post-transcriptional changes/controlling gene expression in mRNA

what creates variety of structure and function seen in cells of different tissues?

• we have 20000-25000 individual genes on chromosome of your cells but only 10000 and 20000 od those genes are actively expressed

• different combinations are expressed in different cells creating variety of structure and function seen in cells of different tissues

how can gene expression be regulated?

• Gene expression can be regulated after an mRNA transcript has been produced.

• expresion of a gene involves two key stages-transcription from DNA to mRNA and translation from mRNA to proteins. Exerting controls at any of the stages of hte process gives control on expression of gene

• In eukaryotes, transcription and translation occur in separate parts of the cell, allowing for significant post-transcriptional modification to occur

how mRNA transcription can be used to control gene expression

• most common way of controlling gene expression is by switching on and off the transcription of certain genes

• transcription is the process by which the genetic code of DNA is copied to a complementary strand of mRNA before protein synthesis can occur

• Messenger RNA transcription is a very effective point at which to control gene expression, because singel mRNA moelcules results in the production of many protein molecules at a ribosome or polysome

what are transcription factors?

• proteins that bind to the DNA in the nucleus and affect teh process of transcribing the genetic material

what are promoter sequences?

regions that enable transcription factors to bind to specific regions on the DNA known as promoter sequences

usually found just above the startign point for trasncription upstream of a gene

jobs of transcription factors that bind to promoter sequences?

• some transcription factors stimulate the transcription of a region of DNA simply by binding to a DNA promoter sequence. This stimulates teh start of transcription of that area of the DNA

• they effec binding of RNA polymerase. Either blocks RNA polymerase from binding or attracts it

what are enhancer sequences

a specific region of DNA to which transcription factors bind and regulate the activity of the DNA by changing the structure of the chromatin. Usually thousands fo base pairs away from gene.

jobs of transcription factors htat bind to enhancer sequences

• other transcription factors bind to regions known as enhancer sequences and control gene expression by changing the structure of the chromatin makign it more or less open to RNA polymerase

• An open chromatin structure is associated with active gene expression; closed chromatin structures are associated with gene inactivity. In this way transcription factors can either stimulate or prevent transcription of gene

• regulartory sites can e on site of gene or long distances from gene they are controlling. This makes it mreo difficult for scientists to work out exactly whats happening

how control over multiple genes can be achieved

• often several different transcription factors will be involved in teh expression of as ingle gne whcih gives many level of control

• or a single trasncription factor may cotnrol the activity of severa diff genes. It may stimulate the expression of on gene and suppress the expression of another

where does control by trascription factors occur?

• control of transcription bytranscription factors occurs in nucleus where transcirption factors control the transcription of regions of DNA into mRNA

what do post-transciptional modification mechanisms include?

• Splicing

• Alternative splicing

what are introns and exons?

• The DNA code within eukaryotic cells contains many non-coding sections

• Non-coding DNA can be found within genes; these sections are called introns, whilst sections of coding DNA are called exons

• During transcription, eukaryotic cells transcribe both introns and exons to produce pre-mRNA molecules

what is pre-mRNA

mRNA that is transcribed directly from teh DNA before it has been modified

process that occurs before pre-mRNA exits the nucleus?

Splicing occurs:

• The non-coding intron sections are removed

• The coding exon sections are joined together by spliceosomes

• The resulting mRNA molecule contains only the coding sequences of the gene

how post trasncription changes to mRNA lead to more variety in the phenotype that is coded for directly in the genotype?

• exons spliced in many diff ways by splicisiomes so exons cna be joined in variety of diff ways. A particular exon may or may not be incorporated into the final mature mRNA

• As a result a single gene may produce several versions of functional mRNA whihc is trasncribed from same section of DNA

• these diff versions of mRNA code for diff arrangements of amino acids which produce diff polypeptid chaisn and diff proteins

• results in single gene producing several diff phenotypes

• This is part of the reason why the proteome is much bigger than the genome

what is post transaltion control?

further modification of proteins may also occur after they have been synthesised. A protein that is coded for by a gen may remain intact or it may be shortened or lengtheend by enzymes to give a variety of other proteins

what is epigeneitcs

• Epigenetics is the control of gene expression by factors other than an individual’s DNA sequence

  • Epigenetics involves the switching-on and switching-off of genes, but without changing the actual genetic code

  • eg RNA splicing as it changes the mRNA and proteins produced from the orig genetic code

can envrionmet inflence gene expresion and phenotype

• phenotype of an organism is a combination of the genetic info in cells and environment in which they grow and develop

• An organism’s internal or external environment can influence gene expression patterns

  • The levels of regulatory proteins or transcription factors can be affected in response to environmental stimuli such as light, and chemicals including drugs and hormones

  • For example, enzymes are activated in response to ultraviolet radiation and increase the expression of melanin-producing genes (and therefore production of melanin), leading to skin pigmentation

what is chromatin

• In eukaryotic cells, nuclear DNA is wrapped around proteins called histones to form chromatin

how can chromatin be chemically modified?

