Site author Richard Steane
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Regulation of transcription and translation

Targetting a gene to be transcribed

All the cells within an organism carry the same coded genetic information, but different tissues and organs express only part of it. In this way they are able to control their specific metabolic activities.

Although the formation of messenger RNA, based on the structure of a section of DNA making a gene, and its function in the coding for the sequence of of amino acids in the resulting polypeptides is well known, less is known about the mechanism by which specific genes are selected for transcription and translation.

The AS specification includes:
the transcription of genes to produce functional mRNA molecules that are then translated by ribosomes to form polypeptides
the involvement in protein synthesis of tRNA molecules that are also encoded by genes.

This is covered in DNA and protein synthesis (links below)

Transcriptional factors

The process of transcription (production of an RNA copy of a section of DNA) takes place within the nucleus, in response to transcription(al) factors which move in from the cytoplasm.

Transcriptional factors are proteins that have a specific tertiary structure or shape and as a result they become attached to a promoter section of DNA in front of a gene ('upstream' from it). This is sometimes called the regulator or enhancer region of the gene.

By binding in this way they flag a position where the enzyme RNA polymerase can attach and start the transcription process.

This diagram shows part of a gene that is being transcribed
transcription_process (8K)
No transcriptional factors visible here

In which direction is the RNA polymerase moving?
> to the right
Why is the DNA shown as a single strand?
>The two strands or helices must separate for transcription to take place
>The diagram shown just the antisense strand

Transcriptional factors can cause stimulation or inhibition of target genes - sometimes described as upregulation or downregulation of gene expression.

What goes around comes around

Being proteins, transcriptional factors are produced by ribosomes in the cytoplasm of eukaryotes, and they are coded for by genes in the nucleus. They pass back into the nucleus to perform their roles in initiating transcription of other genes.

Transcription factors contain a DNA-binding domain (DBD), which attaches to the specific sequence of DNA adjacent to the genes that they regulate. In fact they attach to the outside of the DNA double helix, by means of weak intermolecular forces (electrostatic and Van der Waals forces) between the amino acid sidechains of the polypeptide chain and the the bases at the edge of the DNA backbone, which remain joined by hydrogen bonds between bases in the middle.

For example, the TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box, which has repeated sections of A-T base pairs. These can peel apart more easily than G-C pairs, because they have two hydrogen bonds between them, rather than three. Of course, 'unzipping' of DNA strands is necessary when mRNA is being formed at the gene.

A number of other protein subunits also become attached, and they may cause a notable kinking of the DNA molecule at this point, and the tension may cause the two srands of DNA to peel apart as the enzyme DNA-dependent RNA polymerase becomes positioned on the promoter region.

The role of oestrogen in initiating transcription

Oestrogen is a steroid hormone that affects transcription. It is produced in the ovaries and, being hydrophobic, it easily passes through the cell membrane and enters the cytoplasm of target cells, forming a complex with a specific receptor which then enters the nucleus.

The activated oestrogen receptor (ER) acts as a transcription factor regulating various gene expression events such as development of breast tissue in puberty and pregnancy. This normally involves control of cell division, but it may be compromised in the case of different types of cancer.

Epigenetic control of gene expression

The term epigenetics covers changes in organisms caused by modification of gene expression rather than alteration of the gene itself. Some of it is said to involve heritable changes in gene function, without changing the actual base sequence of DNA.

This may be achieved as a result of two different forms of chemical modification to the structure of chromosome: the DNA and the protein - which are collectively referred to as chromatin.

Methylation of DNA

Methyl groups (-CH3) may be covalently attached to DNA, without changing the base sequence, by enzymes called DNA methyltransferases. Methyl groups may act as markers, changing the possibility of genes being expressed.

CpG sites on DNA

CpG (18K)
Each methylated cytosine has a second methylated cytosine on the partner strand
In particular, cytosine bases can be methylated and pairs of cytosines - 'CpG sites' - are especially important. These sites consist of a dinucleotide section of DNA double helix containing cytosine C then an intervening phosphate p linking to Guanine G. Of course, cytosine pairs with guanine and so there is a second cytosine on the partner strand. Both of these cytosines may be methylated, and there is often a large number of methylated CpG sites in the promoter region of genes that are not active in cells.

