Control of gene expression Flashcards
TRANSCRIPTION REGULATORS
CO-ACTIVATORS
CO-REPRESSORS
THE MEDIATOR COMPLEX
The mediator complex serves a crucial function in gene regulation, forming a link between
gene-specific transcription factors and RNA polymerase II.
The gene regulatory proteins interact with
the mediator complex and may recruit
additional regulatory proteins.
CHROMATIN AND GENE REGULATION
TRANSCRIPTION CIRCUITS AND GENOMIC SWITCHES
POSITIVE CONTROL
A proliferating cell must maintain its identity through subsequent cell division, it has some form of cell
memory, and its pattern of gene expression must be transferred to its daughter cells.
* Positive feedback loops may be used to establish and maintain a heritable pattern of gene expression.
NEGATIVE CONTROL
Positive and negative regulatory feedback loops are common in all cells and can be combined in different
gene regulatory circuits.
* A negative feedback loop is often used to keep the concentration of a protein within a defined range.
Low levels (lack of repressor) → higher expression
High levels (active repressor) → lower expression
COMBINATIONAL CONTROLS
EPIGENETIC MECHANISM
CELL MEMORY
POST TRANSCRIPTIONAL REGULATION
RNA INTERFERENCE
RNAi is induced by a cell detecting double stranded RNA (dsRNA).
* The dsRNA are processed into small 20-30 bp single stranded RNAs, which binds to specific proteins
(Argonaute and PIWI ) and act as guide RNAs to identify other complementary RNAs in the cell.
The three major classes:
microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi interacting RNAs (piRNAs)
CRISPR SYSTEM
CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats
* CRISPR-type clustered repeats were first reported in E. coli (1987), but their functions are only recently
uncovered.
* During infection short fragments of viral DNA are integrated into the bacterial genome.
A later infection with the same / similar bacteriophage will be detected by the CRISPR/Cas9
“surveillance system” and phage DNA degraded.
* A protein complex including the TracrRNA helps processing pre-CRISPR RNA. RNA from the spacers
(of viral origin) are bound to a nuclease (Cas9), which uses the crRNA to seek and destroy viral DNA.
ENHANCERS
INSULATORS
Insulators restrict the range of activators / repressors, so they do not affect nearby genes.
* Insulators function by forming loops of chromatin, bringing genes and control regions in close proximity.
DNA METYLATION
Methylated DNA is recognized and bound by
specific proteins. This may block other gene
regulatory proteins access to DNA.
* A repressive form of chromatin may be established
through histone modifications, by DNA methylases
and proteins binding methylated DNA.
* A histone modifying enzyme is recruited by a gene
regulatory protein (a repressor).
* The modified histone is “read” by a code reader
protein and histone modification is transferred to
neighboring histone by the histone reader-writer
proteins.
* A DNA methylase is recruited and cytosines are
methylated.
* DNA methyl-binding proteins bind methylated
cytosines and cause gene repression.
HISTONE MODIFICATIONS
Histone modifications provide favorable interactions for a number of proteins, (chromatin
remodeling complexes, reader-writer complexes).
* Modifications can be rapidly reversed (genes that needs to be quickly turned on or off), or
modifications can persist and serve as a short and long-term cellular memory.
* Histone modifications can even be transferred to daughter cells after cell division.
LONG NON-CODING RNA
RNAs longer than 200 bp that apparently do not code for any protein.
* Many are transcribed by RNA pol II and have 5’ cap and poly A tails.
* At least 16000 lncRNA have been discovered in humans (GENCODE).
* lncRNAs may function as scaffold RNAs providing interaction between proteins and coordinate their
function or may have guide functions.
XIST
Long noncoding RNAs (lncRNAs) such as Xist are involved in X-chromosome inactivation.
X-chromosome inactivation spreads from the X-inactivation center (XIC) where a long noncoding RNA
(Xist) is expressed.
Only one of the X-chromosomes have Xist
expression.
* The Xist lncRNA diffuses along the Xchromosome and recruit proteins that
induced chromatin modifications and DNA
methylation, resulting in gene inactivation.
RNA DEGRADATION
Decapping and degradation of mRNA takes place at specific locations in the cytosol, so called
Processing bodies (P-bodies).
* If they are not degraded they can be transported over to so called stress granules and be
”restored” for later use.
There is a competition between
mRNA translation and mRNA
degradation.
* If a mRNA is translated with high
efficiency, it is less prone to
degradation.
ALTERNATIVE mRNA SPLICING
Alternative splicing is common in human genes (90 % of the genes).
* Alternative splicing increases the protein complexity.
* Some genes containing many exons can have a large number of splice
variants.
* In many cases alternative RNA splicing is regulated and various splice
forms are produced in different cell types.
In back splicing a single exon is removed as a circular RNA molecule.
The biological functions of circular RNAs (circRNAs) are still not fully
understood but they may regulate function of microRNAs (miRNAs).
Negative control of RNA splicing:
* A repressor prevent the splicing machinery access to the splice site and obstruct mRNA splicing. May
instead result in the use of a “cryptic” splice site.
Positive control of RNA splicing:
* A regulatory protein (splicing enhancer) is required for mRNA splicing. The enhancer binding site can be
located far from the splice site.
RNA EDITING
RNA editing alter the nucleotide sequence of RNA transcripts and can change their coding sequence,
produce stop codons or affect mRNA splicing.
* In animals the most common editing is deamination of adenine to produce inosine (A-to-I editing) and
deamination of cytosine to produce uracil (C-to-U editing).
* A-to-I editing is most common in humans and occur in approx. 1000 genes
The ADAR enzymes (adenosine
deaminase acting on RNA) carry out
the A-to-I editing.
A double stranded RNA structure
produced by the mRNA is recognized
by ADAR enzyme and defines the site
for RNA editing.
Editing take place in the nucleus before
the pre-mRNA are fully processed.
siRNA
The presence of dsRNA in the cell (ex. from a virus)
triggers RNAi by recruiting a protein complex
containing Dicer.
* This protein complex cleaves the dsRNA into ~23
bp fragments called small interfering RNAs (siRNA).
* Binding of the siRNA to the RISC complex
results in degradation of one of the RNA
strands and enable the 5’ end of the RNA to
bind complementary mRNA sequences →
degradation of mRNA.
An alternatively RNA interference response is directed by the RNAinduced transcriptional silencing (RITS) complex.
