Transcriptional regulation of genes

Question 1

What are ways to regulate gene expression?

Answer 1

At the DNA level-transcription
RNA-translation
protein-post modification

Question 2

Explain how the lac operon works

Answer 2

It has several genes that regulate lactose metabolism
Lac z- b-gal- cleaves the lactose into glactose and glucose
Lac y- transports the lactose from PM to cell
Lac O- repressor binds
lac L- codes for repressor
Lac l is constitutively expressed(has it’s own promoter) and binds to the operon, when there is lactose it will bind to the repressor and it will be released, so the lactose digesting enzymes can be expressed

Question 3

How is gene expression regulated in prokaryotes?

Answer 3

Operator- A DNA sequence where the repressor binds
Promoter- Upstream elements, sigma factor, RNA pol
positive control elements and repressor- Bind to DNA and alter transcription levels

Question 4

How is the human genome transcription regulated?

Answer 4

Control of initiation and elongation

Histone modification- chromatin modifying proteins

Question 5

How is the eukaryotic gene regulated after transcription?

Answer 5

RNA editing

Alternative splicing

Question 6

Describe the mechanism of functions of transcriptional regulators

Answer 6

Histone modification-Methylation prevents transcription
Transcription pause factors- DSIP and NELF forces teh DNA pol to pause transcription
Insulators prevent the interaction of enhancers with promoters by recruiting structural proteins
noncoding RNA such miRNA pevent RNA from being translated
and lnCRNA involved in chromatin remodelling and regulation of translation
Translational repressor protein-RNAse

Question 7

Discuss the association of transcriptional regulators and cancer. Give example of it.

Answer 7

Mutation in transcription factors will increase oncogenes if it’s overexpressed
Mutations in the regulatory proteins involved in transcription will lead to genome instability and will in turn deregulate other important genes that will lead to cancer progression.
Mutations in chromatin regulators- such as polycomb
Mice overexpressing c-FOS can lead to osteosarcoma

Question 8

How do transcription factors dimerize?

Answer 8

Via leucine rich zipper domains

Question 9

What’s the difference between GTF and specifc transcription factors?

Answer 9

Required for all transcription and separates the helix

Less specifc

Question 10

Which RNA polymerase transcribes genes? What does RNA pol 1 and 3 do?

Answer 10

RNA pol 2
1- rRNA
3- tRNA

Question 11

What is the promoter made up of?

Answer 11

Basal core element

Distal enhancer element

Question 12

What is the promoter made up of?

Answer 12

Basal core element
Distal enhancer element
Upstream element

Question 13

What is the basal element made up of?

Answer 13

TATA box and initiator element

Question 14

What do enhancers bind to and what do insulators bind to? What is the function of insulators

Answer 14

They bind to the promoter far and close.

Insulators bind to CTCF and TF111C. They prevent teh interaction between enhancers and promoters by recruiting cohesins

Question 15

How to identify enhancers?

Answer 15

By profiling the location of the transcriptional regulators genome wide, test for activity using enhancer reporter vectors

Question 16

Which base is methylated in humans and bacteria?

Answer 16

C and A

Question 17

When in development is DNA methylated?And when is it removed?

Answer 17

Removed during zygote formation and reestablish over time

Question 18

What is a biological purpose of methylation?

Answer 18

Locks cells to their types after differentiation

They prevent the expression of endogenous reteroviral genes

Question 19

What is a biological purpose of methylation?

Answer 19

Locks cells to their types after differentiation
They prevent the expression of endogenous reteroviral genes
Shapes the chromatin

Question 20

What is the gene state associated with methylation of CG promoters of a gene and what’s the ways they can stop transcription?

Answer 20

Methylated CG- repression
Unmethylated- active
It repressed by either directly inhibiting the trancriptional machinery or recruiting co-repressors

Question 21

Give example of transcription factor. What are the two types of transcription factors?

Answer 21

HSF1. Activators and repressors

Question 22

How are transcriptional factors regulated?Give example

Answer 22

They are phosphorylated, ubiquitinated,acetylated. C-JUN phosphorylated at 3 sites prevents it from binding to DNA, but when phosphorylated at 5 can bind and transcribe

Question 23

What is the most frequent amplified oncogene? What does it induce and how?

Answer 23

c-myc, prolferation and growth by recruiting TEFB

Question 24

What are c-jun and c-fos activated by? And what do they induce?

Answer 24

Usually MAPK signallin.
c-jun proliferation and apoptosis
c-fos angiogenesis and invasion

Question 25

Outline how NFKB works and it’s association with cancer and how it comes to be.

Answer 25

It is bound IKB in cytoplasm, when IKB is ubiquitinated and phosphorylated it’s released and translocates to nuclease and transcribes genes. It’s constitutively expressed in many cancer and found in malignant cells because of defects in regulation

Question 26

Explain how PML overexpression can affect a chromatin modification. What is the role of PML in cancer?

Answer 26

PML overexpression can reverse repression of BCL via HDAT. Tumour suppressor

Question 27

Give an example of lncRNA that is mutated in cancer and it’s function.

Answer 27

ANRIL wich recruit PRC1 and 2 and repression of INK, mutations in them will can lead to silencing of tumour suppressor genes