It is thought that this makes the gene inaccessible to transcription factors so the gene is not transcribed. Furthermore, when cells within tissues divide, the pattern of methylation is retained as an enzyme (another DNA methyltransferase) scans the DNA after it is semiconservatively replicated and shared between daughter cells by mitosis, so that methyl groups are added to the newly-added cytosines one space below the methylated cytosine on the other strand. This means that the pattern of methylation is passed down from 'mother cells' to 'daughter cells'. This is one way that epigenetics causes heritable changes in gene function.

This also explains why cells have reduced potency as they become specialised into different tissues.

Increased methylation of DNA inhibits transcription

Methylation of cytosine
cytosine_methylation (20K)
This produces 5-methyl cytosine (right).
In the nucleotide cytidine, nitrogen at position 1 is bonded to deoxyribose (phosphate) and hydrogen bonds (with guanosine) form at (groups at) positions 2, 3, and 4.
Methylation involves addition of a methyl group (-CH3) to the C5 of a cytosine residue. Adenine can also be methylated.

Repeated CpG sequences, referred to as CpG islands, are common at the 5' end of many genes. During development, methylation of these CpG islands 'silences' the affected genes by preventing activation of RNA polymerase.

Acetylation of histones

This causes changes in the winding of DNA onto the histone protein which make up nucleosomes - the 'beads on a string' - which are part of the structure of chromosomes. Although chromosomes contain DNA, most of it is fairly inaccessible to the molecular machinery (transcriptional factors and RNA polymerase, etc) that is needed for individual genes to be expressed. And the basic histone protein can be chemically modified to make the DNA more or less accessible by means of chemical groups - acetyl groups (-CH3CO) which may be joined on to it.

Getting your chromatin to relax

Histone-acetylation-and-deacetylation (71K)
The acetylation process is catalysed by enzymes (histone acetylation acetyltransferases or HATs) and this causes the histone bobbins to be less closely clustered together, exposing a section of DNA and allowing it to be transcribed. Conversely HDAC enzymes (Histone deacetylases) remove acetyl groups from histones, so that DNA is more hidden.

As a result, acetylation of histones causes stimulation of transcription, and deacetylation of histones inhibits it.

Each histone protein 'bobbin' is composed of an octamer of (8) similar subunits (two each of H2A, H2B, H3 and H4), with 'tails' formed from lysine residues, which radiate outwards. Another histone H1 associates with DNA outside the core octamer unit and it is thought to regulate the formation of histone beads into ribbon sections.

When acetyl groups are attached to the tails, the packing of the histones is altered and more DNA is revealed.

Acetyl groups are provided by acetylcoenzyme A (acetylcoA).

Where has acetylcoenzyme A been covered before?

> In the link reaction of aerobic respiration

Epigenetics and the development and treatment of disease, especially cancer

It has been found that some cancer tissue, e.g. colorectal cancer, has less methylation than normal tissue, causing activation of genes that are normally turned off.

On the other hand, too much methylation can undo the work of protective tumour suppressor genes.

This information can be used in controlling cancer.
Demethylating agents can be used to treat acute myeloid leukemia and myelodysplastic syndromes, and histone deacetylase inhibitors may be used for the treatment of cutaneous T-cell lymphomas.
5-aza cytosine
5azacytosine (7K) As N replaces C at position 5, this (base) does not have a site for methylation.
Compare it with methyl cytosine above.

5-aza-2'-deoxycytidine is an inhibitor of DNA methylation.

This nucleotide analogue can become incorporated into DNA which is dividing, and it blocks DNMT (DNA methyltransferase) enzymes from acting, which inhibits DNA methylation.

(5-aza-2'-deoxycytidine is 5-aza cytosine with deoxyribose attached at the bottom.)

RNA interference (RNAi)

As well as producing messenger RNA, DNA in fact also encodes other forms of RNA that are involved in cell regulation. These are transcribed by the same form of RNA polymerase as the enzyme that is involved in building up mRNA - or more accurately pre mRNA. Other forms of RNA polymerase are involved in the transcription of tRNA and rRNA .

This underlines the notion that DNA codes for more RNA than the mRNA that is translated into protein.

Small nuclear RNAs (snRNAs) operate within nuclei, where they are tightly bound to proteins to form small nuclear ribonucleoproteins, or snRNPs (often pronounced snurps), that control the splicing of pre-mRNA. See Action of spliceosomes opposite

Translation of the mRNA produced from target genes can be inhibited by RNA interference (RNAi). This is called silencing the gene.

