eukaryotic TF and methods of study (genomics)

Question 1

describe the structure of transcription factors

Answer 1

bipartate modular structure so has a DNA binding domain at N terminus and effector domain at C terminus

Question 2

at what stage of transcription does most regualtion occur?
A binding
B initiation
C elongation
D termination

Answer 2

binding and initiation!

Question 3

despite having general TF, RNAP unable to recognise promoter - what else does it need?

Answer 3

needs more stimuli to bind to DNA such as short-sequence motifs or CREs

Question 4

how do the different domains of TF function?

Answer 4

Effector domain has enzymatic activity and able to regulate proteins like methylases

ED has an intrinsically disordered region so only forms secondary structures when responding to signal and interacting with proteins

Question 5

what is function of TF?

Answer 5

able to tranduct signals using the different domains

To promote or repress transcription

Question 6

what sort of CREs do lower euk (yeast) have?
> CREs

Answer 6

they have upstream promoter element (proximal, quite close to promoter)

Question 7

what sort of CREs do higher euk have?

Answer 7

as well as upstream promoter elements, they have
> distal
> intragenic
> superenhancers

Question 8

what are CREs?
> strucutre

Answer 8

short motifs (6-8bp) which are binding sites for sequence specific TFs

Question 9

how to TF influence transcription?

Answer 9

they are able to sense signals from in/out of cell and able to activate or repress transcription

> combo of many TF signals influences if gene is on/off

Question 10

what is the stimulus to activate mammalian MT genes?

Answer 10

they respond to cell stress (cortisol) and heavy metal ions inside cell

Question 11

what kinds of TF control MT genes?

Answer 11

3 sequence specific TF which are constituitively bound
2 other Znc-fn TF that bind to DNA when cell is stressed

Question 12

how do the sequence specific TF act when the MT gene is stressed?

Answer 12

cortisol binds to GR which translocates from the cytosol and into nucleus to bind to its motif

Mtf1 will bind to heavy metal ion causing conformational change and will translocate to nucleus

Question 13

how does the regulation of MT gene and globin genes differ?

Answer 13

MT is simple gene regulation, responding to cell stress

globin responds to developmental age, tissue type, altitude so requires enhancers

Question 14

what are the 3 main types of genomics methods?

Answer 14

basic - predictive
functional - like RNAseq
comparitive - similarity

Question 15

what does comparitive genomics tell us?

Answer 15

if there are conserved sequences/regions across different species, very likely it has important function!
> such as exon highly conserved

Question 16

what are the 3 key gene mapping technologies?

Answer 16

ChiP-seq
DNase-seq
ATAC-seq

Question 17

what does ChIP-seq map?

Answer 17

uses antibodies specific to proteins to create a map of genome where that protein is bound

Question 18

what does DNase-seq map?

Answer 18

maps genome accessibility as a protein/something is bound to an area where the DNase is unable to cut

Question 19

what does ATAC-seq map?

Answer 19

maps areas of open chromatin as the transposase is very sensitive to chromatin strucutre and unable to cut inaccesilbe chromatin

Question 20

how do DNase and ATAC seq differ?

Answer 20

uses different enzyme: DNase or transposase

atac uses adaptors too