Lesson 5

Question 1

what was the project created to investigate the “junk” DNA?

Answer 1

the Human Encyclopedia → ENCODE

Question 2

what does ENCODE stand for?

Answer 2

encyclopedia of DNA elements

Question 3

what was project Consortium of ENCODE focused on?

Answer 3

a specific 30 mega base sequence organized as an international consortium of computational and laboratory-based scientist working to develop high throughput approaches for detecting all sequence elements that have biological function

Question 4

what are functional elements?

Answer 4

a discrete genome segment that encodes a defined product or displays a reproducible biochemical signature

Question 5

how does junk DNA work differently than other genes?

Answer 5

genes tend to be highly conserved across species while these regulatory elements are not as conserved

Question 6

what are four major reasons scientists had a hard time identifying junk DNA?

Answer 6

1. junk DNA works differently than other genes
2. functional elements are made of small or fragmented sequences that can be interrupted with other unspecific sequencing
3. can lie in repetitive regions of the genome (hard to recognize)
4. evolve very rapidly or else they can be nearly neutral to evolutionary processes (they become many different things during evolution without having any constrictions)

Question 7

describe DNA methylated regions:

Answer 7

regiones layered with chemical methyl groups which regulate gene expression

Question 8

Describe open chromatin:

Answer 8

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

Question 9

What are RNA binding sites?

Answer 9

positions where regulatory proteins attach to RNA

Question 10

why were RNA sequences an experimental target?

Answer 10

regions that transcribed into RNA

Question 11

why were CHIP-SEQ experiments performed?

Answer 11

revealed where proteins were bound to DNA

Question 12

describe modified histones:

Answer 12

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

Question 13

What are transcription factors?

Answer 13

proteins that bind to DNA and regulate transcription

Question 14

what does it mean if there are “local micro-environments in culture”?

Answer 14

there could be a lot of variation across different places that might cause bias

Question 15

describe an enhancer:

Answer 15

not stable features of the genome → undergo epigenetic changes

Question 16

what are two main challenges of ENCODE?

Answer 16

massive amount of work (have to look for 18,000 transcription factors in each cell type) and each cell type may exhibit a diverse array of responses to exogenous stimuli (environmental conditions or chemical agents)

Question 17

in a Manhattan plot, what does the p-value indicate?

Answer 17

the association between a certain locus in the genome with a certain disease

Question 18

in a Manhattan plot, describe the meaning of the data surrounding the line:

Answer 18

data above the line is significant, data below is not

Question 19

what result is a manhattan plot used to show?

Answer 19

GWAS result - genome wide association studies

Question 20

what do most GWAS identify?

Answer 20

an association between the disease trait and a surrogate marker (tag SNP) rather than a variant - only 3% of variants in the genome of a patient affected with a certain disease are located within genes

Question 21

what are single nucleotide polymorphisms (SNPs)?

Answer 21

enriched with non-coding functional elements with a majority residing in or near ENCODE-defined regions that are outside of protein coding genes

Question 22

when CHIP-SEQ analysis was performed, what was discovered?

Answer 22

found that in various cell lines there were very strong binding sites for GATA2 and in their case for open chromatin (DNase 1) - association with some SNPs that GATA2 was binding

Question 23

what was one major finding of ENCODE related to every gene in the genome?

Answer 23

almost every gene gets alternative splicing

Question 24

when does splicing occur?

Answer 24

during transcription → when the RNA is still bound to DNA, so its a local effect and splicing occurs immediately

Question 25

describe genes with relation to isoforms:

Answer 25

genes tend to express many isoforms simultaneously reaching a plateau at approximately 10-12 expressed isoforms per gene

Question 26

describe the expression when there are many isoforms present:

Answer 26

one is usually most predominant in a given condition and captures a large fraction of total gene expression

Question 27

what is one reason why an alternative 3’ UTR is important?

Answer 27

to define how proteins are localized in the cell

Question 28

what two types of UTR does Cd47 have?

Answer 28

long and short

Question 29

what happens when CD47 has a short 3’ UTR?

Answer 29

protein remains inside the cell and doesn’t translocate to the membrane because the tail doesn’t have anything to bind to

Question 30

what happens when CD47 has a long 3’ UTR?

Answer 30

it binds to the RNA itself and few components, and then two other proteins bring the whole set to the surface

Question 31

in neurons, where do long and short 3’UTRs drive the RNA?

Answer 31

a long poly A drives RNA to remain in the soma and a short poly A drives RNA to the axon

Question 32

what does the 3’ UTR act as?

Answer 32

a scaffold to regulate membrane protein localization

Question 33

besides localization, what else is a shorter 3’ UTR associate with in cancer biology?

Answer 33

increased proliferation

Question 34

how does a shortening of the 3’ UTR effect cancer cells?

Answer 34

activates oncogenes in cancer cells by alternative cleavage and polyadenation

Question 35

why is a shorter 3’ UTR associated with proliferation?

Answer 35

oncogenes choose a shorter poly A so that less microRNA can bind to it and prevent translation / induce eliminaiton

Question 36

how can proteins and transcription factors be compared?

Answer 36

they both always work together in complexes - most transcription factors have a nonrandom association to other transcription factors

Question 37

where are transcription factors found?

Answer 37

on the promotor of actively transcribed genes and intergenic regions (more often)

Question 38

what might transcription factors be bound to in intergenic regions?

Answer 38

maybe bound to regulatory regions exerting some sort of activity

Question 39

what three categories can chromatin modifiers be divided into?

Answer 39

writers, erasers, and readers

Question 40

describe the specificity of chromatin modifiers:

Answer 40

one writer can add many different residues and erasers can remove many different modifications as well → not so specific

Question 41

what is another name for the three chromatin modifiers?

Answer 41

histone modifying genes

Question 42

do histone modifying genes just act on genes inside of the nucleus?

Answer 42

no → some of the sequences of histone 3 are shared by other proteins that have nothing to do with histones

Question 43

what is the most frequent histone modification of promotors (if a promotor gene is active, which methylation are we looking for)?

Answer 43

its the (3) (me)thylation of (lysine) residue number (4) in (h)istone (3) (H3K4me3)

Question 44

what is K4 almost always associated with?

Answer 44

active transcription of genes

Question 45

where does H3K4me3 occur?

Answer 45

trimethylation: on promotors of active genes

Question 46

what is the H3K9me3 methylation?

Answer 46

classical heterochromatin marker → represses chromatin

Question 47

what is the H3K27me3 methylation?

Answer 47

associated with repressed genes

Question 48

what is ATAC-seq used for?

Answer 48

a technique used to find all the chromatin that is open

Question 49

what does it mean if the chromatin is open?

Answer 49

if chromatin is open it implies a region where there is active transcription

Question 50

when do transcription factors bind?

Answer 50

only when the chromatin is open