MicroRNA 'stem loops'
microRNA_stem-loops (15K) The first miRNA discovered (in 1993), lin-4 from Caenorhabditis elegans is an endogenous regulator of genes that control developmental timing.
MicroRNAs (miRNAs) are formed as hair-pin bends of single-stranded RNA that fold back on themselves to give 'stem loops' about 22 to 26 nucleotides long.

One section of this becomes incorporated into a protein-based RISC (RNA-induced silencing complex).

Small interfering RNAs (siRNAs) are formed as double-stranded molecules about 21 to 25 base pairs long. One of the strands becomes incorporated into a protein-based RISC.

When the single-stranded miRNA or siRNA within a RISC binds to a molecule of mRNA that contains a sequence of bases complementary to its own, the mRNA is either hydrolysed or its translation is stopped.

This can be used to degrade mRNA that is no longer needed to produce protein.

It can also act as a defence against infection by viruses.

Action of spliceosomes

Pre mRNA, produced by transcription in the nucleus, consists of exon sections alternating with intron sections. Each of the intervening intron sections are removed by the action of 'spliceosomes', composed of small nuclear ribonucleoproteins - complexes containing catalytic proteins assisted by sections of RNA. Only the exons will be expressed after the splicing process

Structure of U1 snRNA U1_spliceosomal_RNA (8K)
There are several varieties of small nuclear ribonucleic acid (named U1 - U6) and they consist of double-stranded sections, held together by complementary base pairing, with loops, exposing single stranded sections, like transfer RNA. This enables them to target the two ends of each intron, and presumably to bring in the appropriate proteins.

Different snRNAs become attached to the GU nucleotide sequence at the 5' end splice site, and the AG sequence at the 3' end splice site, and these are then brought together as the intervening section is formed into a loop - often described as a 'lariat' - which is cut out as two exon sections are bonded together.

Mature mRNA will eventually be expressed by being translated into protein at the ribosomes in the cytoplasm, and the intron lariats are broken down into RNA nucleotides.

Post-transcriptional gene silencing

This enables removal of mRNA - either originating in the cell (and no longer needed?) or RNA from pathogens such as invading viruses. Alternatively RNA may be introduced into the cell in an attempt to treat genetic conditions.

siRNA and miRNA are processed so as to form a template to bind 'target RNA' to be broken down by various protein complexes.

Action of Dicer

Silencing of mRNA by RNA interference

siRNA_pathway (42K)
This enzyme breaks down double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short double-stranded RNA fragments about 20-25 base pairs long, with two exposed single stranded bases at the 3' ends - small interfering RNA and microRNA.

These fragments are surrounded by a number of proteins to form the RISC. One strand - the 'anti-sense' or 'guide' strand - is retained, and the other 'sense' or 'passenger' strand is degraded.

RNA-induced silencing complex, or RISC

This consists of several proteins, arranged around the short section of RNA, a projecting part of which acts as a template that recognises mRNA to be disposed of. This is attracted as a result of complementary base pairing between the RNA bases. Several of the proteins are RNA-specific endoribonucleases

The protein called Argonaute (Ago) breaks down the mRNA (attached to the anti-sense strand) into short sections of nucleotides.

Other related topics on this site

(also accessible from the drop-down menu above)

DNA and protein synthesis
Nucleic acids

This series (The control of gene expression)
Base sequence alteration
Cell potency
Regulation of transcription and translation
Gene expression and cancer

Interactive 3-D molecular graphic models on this site

(also accessible from the drop-down menu above)

DNA nucleotides cytidine phosphate and guanosine phosphate - rotatable in 3 dimensions

Web references

Epigenetics: Fundamentals - from What is Epigenetics?

Epigenetic Regulation of Osteogenic and Chondrogenic Differentiation of Mesenchymal Stem Cells in Culture

Epigenetics in cancer therapy and nanomedicine

RNA interference (RNAi): by Nature Video - a high quality YouTube animation

siRNA Versus miRNA as Therapeutics for Gene Silencing

Small interfering RNA (siRNA) Therapeutics- Competitive Landscape, Technology and Pipeline Insights, 2015 - A DelveInsight's Report

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