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MSI Unit I > 1-45 Eukaryotic Transcription II > Flashcards

1-45 Eukaryotic Transcription II Flashcards

1
Q

mRNA processing in eukaryotes includes…

where/when do these occur?

A

5’ capping
3’ polyadenylation (poly-a-tail)
splicing
RNA editing

occur in nucleus before shipment to ribosome

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2
Q

5’capping

and three functions?

A

7-methylgunaosine nucleotide added to 5’ end of pre-mRNA.

  1. protects mRNA from degredation
  2. facilitates
  3. allow translation by ribosome
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3
Q

3’ polyadenylation

where does it occur

A

100+ nucleotides added to 3’ end of the pre-mRNA

occurs past the poly (A) addition signal. Provides same benefits as 5’cap

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4
Q

splicing

alternative splicing patterns allow for..

A

intron sequences in pre-mRNA are spliced out, leaving exons

allows for multiple distinct protein products from a single transcribed DNA sequence

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5
Q

mutations involving the splicing process can lead to..

A

disease

progeria - RNA splicing disease

-mutation in area coding for nuclear lamina creates false splice site, more genetic material is spliced out of mRNA than desired

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6
Q

drugs targeting the splicing process have…

A

proven effective against diseases such as Spinal Muscular ATrophy

-drug dislodges the splicing repressor for that exon

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7
Q

non-coding RNA’s can regulate..

A

gene expression

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8
Q

microRNA (miRNA) and gene expression regulation

A

along with RISC proteins, small RNA sequences base pair match with mRNA’s and either inhibit or degrade translation

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9
Q

small interfering RNA (siRNA) and gene expression regulation

A

cleave target mRNA’s

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10
Q

piRNA (Piwi-Interacting RNA) and gene expression regulation

A

prevention of transposition of transposons in the germline

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11
Q

lncRNA (Long Non-Coding RNA) and gene expression regulation

A

Engage in RNA-RNA, RNA-DNA, and RNA-protein interactions to regulate

transcription
splicing
translation
imprinting

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12
Q

RNA sequencing

eQTL’s?

A

is becoming the method of choice for certain diagnoses

detects types/amounts of RNA sequences present in given cell types

eQTL’s - expresision quantitative trait loci take this idea and apply it to disease diagnosis - certian profiles of mRNA expression in certain tissues are associated with diseases

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13
Q

eQTL’s

A

expresision quantitative trait loci apply RNA sequencing and apply it to diagnosing diseases - certain profiles of mRNA expression in certain tissues are associated with diseases

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14
Q

ENCODE

A

encyclopedia of DNA elements aims to map epigenetic sites in the genome and properties of those histones including

  • Transcription factor binding sites
  • cis-acting enhancers
  • Nucleosome positioning
  • Histone modifications
  • RNA splicing signals
  • Non-coding RNA’s
  • Chromosome looping interactions
  • Replication origins
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15
Q

recent nobel prize-winning studies have shown that..

A

differentiated cells can be reprogrammed back into stem cell state OR directly into other kinds of differentiated cells using a few transcription factors

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16
Q

RNA interference, two types

A
  1. a perfect base match will recruit factors to destroy the mRNA
  2. a near-perfect base match will recruit inhibitory factors
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17
Q

Many gene activator proteins are comprised of an “activation domain” which is separate from a DNA-binding domain. TF

A

True

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18
Q

A 2’-5’ phosphodiester bond is formed in which of the following processes:

A

RNA splicing. G cap

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19
Q

what is the enzyme/protein required for recognition of the TATA box by the RNA polymerase II transcriptional machinery.

A

TFIID -factor specific for binding to the TATA box; one of its subunits is TBP- TATA-binding protein.

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20
Q

enzyme/protein directly required for gene expression by unpacking DNA in nucleosomes.

A

Histone Acetyltransferase

HAT enzymes activate transcription by aceytylating nucleosomes, reducing their positive charge and thereby their hold on DNA wrapped around them, thereby exposing nucleotide sequences such as the TATA box for protein binding (in this case by TBP, which initiates the cascade of binding by general transcription factors for ultimate binding by PolII).

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21
Q

guanyl transferase methyl trasnferase

A

puts ‘5 G cap on backwards in 5’-5’ linkage

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22
Q

poly A polymerase adds

A

adenisines at 3’ tail

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23
Q

alternative splicing allows…

A

a single gene to generate different isoforms of teh same proteins. Important because we have fewer genes than a housefly, but we do more splicing.

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24
Q

a big gene is more likely to…

A

recombine with its homologue than a small gene.

this helps create diversity

25
Q

the sequences required for intron removal

A

donor, acceptor, and branchpoint are cis-acting sequences

26
Q

way to cure spinal muscular atrophy?

A

in normal neurons, functional SMN1 and nonfucnctional SMN2 are spliced differently, leading to their differential functionalities

In SMA, the SMN1 splicing pattern is lost due to a mutation, and the only splcing pattern available (SMN2) creates unstable proteins only.

the idea is to change the splicing of SMN2 RNA to the splciing pattern of SMN1 with drug therapies

27
Q

how do SMA drugs work?

