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Regulation Of Gene Expression > Lesson 8 > Flashcards

Lesson 8 Flashcards

1
Q

describe the central dogma in depth:

A

dna which can be replicated, is transcribed into RNA which is translated into proteins that are major players in regulating gene transcription

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2
Q

non-coding dna consists of what elements?

A

repetitive sequences (repetitive DNA and transposomes) and dna coding for noncoding RNA (long and small)

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3
Q

what are three types of small non-coding RNA?

A

miRNA, ribozymes, and tRNA

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4
Q

what does RNA interference lead to?

A

RNA silencing pathways

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5
Q

what does it mean when RNA silencing pathways are triggered?

A

negative regulation on gene expression

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6
Q

describe the origin of small interfering RNAs (siRNA):

A

endogenous or exogenous with respect to the cell they act on

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7
Q

what is the origin of miRNAs?

A

endogenous (cellular products) → any cells and somatic cells

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8
Q

what is the origin of Piwi-interacting RNAs?

A

endogenous → only germline cells

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9
Q

where was RNA interference first discovered?

A

C. elegans

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10
Q

the regulation of gene expression comes from an interaction within the genome at what level?

A

the level of DNA or chromatin modifications

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11
Q

what are most of the fundamental processes regulated by, such as development, differentiation, and cancer?

A

proteins together with microRNAs

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12
Q

why does the level of gene expression by RNA interference not occur at the level of initiation of transcription like with repressors?

A

mRNA is already transcribed but will not be expressed

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13
Q

describe the location of siRNAs:

A

both endogenous and exogenous

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14
Q

are miRNAs endogenous or exogenous?

A

endogenous → small guide RNAs that repress the expression of target genes

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15
Q

how to miRNAs differ from siRNAs?

A

in biogenesis but not function

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16
Q

where are miRNAs abundant?

A

in ssRNA

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17
Q

describe the effect of miRNAs on mRNA:

A

one miRNA can regulate many different mRNAS

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18
Q

what does the presence of multiple binding sites for different miRNAs at the 3’ UTR determine?

A

that several different miRNAs can target the same 3’ region, meaning that each mRNA can be regulated by different miRNA

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19
Q

what does the complex regulation of miRNAs allow?

A

for combinatorial control and system abundancy

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20
Q

how does the complex regulation of miRNAs allow combinatorial control?

A

more than one miRNA can regulate the same mRNA

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21
Q

how doest the complex regulation of miRNAs allow system abundance?

A

losing one miRNA due to mutation or deletion does not impact the regulation of the genes as there are many other that can get the job done

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22
Q

what is the structure of miRNAs?

A

21-24 nt regulatory RNAs with a hairpin secondary structure

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23
Q

list some functions of miRNA:

A

participate in the regulation of many important processes such as the regulation of signaling pathways, apoptosis, metabolism, development, cancer → they are important as well as proteins for the regulation of gene transcription at the post-transcriptional level

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24
Q

since an miRNAs mechanism of action is based on matching, what can occur?

A

the targets in the genome can be predicted by sequencing them

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25
Q

what are two roles of miRNA in biological processes?

A

help to confer robustness to transcriptional programs operated by regulatory proteins and since they do not interfere with the product, their tole can also be to regulate aberrant transcripts in the cell

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26
Q

at what point during development does miRNA expression increase?

A

during embryonic development

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27
Q

in animals, what correlation has been found with miRNA?

A

the more complex the organism, the more diverse the miRNA populaiton

28
Q

genes with tissue-specific expression have a longer 3’ UTR meaning what?

A

they have more miRNA binding sites → the genes encoding for proteins specifically expressed in a tissue during a certain step of differentiation require more regulation by miRNA

29
Q

LEARN RNAi PATHWAY

A
30
Q

what are miRNA’s function essential for?

A

sustaining life

31
Q

what is the prototype of genes coding for miRNA in C. elegans?

A

lin-4

32
Q

what does Lin-4 miRNA regulate?

A

lin-14 mRNA

33
Q

why are there multiple binding sites in the 3’ UTR?

A

we have different levels of complimentary, so no perfect match is needed (but some regions need to be matched)

34
Q

describe the structure of Lin-4 miRNA:

A

transcribed as a single molecule and thanks to its intra-strand complimentary regions formed a double-stranded RNA (forms kind of a hairpin structure)

35
Q

where are the genes encoding miRNAs located?

