Lecture 9 Control of gene expression Flashcards
How is the genome in your neuron different then the genome in your hepatocyte (liver cell)?
It is not. The genome (human genome) is the same in all cells.
What is different in different cells?
The expression of genes is different, thus the identity and the amounts of active molecules (protein, RNA, metabolites) is very different.
A genome contains …
all the information needed to make a multicellular organism
housekeeping genes
All cells have a set of principles and processes that are general (common to all cells), such as processes that maintain the structural features of the cell, general energy utilization, DNA metabolism etc. Genes that code for those are called housekeeping gene
At any time, any human cell expresses …
30-60% of the genes (out of 25 000).
actin filaments vs enzyme in liver cell
actin filaments is needed in all cells, therefore the transcription level is the same for all cells (equally expressed)
the enzyme is only needed in the liver cell, therefore the transcription level is much higher there (but the gene is still present in all the other cells)
regular spots for gene expression in Eukarya
transcription control RNA processing control RNA transport and localization control mRNA degradation control translation control protein activation control
transcription control
Proteins that regulate gene transcription “compete” with histones for DNA binding
eg helix-turn-helix proteins leucine zipper proteins helix-loop-helix proteins zinc finger proteins
gel-mobility shift assay
Answers the question: does THIS protein bind THIS DNA?
Retardation in gel, DNA + protein moves slower than just DNA
Chromatin Immunoprecipitation
Answers the question: which DNA sequence is recognized by a specific, known transcription regulator, in vivo.
crosslinks, antibodies
Regulation of initiation of transcription,
Example 1: the Trp operon switch in E. coli
- tryptophan low: repressor inactive -> operon on
and RNA polymerase can bind - tryptophan high: repressor activated by tryptophan
-> operon off
and RNA polymerase can not bind
Activators
bind typically upstream of promoters and help with RNA polymerase binding or activity
Regulation of initiation of transcription,
Example 2: Dual control of the Lac operon in E. coli
glucose vs lactose
repressor and activator
General concepts of gene expression in bacteria
repressors and activators, either addition or removal of ligand
Induction of gene expression from a distant cis-regulatory sequence
rare in bacteria, common in Eukarya
more complex in Eukarya
distant cis-regulatory sequence with regulator activates transcription by contacting RNA polymerase (involves folding)
Regulation of termination of transcription,
Riboswitch
low guanine:
genes for purine synthesis on
high guanine:
the riboswitch reform (by the present of guanine) and forms a terminator
-> genes for purine synthesis off
Regulation of translation (but still at mRNA
level)
eg structures only stable in low temp
gene regulation: Eukarya vs Bacteria
Euakrya: - Many inputs (100s) - RNA Pol II needs 5 general TFs (27 proteins) - Regulation of individual genes - Mediator (24 subunits) at the interface of RNA Pol and regulatory proteins - Regulation via chromatin structure/modifications
Bacteria:
- Few inputs
- RNA Pol needs 1 TF (σ)
- Operons as transcription units
- No mediator
- No regulation via chromatin
Dosage compensation
X-chromosomes much larger than Y-chromosomes, therefore one of the X-chromosomes gets condensed (inactivated)
How to shut down a chromosome
XI C, X-inactivation center (locus), codes for an RNA called X- inactivation specific transcript (Xist)
Xist spreads along the base of chromosome loops and silences genes
