lecture 7 (2016)Apunte Inglés
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Molecular biology – Lecture 7
MULTILEVEL TRANSCRIPTIONAL CONTROL
1. DNA-BINDING DOMAIN AND ACTIVATING DOMAIN
The specific transcription factors that bind enhancers (sequences that
allow the gene to be expressed) can bind and activate them because
they have two specific domains: DNA binding domain and activating
domain. The activating domain can bind the basal complex and with
the action transcription would start. A connecting domain links both
We have to take into account that transcription factors don’t need to be close to the promoter to start transcription because as DNA is a flexible molecule, by making a loop they can contact and activate or repress transcription. Thanks to the capability of these proteins to act in large distances, lots of proteins can bind the basal complex and cooperate and interact among each other to activate or repress gene expression.
The activating domain apart from binding the basal complex has other functions such as: - - Histones have positive charge tails and these help the histones to bind phosphate groups of DNA. If the tails are modified, the positive charges disappear and the histones go away from DNA allowing it to be transcribed. A function of the activating domains is also to recruit enzymes (co-activators) that will acetylate the tails of histones to relax chromatin, allowing the basal complex to initiate transcription.
They also can recruit other proteins (co-repressors) that remove the acetyl group, helping the chromatin to be packed and like this repressing transcription.
Molecular biology – Lecture 7 2. PROTEINS INVOLVED IN TRANSCIPTION We don’t know the cause of many illnesses but in many tissues, we see that they lose the capability of functioning as they are supposed to function. Often this happens because cells are not able to differentiate properly to fulfil the specific tissue requirements. In many experiments it has been proved that the inactivation of a single transcription factor can cause severe distortions on the function of tissues in multicellular organisms. Ex: the inactivation of one protein in the genome of a fly caused the duplication of the fly wings.
We can see that are lots of proteins involved in transcription. The expression of a gene depends on the presence or absence of the specific transcriptional factors but this is not the only factor. If the presence or absence of specific transcriptional factors were only mechanisms implied in transcription, a circular argument would be created because the activation of a gene would imply the synthesis of a specific transcription factor which in turn.
Would imply the activation of other gene and successively.
To solve this circular argument, we need the presence of additional mechanisms.
3. REGULATION OF TRANSCRIPTION FACTORS Different examples: 1. Protein synthesis: the synthesis of a certain transcription factor causes the expression of the gene. Ex: homeoproteins 2. Protein phosphorylation: there are some transcription factors that can’t bind DNA and the can only do it if they are phosphorylated. Phosphate groups cause strong structural changes that make the protein capable of binding. Ex: HSTF 3. Protein dephosphorization: there are some transcription factors that can’t bind DNA if they are phosphorylated so the need to be dephosphorylated to be capable of binding DNA.
Molecular biology – Lecture 7 4. Protein ligand binding: when the protein is outside the nucleus, it needs a special molecule (ligand) that binds the protein and transports it into the nucleus. Once in the nucleus, the protein will be able to bind DNA. Ex: steroid receptors 5. Protein cleavage to release active factor: when a protein is processed by a protease the specific transcription factor is released and it can bind DNA to start transcription.
Ex: sterol response 6. Protein release by inhibitor: when a specific transcription factor is bound to an inhibitor factor it can’t bind DNA. When this inhibitor factor releases the protein, it can bind DNA and start transcription 7. Protein change in partner: when a specific transcription factor is bound to an inhibitor factor it can’t bind DNA. When an activating factor binds the protein and the inhibitor factor releases it, the protein can bind DNA and start transcription.
4. HOW OUR CELL REACT IN FRONT OF SEXUAL HORMONES Steroid hormones are molecules that can cross membranes, entering to the cytosol. They don’t need special proteins outside to transport them. These molecules enter the cell and bind receptor proteins (a class of specific transcription factors) that are within the cell already. The binding domain of the hormone to the protein is direct. Once the hormone is bound, the receptor proteins can enter to the nucleus and bind DNA to start transcription.