A

prevent binding of “splicing repressors” which prevent exon 7 of 6-7-8 from being spliced out like in the SMN2 splice pattern

28
Q

splicing

A

U1 snRNP binds to 5’ splice site

U2 binds near 3’ splice site

these come together, loop out, and cut out the extraneous introns.

29
Q

lariat

A

the resulting loop of introns

30
Q

lariat biology is being pursued for the treatment of..

A

ALS

31
Q

functions of RNAi

A

some genes downregulated by transcribing small RNA’s that are complementary to the RNA’s you want to destroy

ssRNA forms complex that targets RNA by way of complementarity. Small RNA base pairs with target RNA and brings along regulatory complex to destoy it

32
Q

2 ways that RNAi can inhibit

A

destroy given mRNA or inhibit translation without destroying it

33
Q

miRNAs and siRNAS form distinct..

A

complexes and downregulate mRNA by distinct mechanisms

34
Q

what do miRNA’s do?

A

they are mostly base paired, repress translation

35
Q

what do siRNA’s do?

A

perfectly base paired, cleaves target RNAs

36
Q

what is “IncRNa’s can act in cis or trans” mean?

A

long non coding rna’s can work in cis by regulating genes nearby, or in trans by regulating genes far away.

37
Q

eQTL

A

expresssion quantitative trait loci

you can use expression level of agene as a marker like any other marker
-compare expression level of mRNAS in normal vs diseased using RNA-sequenceing

may see that some expression patters are related to certain diseases

38
Q

eqtl’s are tissue

A

specific…wont get overexpression of liver cells in kidney

39
Q

eqtl’s are heritable. TF

A

heritable, you can track high expression of a gene through a pedigree like any marker

40
Q

splicing occurs via ___ acting sequences

A

cis

41
Q

relative amount of coding and non coding RNA?

A

non coding RNA outnumber, important regulatory functions

42
Q

small noncoding vs large noncoding strategy

A

lnc - large, bigger, more complex, and can do more. act as scaffolds to assemble protein complexes and take them to particular locations. can work cis or trans

small noncoding target RNA by complementarity

43
Q

2 ways you can inhibit RNA.

A

with siRNA’s - perfectly base paired, recruits desctuction complex

with miRNA’s - mostly base paired, recruits complex to block translation and condense

44
Q

cis vs trans interaction

A

cis - RNA made works right next door

trans - rna made on one crhomsome works on distant chromsome

45
Q

microarrays vs RNA-seq

A

rely on having to put specific gene probes that you already know are important. must already know the gene that is important.
-only measures the RNAs whose genes you have put on the array

Rna-seq - blind method where you look at everything. measures ALL rnas in the cell

46
Q

what do microarrays tell you

A

compare expression of normal tissue genes and diseased genes. must know what genes to use (a.priori knowledge)

47
Q

Rna seq

A

will become method of choice - way to sequency and quantify total RNA in the cell. entire genome, including non-coding

48
Q

advantage of SNP’s vs eQTLs?

A

eQTL’s are tissue specific, SNPS are in every cell.

eQTL’s may indicate a function in that particular tissue. may also help insignt into disease by discovering tissue specific eQTLs

49
Q

2 uses of IPS cells

A

induced pluripotent stem cells

  • disease modeling - mimic condition of the disease on cells to try drugs
  • treatment - take own cells, convert to IPS cells and then heathyl speicalized cells, and put back into body
50
Q

gene regulation relies on

A

expression of cell type and gene specific trasncription factors

AND non-coding RNa’s

51
Q

describe transcription factors

A

modular and bind to specific enhancers

52
Q

transcription factors help recruit

A

RNA pol II or enzymes that modify chromatin structure/chemistry

53
Q

cells can be reprogrammed by

A

transcription factors, as few as four, for therapeutic potential

54
Q

D. Gene activator proteins may function by either

A

recruiting the transcriptional machinery to the promoter or by changing chromatin structure around the promoter.

55
Q

How do HAT activate transcription?

A

HAT enzymes activate transcription by aceytylating nucleosomes, reducing their positive charge and thereby their hold on DNA wrapped around them, thereby exposing nucleotide sequences such as the TATA box for protein binding

56
Q

TBP does what?

A

it is a subunit of TFIID, reponsbible for TFIID binding to the TATA box

TBP = tata binding protein

57
Q

describe eQTL specificity

A

whole blood and lymphoid cells had strong eQTLs for autoimmune diseases (chrohns) consistent with these tissues being involved. In contast, blood did not show eQTL’s for bipolar disorder or type 2 diabetes.

58
Q

example of how eQTL’s could be ussed to expand our understandign of certain diseases

A

A high BP SNP is associated with an eQTL in arteries as expected, but the eQTL is also high in adipose tissue and skin - suggesting these might be important tissues to look at in hypertension studies

MSI Unit I (52 decks)

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