A

the nucleus

36
Q

what is the final product of transcription?

A

pri-miRNA

37
Q

what is pri-miRNA?

A

a single stranded molecule that has a 5’ end and a 3’ end, and a quite extended region of intrastrand homology with a small loop a the end

38
Q

in the nucleus, what is pri-miRNA processed by?

A

Drosha

39
Q

in mammals, what is Drosha coupled with?

A

DGCR8

40
Q

what is the function of Drosha + DGCR8? (after transcription)

A

responsible for the first major processing, which consists of cleavage and generation of the 3’ overhang

41
Q

after pri-miRNA is processed by Drosha, what does it become?

A

pre-miRNA

42
Q

where must the regulation of miRNAs occur?

A

cytoplasm

43
Q

how do pre-miRNAs get to the cytoplasm?

A

exported from the nucleus through nuclear pores by RAN-GTP/exportin 5 complex

44
Q

what enzyme processes pre-miRNA in the cytoplasm?

A

DICER

45
Q

what is the function of DICER?

A

the enzyme which is responsible for trimming the pre-miRNA

46
Q

what is the main modification from pre-miRNA to mature miRNA?

A

the loop is lost and the 3’ overhang on both sides of the strands are formed

47
Q

which are the only types of mature miRNA included in RISC complexes?

A

double strand structure of mature miRNA

48
Q

once miRNA is mature, describe the structure:

A

two different strands called Duplex miRNA/miRNA*→ one will be retained by the RISC complex and the other will be released and degraded

49
Q

in what three ways are miRNAs present in the genome?

A

in an intergenic position, intragenic position, or in clusters

50
Q

describe in intergenic position:

A

transcription is regulated by specific elements such as promotors (is a single transcription unit)

51
Q

describe an intragenic position:

A

transcription miRNA is regulated by the “host” gene elements → miRNA are included in introns so transcription will occur under the control of the promotor of the gene in which they are contained

52
Q

describe clusters in relation to miRNA genes:

A

in Drosophila: processed as polycistroninc RNAs and can be transcribed as polycistronic mRNA

53
Q

in the intragenic position, are the miRNAs going to regulate the transcript in which they are included?

A

yes but not always

54
Q

describe Drosha:

A

a nuclear enzyme with RNAse activity (trims long transcripts)

55
Q

in drosophila, what does Drosha work with instead of DGCR8?

A

Pasha

56
Q

describe the processing of pri-miRNA:

A

during processing all the inferior stem is lost while all the superior stem is retained, the loop is lost as well

57
Q

describe the structure of Drosha:

A

double-stranded RNA binding domains, two domains with RNAse activity, a N-terminal domain and a nuclear localization signal

58
Q

why does drosha need a partner (DGCR8 or Pasha)?

A

it is not able to selectively cut the pri-miRNA the correct way

59
Q

where is the 3’ overhang on pre-miRNA?

A

2 nucleotide overhang on the 3’ end

60
Q

where does dicer cut the miRNA?

A

recognizes the double strand end of the loop and cuts both ends of the duplex

61
Q

what does RISC stand for?

A

RNA induced silencing complex

62
Q

describe the structure of dicer:

A

helices domain, two RNAse III domains, a dsRNA binding domain and a PAZ domain

63
Q

when is the RISC complex transformed into an active form?

A

only when there is the unwinding of the siRNA or miRNA duplex and one strand is lost → when the miRNA is still bound the complex is inactive

64
Q

what is the mechanism of action in RISC assembly?

A

RISC recognizes the target mRNA and this recognition is mediated by the match between miRNA and the mRNA

65
Q

name two ways in which miRNA silencing can occur:

A

if the cut of mRNA is in a very specific position (mRNA is cut at the level of nucleotides complimentary to th exposition of nucleotide 10 and 11 in the miRNA) OR the inhibition of translation due to the absence of a perfect match

66
Q

what is the choice between the two silencing mechanisms of miRNA dependent on?

A

the level of complementarity between miRNA / siRNA and the target mRNA

67
Q

name 5 possible mechanisms for miRISC-mediated repression (inhibition of translation):

A

compete for cap binding, promote degradation, compete for eiF2/60S, block circulation, or cause ribosome dropoff

Regulation Of Gene Expression (28 decks)

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