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3597A Final > Week 11 - micro RNA and RNA-epigenetic > Flashcards

Week 11 - micro RNA and RNA-epigenetic Flashcards

1
Q

Heterochronic genes

A

mutants affect timing of divisions

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2
Q

lin-14 (lf)

A

lineage is disrupted; precocious development of L2 lineage
- 2 rounds of division in L1 larval stage

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3
Q

lin-14 (gf)

A

suppression of L2 lineage and replacement with L1 lineage
- continuous reiteration of L1 lineage

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4
Q

lin-4 (lf)

A
  • result in same suppression of L2 lineage as Lin-14 gf
  • continuous reiteration of L1 lineage
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5
Q

Double mutants;
lin-4 (lf) lin-14 (lf)

A

demonstrated lin-14 phenotype

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6
Q

Lin-4 ____ lin-14

A

represses

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7
Q

lin-14 encodes a _______

A

nuclear protein

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8
Q

lin-4 encodes a _______

A

non-coding RNA, a miRNA the first found

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9
Q

lin-4 RNA ____ with Lin-14 _______

A

base pairs, 3’ UTR

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10
Q

in lin-14 gf mutants, ________ are deleted

A

lin-4 binding sites

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11
Q

lin-14 mRNA is expressed ______ larval stages, however lin-14 protein is expressed in _____ larval stages

A

throughout, L1

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12
Q

lin-4 mRNA is expressed at ______ larval stages

A

L2, L3 and L4

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13
Q

Let-7 and Lin-29

A

required for suppressing L4 events
- let7 (lf) and lin-29 (lf) depicts lineages dividing past adult stages
- lin-29 stops juvenile lineages from occurring and establishes adult lineages

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14
Q

let-7 encodes ____ and can bp at the _____ of RNA

A

non-coding RNA, 3’ UTR

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15
Q

miRNAs

A
  • everywhere
  • very short; 20 odd bases long
  • sequencing 20 base RNAs uncovered many miRNAs
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16
Q

miRNA transcription

A
  • transcribed by RNAPII
  • processed to form pri-miRNA
    • PASH-1 and DRSH-1 bind
  • formation of hairpin structure = pre-miRNA –> EXPORTED TO CYTO and processed by dicer
    • forms 20 nucleotide miRNA that will form a complex with AGO where complex searches for mRNA that contain complementary RNA sequences
  • RNA-induced silencing complex (RISC) forms –> brings silencing of translation of message
  • miRNA turnover = miRNA have a lifespan
    • will be POLYURINATED –> uracils added to 3’ end for degradation
16
Q

miRNA suppresses ________

A

translation

17
Q

RNAi degrade _____ through _____

A

mRNA, cleavage

17
Q

miRNA guide ____ to ____ and ___ suppresses _____

A

RISC,
specific mRNAs,
RISC,
translation

(MODEL SUGGESSTS miRNA HAVE NO ROLE IN ACTIVATING RISC)

17
Q

Experiment to understand miRNA role in RISC proteins

A

1) tether AGO to RNA binding protein (ex: lambda N protein -> recognized b -box)

2) Two experiments,
1. mRNA with no b-box = TRANSLATION

  2. mRNA with b-box that N protein     can bind to = NO TRANSLATION
17
Q

Activate state –> Repressed state

A
  • gene transcribed by RNAP
  • RNA info converted into mRNA
  • mRNA binds to AGO
  • AGO with mRNA finds transcript and recruits enzymes important for regulating chromatin structure
  • SILENCES CHROMATIN
17
Q

New definition of epigenetic:

A

gene expression changes that are mutation independent and heritable in the absence of the triggering event

17
Q

paramutation

A

an allele of a gene can permanently and heritably change the expression or behavior of another allele of the same gene, even without any changes in the DNA sequence

17
Q

Paramutation in corn

A

the presence of B’ alters B-I
- B-I that has been exposed to B’ can now alter B-I alleles