• Chromatin can be chemically modified in different ways to alter gene expression, including:

  • Methylation of DNA (chemical addition of -CH₃ groups)

  • Histone modification via acetylation of amino acid tails

  • Such modifications are called epigenetic tags and collectively, all the epigenetic tags in an organism is called the epigenome

what environmental changes can cause changes in epigenome

• Smoking, stress, exercise and diet can cause epigenetic changes

• Internal signalling from the body's own cells can also cause modifications to occur

is epigenetic modification indepdendent or no

• Epigenetic modification is independent (i.e. DNA methylation or histone modification in one area is not linked to modification in another)

what does chemical modification of histones and DNA control?

• The chemical modification of histones and DNA controls how tightly the DNA is wound around them as the intermolecular bonding between the histones and DNA changes

  • If the DNA is wound more tightly in a certain area, the genes on this section of DNA are 'switched off' as the gene and promoter regions are more hidden from transcription factors and RNA polymerase

why modification of histones be diff in cell types

• The modification of histones is reversible and therefore can be different in different cell types and can vary with age

what is DNA methylation?

• One method of epigenetic control involves the methylation of DNA

• Methyl groups (-CH₃) can be directly added to DNA to change the activity of a gene by a DNA methyltransferase enzyme

• Direct addition of a methyl group to cytosine bases which can influence gene expression

• can also modify structure of histones so have an epigenetic effect in more than one way

how methylation of DNA suppresses trasncription of gene

• Methylation of DNA suppresses the transcription of the affected gene by inhibiting the binding of transcription factors and enzymes needed for transcription (e.g. RNA polymerase) by hanging arrangement of DNA molecule

  • Cells use this mechanism to lock genes in the ‘off’ position-rerpessing of inactivaitng them

• DNA methylation can be affected by many environmental, lifestyle or age-related factors. in many specialised cels ina dults genes silenced by DNA methylaiton eg X chromosome inactivation

what is DNA demethylation

• removal of methyl group from methylated DNA enabling genes to become active so they can be transcribed

job of histones

the histones determien teh structure of the chromatin

heterochromatin

densely supercoiled and condensed chromatin where the genes are not availabel to be copied to make proteins

what is active chromatin?

active chromatin is more loosely held together with uncoiled regions of DNA making more genes available for transcription so that new proteins can be made. Heterochromain and active chromatin is one way in which cells of diff types produced

what is histone acetylation

• Acetyl groups (-COCH₃) can be added to lysine amino acids on histone proteins

• Lysine has a positively charged R group, this forms ionic bonds with the negatively charged phosphate backbone of DNA

  • This helps DNA to coil tightly around the histone protein core

• Adding acetyl groups (acetylation) to lysine residues removes the positive ion and therefore removes a bond between the histone protein and the DNA, this causes the DNA to be less tightly wrapped

  • When the DNA is less tightly wrapped, RNA polymerase and transcription factors can bind more easily and therefore gene expression can occur

  • The gene is said to be activated

  • removing acetyl group produces heterochromatin again

what is histone methylation

• a methyl group is added to a lysine in the histone

• depdengin on the posiiton of the lysine )there are 2 lysines) methylation may cause inactivation of the DNA or activation of a region

• methylation is often linked to the silencing of a gene and even whole chromosome

• Like the genome, the epigenome is heritable (i.e. when a cell divides and replicates, epigenetic changes affecting the expression of genes in the DNA of that cell may be passed on to daughter cells)

  • For example, during gamete production, DNA in the parent cell usually undergoes de-methylation (the methyl groups are removed) but often methyl groups are not removed and therefore are present in the DNA on the sperm or egg cells

  • One potential explanation for why this occurs is that if an epigenetic change occurs in response to an environmental factor, it may be beneficial for this epigenetic change to also occur in daughter cells (or gametes, for example) so that they are also better adapted for the environmental factor (in the same way the parent cell was)

  • Mounting evidence demonstrates that modifications to the epigenome in one generation can be passed on to the next generation at the cellular or whole organism level

what is epigenome and its in heritability?

The epigenome is heritable, meaning epigenetic changes that affect gene expression can be passed on to daughter cells during cell division. This could be as if an epigenetic change occurs in response to an environmental factor it may be ebenficial for this epigenetic change to occur in daughter cells so they are better adapted to enviroenmental factor in same way parent cell was.

difference between epigenetic and mutations

both of which lead to changes in the expression of genes - whilst mutations affect the genetic code itself, by altering nucleotide sequences, epigenetic changes only affect the way the code is read.

what is non coding RNA

98% of the RNA which does not code for proteins but affects the transcription of the DNA code, modifies the chromatin structure or modifies the products of transcription eg silencing of one of the X chromosomes in fmales due to rpescense of ncRNA alled Xist

another tole of ncRNA in epigenetics seems to be in chromatin modification where it acts on the histoens ot make areas of DNA available or unavaibale for transcriptione