Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Regulation of Gene Expression > Tonon: Lecture V > Flashcards

Tonon: Lecture V Flashcards

Functional Elements of the Genome

1
Q

What was the main focus of the ENCODE Project Consortium (ENCyclopedia Of DNA Elements)?

A

to develop and apply high-throughput approaches to detect all sequence elements that have a biological function

focused on 30 megabases (∽1%)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What tools did ENCODE use to have a full perspective of the “junk” DNA?

A

DNAse digestion
microarray hybridization
DNA replication sites
Chip-chip
cis-regulatory elements (promoters, transcription factors binding sites)
long-range regulatory elements (enhancer, repressors/silencers, insulators)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Name the steps scientists took to identify “junk” DNA and what they found:

A
  1. chose 44 genomic regions
  2. chose 30 megabases (15 known, 15 unknown)

they found “functional elements”, which is a genome segment that actually encoded for a defined product

DNA is no longer thought to be composed of mainly “junk”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How are the important elements of a genome identified?

A

by comparing the homology of organisms

signatures are important, whether alone or in combination, in order to identify sequences with important functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Why did it take scientists so long to detect “junk” DNA? List the 4 reasons:

A
  1. genes are not as conserved
  2. functional elements were made of small or fragmented sequences that can be interrupted with other unspecific sequences
  3. can lie in repetitive regions of the genome, making their recognition difficult
  4. evolve very rapidly and can be nearly neutral to evolutionary processes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What were the experimental targets of ENCODE in relation to the 2012 experiment?

A

assign functions to as many DNA regions as possible

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

DNA methylation

A

regions layered with chemical methyl groups, which regulate gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

open chromatin

A

areas in which the DNA and proteins that make up chromatin are accessible to regulatory proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

RNA binding

A

positions where regulatory proteins attach to RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

RNA sequences

A

regions that transcribed into RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

CHIP-SEQ experiment

A

technique that reveals where proteins bind to DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Modified Histone

A

histone proteins, which package DNA into chromosomes, modified by chemical marks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Transcription Factors

A

proteins that bind to DNA and regulate transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What was a limitation to the ENCODE approach?

A

some cells could be open and others closed, so the cells would be replicating at different points resulting in the analyzation of the average

also the preparation across different countries was not uniform even if the protocol was in place due to the slight variations that could occur in materials

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is an observation based on the image in regards to H3K27ac?

A

H3K27ac is a marker used for enhancer expression

what can be observed is that the enhancers undergo silencing, so they are not a stabilizing feature of the genome as they can undergo epigenetic changes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are 2 limitations to this study?

A
  1. transcription factors were not taken into consideration
  2. they overlooked the complexity of the organism and simply focused on definite cells and definite cell lines
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What did ENCODE find?

A

80.4% of the human genome participates in at least 1 biochemical RNA and/or chromatin-associated event in at least one cell type

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Explain the Manhattan plot and why it is used:

A

it represents the position of the gene in the genome in relation to its p-value

the red line is the threshold and everything above the red line is significant

used to see the association between a certiain region of the genome with a certain disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Explain the Manhattan plot and why it is used:

A

it represents the position of the gene in the genome in relation to its p-value

the red line is the threshold and everything above the red line is significant

used to see the association between a certain region of the genome with a certain disease

used to show Genome Wide Association Studies (GWAS)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is GWAS?

A

https://www.youtube.com/watch?v=b7VTJv77f24

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What should be used as an enhancer for a manhattan plot studying GWAS?

A

microarray to visualize intergenic regions (Regions outside of the genes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What does GWAS identify?

A

association between disease trait and surrogate marker (tag SNP)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is interesting about the findings related to GWAS?

A

only 3% of the genomic variants are located within genes

most are found in intronic or intergenic genes

24
Q

How do we analyze Crohn’s patients?

A

find associations with SNPs that are overlapping GATA2-binding site

25
Q

What was found out about alternative splicing with ENCODE?

A

most genes undergo alternative splicing, during transcription with a local effect when the RNA is still bound to DNA

26
Q

What is known about Poly(A)?

A

there are many poly(A) for certain genes

27
Q

How many human genes have a Poly(A)?

A

at least 50%

28
Q

In the example with CD47, what happens if the poly(A) tail is on a short 3’UTR?

A

CD47 protein doesn’t translocate to the membrane because the tail has nothing to bind to

RNA is driven to the axon

29
Q

In the example with CD47, what happens if the poly(A) tail is on a long 3’UTR?

A

binds the RNA to a few components and brings the whole set to the surface

RNA remains in the soma

30
Q

What do 3’UTRs act as?

A

a scaffold to regulate membrane protein localization

31
Q

Highlight 3’UTR to cancer:

A

short 3’UTR → increased proliferation → alternative cleavage and polyadenylation → oncogenes activated in cancer cells

32
Q

Why is the shorter 3’UTR associated with proliferation?

A

ncRNAs will have the ability to bind to it and prevent translation or induce elimination

33
Q

What are 2 important factors in the discovery of transcription factors with ENCODE?

A

transcription factors work together

found in both promoter regions and in intergenic regions, where apparently there are no genes (probably bound to regulatory regions, exerting some activities)

34
Q

Describe the hierarchy of chromatin modifications in epigenetics:

A

DNA sequence & DNA methylation → nucleosomes → histone modification (compactin of chromatin) → nuclear organization and transcription factors

35
Q

What is the nomenclature of histones?

A

first letter: histone (with number)
second letter: residue
number: number of histone
type of modification
number of residues

36
Q

What are some exceptions for the nomenclature of histones?

A

acetylation does not have a number for the number of residues because there can only be 1

37
Q

What is H3K27ac a typical modification of?

A

enhancers

38
Q

What are the 3 types of chromatin modifiers and what do they do?

A

writers: put residue on lysine 4
erasers:
readers

39
Q

What is the most important histone?

A

H3

40
Q

What are the most important residues?

A

K4, K9, K27, and K36

41
Q

Are writers and erasers specific in their activity?

A

no, they add many different residues to different amino acids or remove many different histone modifications

42
Q

What composes histone modifying genes?

A

writers
erasers
readers

43
Q

What is the most frequent histone modification of promoters?

A

it is the 3 methylation of lysine residue number 4 in histone 3 (H3K4me3)

44
Q

Which lysine residue number is almost always associated with active transcription of genes?

A

K4

45
Q

What is on the promoters of active genes?

A

H3K4me3 (trimethylation)

46
Q

What is typical of active enhancers?

A

H3K4me1 (monomethylation)

47
Q

What is a classical heterochromatin marker that represses chromatin?

A

H3K9me3

48
Q

What is associated with repressed genes?

A

H3K27me3

49
Q

Review the chart of active and repressed transcription in a normal cell:

A
50
Q

active gene promoter →

A

H3K4me3

51
Q

gene promoter not expressed →

A

H3K27me3

52
Q

What is the function of chromatin in regards to histones?

A

it is an accessibility barrier, so if there are no histones near the promoter, there is no H3K4me3, so it’s marker for active promoters are “on their side”

53
Q

What is a technique that is used to find all chromatin that is opened?

A

ATAC-seq, which is a DNA-seq

54
Q

Why is ATAC-seq important?

A

if chromatin is open, it almost always implies there is active transcription in that region

55
Q

What happens when you look at CHIP-seq for H3K4me3?

A

since there are no histones, signals are not present

56
Q

What does it mean if important genes have bivalent promoters?

A

they have both H3K27me3 and H3K4me3 on the same region in order to go both directions

(about 20% in ES cells)

Regulation of Gene Expression (28 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions