE

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12
Q

Inverted duplication and small RNAs

A

inverted duplication gene structure– mRNA forms loop structure
- major mode for how siRNA and miRNAs form de novo

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13
Q

lncRNAs

A

long non-coding RNAs

  • ~200nt and not translated into proteins
  • many intergenic, some overlap with protein coding genes
  • most recently identified
  • some function in chromatin remodeling complexes to help regulate gene expression
  • sequences evolve more rapidly than protein coding genes
  • tissue specific
  • less conservation
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14
Q

Xist

A

lncRNA and x-chromosome inactivation

  • expressed from inactive x chromosome
  • 17kb= unusually large
  • accumulates along x- chromosome to be inactivated and helps reduce heterochromatin formation
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15
Q

functions of lncRNAs

A
  • chromatin remodeling
    • recruitment of chromatin modifying complexes
    • decrease expression
  • transcriptional control (recruit or block TF or bind promoter)
    • positive, negative, or negative by binding to promoter to form triplex (not common)
  • reduce or inhibit function of miRNAs
    • bind miRNAs so fewer miRNAs available to reduce target gene
  • – positive effect on gene regulation
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16
Q

evolution of small RNAs

A

lncRNAs much less highly conserved than protein coding and less than small RNA precursors

  • conservation = protein coding> small RNA> lncRNA
  • lncRNA more recently evolved
17
Q

housekeeping vs regulatory ncRNAs

A 
housekeeping
- constitutively expressed
- tRNA, rRNA, snRNA, snoRNA
regulatory
-lncRNA and small ncRNA
- 200 nt is cut off
18
Q

evolution of lncRNAs vs protein coding genes

A 
lncRNA
- low sequence conservation
- maintain function by preserving short sequence stretches or structural motifs that serve as functional domains
protein coding
- high sequence conservation
- must preserve ORF to maintain function
19
Q

4 ways new lncRNAs can form

A
  1. gradual transformation of protein coding to functional lncRNA
  2. chromosome rearrangement of 2 un-transcribed regions
  3. duplication of lncRNA to give rise to 2 lncRNA
  4. TE insertion
20
Q

5S-OT

A

acts as a lncRNA
cis in mammals and trans in humans
- in mammals has cis and trans effects
- acts in cis to regulate its own expression
- acts in trans to modulate AS by interacting with the splice factor

21
Q

lncND

A

regulates itself and sequesters miRNA

- acts as a miRNA sponge

22
Q

3 ways miRNAs can originate

A
  1. local or tandem duplication of existing miRNA followed by sub/neofunctionalization
  2. gradual evolution of unstructured transcripts to form hairpin structures
  3. antisense transcription of existing miRNA gene
23
Q

miRNA vs siRNA

A

same length

  • mi= ENDOGENOUS
  • si= exogenous and endogenous
  • mi- don’t have to be fully complementary
  • single stranded
  • always have stem loop
  • si - completely complementary
  • single stranded
  • no dedicated genes to them
  • both use RISC complex
  • doesn’t need to form a stem loop structure but can

Biology 430 (16 decks)

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