Gene Regulation in Eukaryotes
Other roles of histone variants
-histone cenH3, the variant of histone that is found at the centromeres of each chromosome -Histone macroH2A is found in inactivated X chromosomes (forms barr bodies --spH2B is found at telomeres in sperm cells -certain histone variants also play a role in DNA repair
Common contributing factors to combinatorial control
1) activator proteins 2) repressor proteins 3) binding of small effector molecules, protein-protein interactions and covalent modifications 4)alter the composition or arrangement of nucleosomes 5) DNA methylation
Three ways that regulatory transcription factors are regulated
1) binding of a small effector molecule 2) protein-protein interactions 3)covalent modifications
three affects of chromatin remodelers
1) change in nucleosome position/spacing 2) Histone eviction 3) Replacement with variant histones
What does Histone acetyltransferase and Histone deacetylase do?
A-loosens the DNA from the histones D-retightens the DNA around the histones
Control/Regulatory Elements
DNA sequences located near the core promoter that regulatory transcription factors recognize and bind to, affecting transcription (similar to operator sites found in bacterial promoters)
Key Role of Histone Variants
Histone genes that have accumulated mutations that change the amino acid sequence of the histone proteins. The create functionally specialized regions of chromatin. The key role is to regulate the structure of chromatin, influencing gene transcription.
What usually moves in front and behind RNA polymerase II as it is transcribing?
Histone-modifying enzymes usually move in front for removal and replacement of histones during elongation. Histone deacetylase removes the acetyl groups, which rebinds histones to the DNA
What is the function of TFIID in transcription pre initiation complex?
It helps bind to the TATA box. sets everything up and affects all the other transcription factors
Phosphorylation mechanism
Phosphorylation has different affects. The Phosphorylation of eIF2 inhibits translation, where the phosphorylation of eIF4 increases translation.
Repressor
Regulatory transcription factor, binds to elements called silencers
Chromatin Remodeling Steps
The gene has a NFR region, activators bind to enhancer (which can be near the NFR or far from it), Activator recruits chromatin remodeling complexes, nucleosomes may move and histones may be evicted, some histones are subject to covalent modification, next the pre initiation complex forms by transcription factors and RNA polymerase II binding to the core promoter, during elongation histones are covalently modified or partially displaced in front of the open complex, behind the open complex histones are deacetylated and become tightly bound to the DNA again
How can repressors and activators affect the function of mediators?
The mediator and activator bind by creating a loop within the intervening DNA , which allows the RNA polymerase to proceed to elongation. Whereas if a repressor binds to the mediator, than transcription will not be able to go onto elongation because it is in a closed complex right now.
Effect of splicing repressor
The repressor prevents the recognition of a splice junction, therefore some exons will be skipped and not included in the mRNA
What is the significance of a gene having a well-positioned nucleosome followed by an NRF at the end of it?
This arrangement at the ends is probably important for transcriptional termination
AU rich element
a destabilizing element found in the UTR, it is recognized by cellular proteins that attach to the ARE, influencing whether or not the mRNA is rapidly degraded.
Motif
a domain that has a similar structure in many different proteins
helix-loop-helix motif
a short alpha helix and a longer alpha helix are connected by a loop. The longer alpha helix binds to the DNA. (this is not a dimer on its own, if there was another helix-loop-helix motif connected as well then it would be a homodimer)
How can an activator enhance the ability of TRIID?
activators could help recruit TFIID to the TATA box, or the activator could exert its effects by interacting with coactivators
Alternative Splicing in Gene Regulation
alternative splicing produces two or more polypeptides with differences in their functions, and amino acids within a polypeptide determine the structure and function of a protein
constitutive exons
always found in mature mRNA from all cell types
Why are alpha helix structures common in transcription factors?
an alpha helix is the proper width to bind into the major groove of the DNA double helix. Since the major groove is where the double helix makes contact with water, hydrogen bonding is one way that the transcription factor can bind. Alpha helixes also has many positively charged amino acids, which interacts well with the negatively charged DNA backbone.
CpG islands
commonly 1000 to 2000 bp in length and contain a high number of CpG sites (the dinucleotide of C and G in DNA that is connected to a phosphodiester linkage) they are near the promoters of genes and they are unmethylated
DNA methyltransferase
enzyme that attaches a methyl group to the number 5 position of the cytosine base, forming 5-methylcytosine
Iron Response element
example of the regulatory effect of RNA-binding proteins on translation: when iron is low, IRP binds so that more transferrin receptors are made which promotes the uptake of iron. When iron is abundant, the IRP is removed and the mRNA becomes rapidly degraded
TFIID
general transcription factor that binds to the TATA box and is needed to recruit RNA polymerase II to the core promoter
high iron, no translation, less receptor (transferrin)
high iron, more translation, more ferritin
mediator
mediates the interaction between RNA polymerase II and regulatory transcription factors. it controls the ability of RNA polymerase II to progress to the elongation stage of transcription
alternative exons
not always found in the mRNA after splicing has occurred.
