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Applied Genetics > Regulatory Regions > Flashcards

Regulatory Regions Flashcards

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1
Q

what is the TSS

A

transcription start site

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2
Q

what is cis acting

A

function that occurs on same chromosome

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3
Q

what is trans acting

A

function that occurs on opposite chromosome

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4
Q

what are enhancers

A

short region (50-1500bp) of DNA that can bind activator proteins to trigger transcription of a gene

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5
Q

what are TADs

A

Topological Association Domains a way to understand organisation of a genome

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6
Q

what are promoters

A

regulatory regions of DNA upstream of a gene, which provide a control point for regulated gene transcription

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7
Q

what is in the coding region

A
  • 3’ end has the Poly A

- 5’ end has the cap structure

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8
Q

structure of prokaryotes replicated DNA strand -polycistronic mRNA

A

promoter
5’ end non-coding region
coding region for multiple proteins - cistrons
terminator

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9
Q

structure of eukaryotes replicated DNA strand - mRNA

A 
promoter
transcription start
5'cap
5' non-coding
coding region for one protein (exons)
introns
3' non-coding
poly A tail
transcription end point
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10
Q

what is the consensus sequence

A

segment of DNA that is conserved where different proteins bind to it

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11
Q

what make up the promoter elements

A

core promoter and proximal promoter

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12
Q

what is the core promoter

A

minimal portion of the promoter required to properly initiate transcription. Located around position -34

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13
Q

what is the proximal promoter

A

proximal sequence upstream of the gene that contains primary regulatory elements. Located around position -250

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14
Q

what does the prokaryote promoter consist of

A

TTGACA -35 element
TATAAT -10 element prinbow box
TSS (transcription start site)

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15
Q

what do most eukaryotic core promoters consist of

A
  1. a TATA (TATAA) box, usually within 50 bp from Transcription State Site, that binds to the TATA protein to begin transcription
  2. a CAAT box (CCAATC), general transcription factors bind to it and it is frequently absent from ubiquitous genes. Located in the proximal promoter
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16
Q

what does RNA polymerase II bind to

A

transcription factors

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17
Q

what transcription factor binds to TATAbox

A

TF II D -complex of 15 proteins that binds to TATA box

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18
Q

what transcription factor binds to another transcription factor

A

TF II B binds immediately upstream of TFIID

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19
Q

when can RNA polymerase interact with DNA

A

when TFIID on TATA and TFIIB on TFIID

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20
Q

how many proteins is RNA polymerase II made of

A

12

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21
Q

where is the proximal promoter

A

outside region where RNA polymerase binds

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22
Q

how is the proximal promoter formed

A

> CAAT box, found in many animal and some plant genes
Sp1 box and GC box in animals and AGGA box in plants
Bind transcription factors so DNA loops around to bring these into contact with the RNA polymerase

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23
Q

what makes up the minimal promoter

A

Core promoter and proximal promoter

24
Q

what is the minimal promoter for

A

necessary for expression

25
Q

what makes expression levels low

A

without presence of extra control sequences located in distal promoter

26
Q

where is the distal promoter

A

very ill defined area which can range from beyond 3’ end of the gene, through coding region of the gene, through core promoter, through proximal promoter, right up to and even into next gene

27
Q

how long are enhancers and what do they do

A

Enhancers are short (50-1500 bp) regions of DNA that can bind to proteins to activate transcription or increase expression of gene

28
Q

characteristics of enhancers examples

A

generally cis-acting
can be upstream or downstream from the start site, even in introns
orientation independent
sometimes not located on same chromosome as gene they’re regulating

29
Q

why are enhancers important examples

A

evolution of species role
development, differentiation and growth of cells and tissues
development robustness: survival of fruit flies when environmental disturbances take place

30
Q

what are promoter silencers and what do they do

A

Silencers are antagonists of enhancers that, when bound to its proper transcription factors – repressors

31
Q

how do silencers and enhancers differ

A

Silencers and enhancers may be in close proximity to each other or may even be the same region only differentiated by the transcription factor region binds to

32
Q

how do silencers work

A

when repressor protein binds to silencer region of DNA, RNA polymerase is prevented from binding to promoter region

33
Q

characteristics of promoter silencers

A
  1. generally cis-acting
  2. located between -20 to -2000bp upstream from gene
  3. most commonly found upstream from start site; some maybe located in introns or exons of gene itself. Also present in 3’ UTR
  4. there are two types
34
Q

what are the two types of promoter silencers

A

classical silencer element

non-classical regulatory element

35
Q

what is classical silencer element

A

gene is actively repressed by silencer element by interfering with general transcription factor GTF

36
Q

what is the non-classical regulatory element

A

NRE passively repress the gene by inhibiting other elements upstream of the gene. Some are orientation dependent

37
Q

what are promoter insulators

A

genetic boundary elements that block the interaction between enhancers and promoters

38
Q

what do promoter insulators do

A
  • determine set of genes and enhancer can influence
  • act by forming loops
  • prevent spread of heterochromatin from silenced gene to an actively transcribed gene
39
Q

when are promoter insulators made

A

formed when two adjacent genes in chromosome have different patterns of transcription

40
Q

where are the promoter insulators

A
  • occurs via 3D structure of DNA

- present at boundary of topological association domains (TADs) which divide chromosome in ‘chromosome neighbourhoods’

41
Q

what can lead to transposon duplication

A

Transposition often results in duplication of transposon

42
Q

how many types of transposons are there

A

2

43
Q

what are the types of transposons

A 
class I or retrotransposons
class II (DNA transposons)
44
Q

what is the function of class I or retrotransposons

A

copy and paste; copied in 2 stages DNA to RNA; RNA is reversed transcribed to RNA (i.e. retroviruses, as HIV)

  • transposons with long terminal repeats
  • line I (transcribed by RNA pol II)
  • SINEs (transcribed by RNA pol III)
45
Q

what is the function of class II (DNA transposons)

A

cut and paste; does not involve RNA intermediate. Transpositions catalysed by several transposase enzymes

46
Q

what are transposase enzymes

what can they cause

A

mutagens that can damage genome and produce diseases like haemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy

47
Q

what does epigenetics study

A

variations that are caused by external or environmental factors that turn genes on or off affecting how the cells read this genetic information
changes that can be inherited or not
changes that epigenetics study in relation to gene expression or cellular phenotype are not based in changes in sequences of DNA

48
Q

what are covalent modifications

A

DNA methylation and hydroxymethylation; protein acetylation, methylation, phosphorylation, ubiquitination and sumoylation

49
Q

what are RNA transcripts

A

product that (directly or indirectly) maintains the activity of that gene

50
Q

what are microRNAs

A

Non-coding RNAs of 17-25 nucleotides long

51
Q

what is mRNA methylation

A

mRNA plays a critical role in human energy homeostasis, sRNAs

52
Q

what are sRNAs

A

(50-250 nucleotides) virulence genes in pathogens

53
Q

what are prions

A

infectious forms of proteins

54
Q

what is structural inheritance

A

seems existing structures act as templates for new structures

55
Q

what is nucleosome positioning

A

isn’t random

determine DNA accessibility to regulatory proteins determines differences in gene expression and cell differentiation

Applied Genetics (20 decks)

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