*NON-MENDELIAN INHERITENCE**
- inherited in a transgenerational manner

  • expression of b1 locus of B-I allele is regulated by a B-I enhancer (Tandem repeats) approx. 1 kb 5’ from b1 locus
    • in the B’ locus, tandem repeats are associated with B’ silent chromatin
17
Q

RNAe (RNA epigenetics)

A

involves use of miRNA to recruit protein involved in modification of chromatin to specific genes

17
Q

A. thaliana (plants) RNAe

A
  • uses RNAP 4 and 5
  1. RNAP 4 transcribes region of genome
  2. bound by RNA-dependent RNAP and a DS copy made
  3. transcript diced
  4. 20b miRNA sequences produces
  5. AGO recognizes miRNA and forms complex
  6. complex enters nucleus
  7. Pol 5 transcribes region and recruits methylases
  8. area of DNA is methylates
    = SILENT STATE
17
Q

S. pombe (yeast) RNAE

A
  1. area of heterochromatin induces transcripts (using Pol2)
  2. transcripts bound by RNA-dependent RNAP
  3. copy of RNA made
  4. copy recognized by dicer
  5. 20 base long nucleotides produced
  6. AGO recognizes 20b seq. and finds binding site and forms RNA scaffold
  7. enzymes to modify histones are recruited
    = REPRESSIVE STATE (HETEROCHORMATIN MAINTAINED)
17
Q

C. elegans (nematode)

A
  1. RNAs diced
  2. placed in worm-specific AGO protein
  3. enters nucleus and finds target transcript
  4. recruit enzymes to modify chromatin structure
    = REPRESSIVE STATE (HETEROCHORMATIN MAINTAINED)
17
Q

Tandem repeats RNAe

A

when tandem repeats are transcribed, siRNA are produced which are recognized by AGO and enters the nucleus again where it binds to transcript produced from tandem repeats
- Repression enzymes are brought in which change the structure of TR from open to silent and now TR cannot act as an enhancer

18
Q

mop

A
  • characterization of genes required in trans
  • mop recognizes Pol4 and produces a RNA copy of transcripts, DS RNAs are then diced, associate with AGO and re-enter nuc to maintain silent chromatin
19
Q

transgenerational silencing in the germ line can last for ______ generations

A

> 10

20
Q

transposable element gene silencing

A

cause massive gene rearrangements
- activation of P element through transposition in flies leads to sterile phenotype

21
Q

Piwi pathway –> Piwi RNA expression

A

P-element Induced Wimpy testis

  • surpresses expression of transposable element transposons
  • pre-cursor piRNA transcript transcribed using RNAPII
  • Rhino protein shuttles between chromatin and RNA
  • when Rhino on RNA, it marks transcripts to be taken into cytoplasm where it is cleaved
22
Q

Piwi RNA function

A
  • short RNA seq that piwiAGO recognizes , moves into nucleus
  • piwiAGO RNA complex will hybridize to transposon RNA
    = silencing of TE transcription and degradation of transposon mRNA
    • therefore NO TRANSPOSONS ARE BEING PRODUCED
23
Q

Piwi conversion

A
  • new TE can be used to produce loci that will produce PiwiRNA

Transposon RNA –> piwiRNA locus (suppress expression of transposon)

24
Q

transgeneration avoidance of Pseudomonas

A
  • C.elegans originally attracted to pseudomonas (pathogenic)
  • however once on pseudomonas, c. elegans learn to avoid it which can last for many generations
  • learning index maintained for 4 generations, lost in the fifth

REQUIRES USE OF miRNA

25
Q

P0 HK9me3 methyltransferase

A

methylates histones and loses the organisms’ ability to learn

26
Q

Prions

A
  • protein disease, infectious agent

non prion (has same aa seq as prion) -> exposed to prion protein –> changes structure of protein to become –> prion

PERMITS TRANSGENERATIONAL CHANGE IN PROTEIN CONFORMATION

27
Q

mot3

A

TF mot3- = suppresses expression

MOT3+ (prion form) = INACTIVE, allowing expression
- MOT3+ is stuck in an aggregate such allows expression of gene

  • MOT3+ can convert mot3- to MOT3+ for generations

3597A Final (11 decks)

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