What has been shown about nucleosomes in cells that express a particular gene compared with cells in which the gene is inactive?
nucleosomes have been shown to change position in cells that normally express a particular gene
DNA methylation
occurs on the cytosine base, covalent attachment of methyl groups, which modifies DNA structure in a way that usually silences gene expression
mircro RNA (miRNA)
partially complementary to certain cellular mRNAs and inhibit their translation
what part of the histone is subject to several types of covalent modifications?
particular amino acids in the amino-terminal tails of both standard and variant histones
short-interfering RNAs (siRNAs)
perfect match to specific mRNAs and cause the mRNAs to be degraded
Mechanism of RNA interference
pre-miRNA or pre-siRNA is transcribed from a gene, it is cut to a double-stranded RNA about 21-23 bp long, then it is recognized by a protein that associates with other proteins to form a RNA-induced silencing complex, one of the RNA strands is degraded, RISC recognizes cellular mRNAs due to completmentarity, the mRNA is either unable to be translated or degraded(high complementarity)
histone code hypothesis
the pattern of histone modification acts like a language or code in specifying alterations in chromatin structure. The pattern of the modifications to amino terminal tails provides binding sites for proteins, which affects the degree of transcription.
combinatorial control
the phenomenon that most eukaryotic genes are regulated by many factors
Effect of PolyA-binding protein
the polyA tail is recognized by this protein, and the binding of this protein enhances stability (remember the stability of mRNA is dependent on the length of the polyA tail, the longer the tail, the more stable)
If genes are highly regulated and only occasionally expressed, what could you infer about the CpG islands near them? called tissue specific genes
they are probably methylated, inhibiting transcription
How do repressor proteins affect TFIID?
they inhibit the binding of TFIID to the core promoter and therefore transcription is repressed
Nucleosome-free region (NFR)
this is a site that is missing histones, core promoter is found at a NFR for active genes or genes than can be activated it is about 150 bp in length it is required for transcription, however by itself it is not sufficient for gene activation it lies between two well positioned nucleosomes termed the -1 and +1 nucleosomes
Activator Protein
transcription factor that increases the rate of transcription, binds to the enhancer sequence
what is the result of a phosphorylation is eIF2
translation is inhibited because the initiator tRNA(met) does not bind to the 40S subunit
Helix-turn-helix motif
two alpha helices connected by a turn and lie in the major groove of the double helix
heterodimer
two different transcription factors
homodimer
two identical transcription factors
Effect of splicing enhancer
binding of a splicing enhancer promotes the recognition of poorly recognized junctions. Therefore an exon that was not included in the mRNA before and now it is included
function of RNAi
can be a defense mechanism against viruses and transposable elements, and also acts as a moral cellular process for regulation of gene expression
what change in nucleosome position and histone composition has to do with gene regulation?
changes in chromatin structure from the closed to the open conformation
housekeeping genes
genes that encode proteins required in most cells of a multicellular organisms, so they are expressed. CpG islands near them are unmethylated then
Where must methylation occur to have an effect on transcription?
in the vicinity of the promoter, coding regions downstream from the core promoter usually contain methylated CpG regions and are not affected
How does the binding of IRP to the IRE of ferritin affect translation?
it inhibits it
How does the binding of the IRP to the IRE of transferrin receptor affect translation?
it promotes it
Methylation inhibits transcription by
preventing the binding of regulatory transcription factors to the promoter region or methyl-CpG-binding proteins may bind to the DNA and then recruit inhibiting proteins. Ex) recruiting histone deacetylase will remove acetyl groups from histone proteins, inhibiting transcription
coactivator
proteins that increase the rate of transcription but do not directly bind to the DNA itself
transcription factors
proteins that influence the ability of RNA polymerase to transcribe a given gene
Key role of some transcriptional activators
recruit chromatin-remodeling enzymes and histone modifying enzymes to the promoter region
domain
regions of transcription factors that have specific functions ex) DNA-binding function or binding site for an effector molecule, ext
regulatory transcription factors
regulate the rate of transcription of target genes
3'-untranslated regions
sequences that act as destabilizing mechanisms, located between the stop codon and the polyA tail
histone acetyltransferases
the attachment of the acetyl group eliminates the positive charge on the lysine side of the chain, therefore disrupting the electrostatic attraction between the DNA and the histone. It essentially loosens the DNA around the histone proteins
chromatin remodeling
the energy of ATP hydrolysis is used to drive a change in the locations and/ or compositions of nucleosomes, thereby making the DNA more or less amenable to transcription, so it can activate or repress transcription
What is cis and what is trans?
the enhancers and silencers are cis because they are part of a DNA sequence. the activators and repressors are trans because they are proteins
is H2A.Z or H2a thought to be more easily removed from the DNA?
the histone variants are known to be more easily removed from the DNA
relationship between transferrin, ferrin and iron
when iron is high, you want to decrease the transferrin, when iron is low you want to decrease the ferritin