Molecular biology – Lecture 7 The different receptors are capable of recognizing similar enhancers (sexual hormones) but the difference in bases of the different enhancers is sufficient for the proteins to distinguish one enhancer from each other. Each enhancer will activate different sets of genes and create specific responses.
5. HLH PROTEINS They are specific transcription factors that are important in differentiation of cells during all our life. In tissues that are renewed very fast, we have lots of cells that are being differentiated, and in this differentiation is regulated by HLH proteins. HLH proteins with basic DNA-binding domains bind to each other forming a dimer capable of binding DNA. If the HLH protein doesn’t has a basic DNA-binding domain, although it can from a dimer with another HLH protein with a DNA-binding domain, the dimer will not have enough affinity and it will not bind DNA.
Molecular biology – Lecture 7 6. THE ALGEBRA OF THE GENES Specific transcription factors may interact among them to define decision models offering a wide range of functional responses to fulfil extremely complex requirements in eukaryotes.
We can find other situations: 1. The two specific transcription factors (A and B) must be present to activate transcription. A has the DNAbinding domain and the activation domain that will be in B 2. Any of the two specific transcription factors (A or B) is able on itself to activate transcription. Both A and B can recognize the same enhancer and the both contain an activation domain.
3. Factor B doesn’t contain an activation domain and behaves as a repressor by replacing activating factor A at it DNA-binding domain, and substitutes the specific transcription factor A (that has enhancer and activating domain). Like this, transcription doesn’t occur.
7. HOW CAN TISSUES ORIGINATE All our tissues originate from on cell and this process mostly depends on transcription factors. The scheme proposes that, in the first division of the embryonic cell, the two daughter cells are not exactly the same. Cell A is different from cell B by the only presence of one single transcription factor. In the second division, from A we will have two cells that are going to be different as in the first division. The two cells that came from B will have the transcription factors from the mother. Like this the number of transcription factors increases exponentially. By this simple rule, we end up in three divisions with 8 cells with different combinations of transcription factors. We can obtain like these more than 10.000 different cells with just 25 different transcription factors. Our genome has hundreds of transcription factors so it is not that difficult to produce such a complex organism like us.
Molecular biology – Lecture 7 8. METHYL IMPRINTING Genetic imprinting is a phenomenon in which a gene is either expresses or not expressed in the offspring depending on which parent it is inherited from. Genes in the X chromosome particularly show this behavior in females. Methylation is an important mechanism of transcriptional regulation. In the early embryo, genes subject to imprinting are marked by methylation. In this way DNA methylation is used as a mark to distinguish two copies of a gene that may be otherwise identical. This methylation will affect the two strands of DNA and it usually takes place in promoters. In most cases, the methyl imprints silences nearby gene expression (acing as repressor). In some case, the methyl imprint can activate expression of a gene.
Normally what happens is that enzymes that add methyl groups are only expressed in the egg cells (germ cells) in females. A random combination will generate an embryo that will only have methyl groups that come from the female (maternal imprinting).
In other genes the methylations occur only in the male germ cells (paternal imprinting)- so methylation is maintained over successive cell divisions and explains maternal or parental genetic dominance. In this case the Mendel’s laws don’t work.
Molecular biology – Lecture 7 9. STABILITY OF mRNAs The stability of mRNAs is a mechanism of gene control at a post-transcriptional level.
We ca distinguishes 3 different types of mRNAs: 1. Stable mRNA: if the mRNA is a final destination, it’s better to have an mRNA very stable because the cell will be able to use the mRNA to produce proteins for long periods of time.
2. Unstable mRNA: if mRNA codes for growth factor (proteins segregated by the immune cells that tell the cells that they have to proliferate), it’s usually an unstable mRNA.
When you want mRNA for a transient response, those mRNAs are very unstable. If this mRNA was stable, proliferation would occur during too much time and it could produce tumors.
3. DNA synthesis modulates DNA stability: a very extreme example is the histone mRNA.
The requirements of histones of a cell are very special. Depending on the situation of the cell, you will need more or less histones. And that’s why the histone mRNAs only last 12 minutes when it’s not synthetizing histones but if it’s synthetizing histones, it last until 1 hour so the DNA synthesis modulates stability.