pastpaperbd/ Biology/ Notes/ Gene Expression
T8

Gene Expression

AQA spec ref: 3.8 - The control of gene expression

Every cell in an organism contains the same DNA and therefore the same genes. Yet a liver cell looks and behaves completely differently from a neuron, a red blood cell, or a muscle cell. The reason is differential gene expression - different cells express different subsets of their genes. Understanding how this is controlled is one of the most important areas of modern biology, and is directly relevant to development, disease, and treatments like gene therapy.

What is Gene Expression?

Gene expression means producing a functional product from a gene - usually a protein (via transcription → translation), but also sometimes a functional RNA molecule. A gene that is being expressed is said to be "switched on" or "active."

Since all cells have the same genome, differences between cell types arise entirely from differences in which genes are expressed - which genes are transcribed into mRNA, and which mRNAs are translated into protein. The control of gene expression is therefore the basis of cell differentiation during development.

Transcriptional Control

The most important level of gene expression control is transcription - whether or not a gene is transcribed into mRNA.

Chromatin Structure and Accessibility

DNA in the nucleus is wound around histones, and this chromatin can exist in two states:

Euchromatin - loosely coiled, DNA is accessible to RNA polymerase and transcription factors. Genes in euchromatin are available for transcription (active/expressed genes).

Heterochromatin - tightly coiled, DNA is inaccessible. Genes in heterochromatin are silenced.

The degree of chromatin compaction is regulated by modifications to the histone proteins:

  • Histone acetylation - acetyl groups are added to the positively-charged lysine tails of histones by histone acetyltransferases (HATs). This reduces the positive charge on histones, weakening their attraction to the negatively-charged DNA. The chromatin opens up (euchromatin) → gene transcription is activated. Histone deacetylases (HDACs) remove acetyl groups → chromatin condenses → transcription silenced.
  • Histone methylation - methyl groups added to histones. Depending on which histone and which position, methylation can either activate or repress transcription.

These modifications are part of epigenetics - heritable changes in gene expression that do not involve changes to the DNA sequence itself.

Transcription Factors

Transcription is controlled by transcription factors - proteins that bind to specific DNA sequences near a gene (in the promoter region) and either activate or repress transcription:

  • Activators - bind to enhancer sequences and interact with RNA polymerase or general transcription factors to increase transcription rate
  • Repressors - bind to silencer sequences or to the promoter, blocking RNA polymerase from binding

The activity of transcription factors can be regulated by:

  • Phosphorylation (by signalling cascades - e.g. a hormone binding to a cell surface receptor ultimately activates transcription factors via second messengers)
  • Direct binding of a small molecule (e.g. steroid hormone - receptor complexes act as transcription factors directly)
  • Availability - some transcription factors are only synthesised at specific developmental stages

This means gene expression is ultimately controlled by the environment (via signalling molecules) and by the developmental programme (which transcription factors are present).

DNA Methylation

DNA methylation is the addition of methyl groups directly to cytosine bases in the DNA, typically at CpG sites (cytosine followed by guanine). Methylation of promoter regions generally silences genes - it can directly block transcription factor binding, and also recruits proteins that compact the chromatin further.

Importantly, DNA methylation patterns are:

  • Heritable - when cells divide, the methylation pattern is copied to the new strand
  • Potentially reversible - demethylases can remove methyl groups
  • Environmentally influenced - diet, stress, toxins can alter methylation patterns

DNA methylation is therefore a major mechanism of epigenetic inheritance - changes in gene expression that are passed from parent cell to daughter cells without altering the DNA sequence.

Post-Transcriptional Control: RNA Processing

In eukaryotes, the initial RNA transcript (pre-mRNA) undergoes processing before it leaves the nucleus:

Splicing: non-coding introns are removed and exons are joined together. The AQA-relevant point is that alternative splicing allows different combinations of exons to be joined, producing multiple different mRNAs (and proteins) from the same gene. Approximately 90% of human genes are alternatively spliced, massively expanding proteome diversity beyond genome size.

mRNA stability: different mRNAs have different half-lives in the cytoplasm. mRNA is degraded by nucleases, and sequences in the mRNA's 3' untranslated region (UTR) can make it more or less stable. More stable mRNA = more translation = more protein.

Post-Translational Control: Protein Activity

Even after translation, protein activity can be regulated:

  • Phosphorylation by kinases activates or deactivates many proteins (e.g. enzymes, transcription factors)
  • Ubiquitination tags proteins for degradation by the proteasome, controlling how long a protein persists

Epigenetics

Epigenetics is defined as heritable changes in gene expression that do not involve changes to the DNA base sequence. The molecular mechanisms are histone modification and DNA methylation, described above.

Why epigenetics matters:

  • Development: during embryonic development, cells differentiate from a single fertilised egg into hundreds of cell types. This differentiation is largely driven by epigenetic changes - different genes are epigenetically silenced in different cell types. Once silenced, the pattern is inherited by all daughter cells of that lineage.
  • Environmental effects: external factors can alter epigenetic marks. Diet, stress, toxins, and exercise have all been shown to influence DNA methylation and histone modification patterns. Some of these changes can persist across cell generations.
  • Disease: many cancers involve aberrant epigenetic changes - silencing of tumour suppressor genes by hypermethylation, or inappropriate activation of oncogenes. HDAC inhibitors and DNA methylation inhibitors are being developed as cancer treatments.
  • Transgenerational epigenetics: some epigenetic marks can be inherited across generations (parent → offspring), though this is controversial and the mechanisms in humans are not fully established.

Key example - X-inactivation: in female mammals (XX), one X chromosome is randomly inactivated in each cell during early development, forming a Barr body (condensed, transcriptionally silenced heterochromatin). This is maintained in all descendant cells. X-inactivation is controlled by the XIST gene, which produces an RNA (not a protein) that coats and silences one X chromosome via epigenetic mechanisms. Since X-inactivation is random, females are genetic mosaics - different cells may express the maternal or paternal X.

Stem Cells and Differentiation

A stem cell is an undifferentiated cell capable of:

  1. Self-renewal - dividing to produce more stem cells
  2. Differentiation - dividing to produce specialised cell types

Totipotent cells - can differentiate into any cell type, including extra-embryonic tissues (placenta, yolk sac). Only the fertilised egg (zygote) and the first few cell divisions are totipotent.

Pluripotent cells - can differentiate into any cell type of the embryo proper, but not extra-embryonic tissues. Embryonic stem cells (ESCs) from the inner cell mass of the blastocyst are pluripotent.

Multipotent cells - can differentiate into a limited range of related cell types. Adult stem cells (e.g. haematopoietic stem cells in bone marrow producing all blood cell types) are multipotent.

Unipotent cells - can only differentiate into one cell type.

Differentiation involves permanent changes in gene expression - epigenetic silencing of the pluripotency genes and activation of tissue-specific genes. Once a cell is differentiated, it generally cannot reverse (with some exceptions - see induced pluripotent stem cells below).

Therapeutic Uses of Stem Cells

Stem cells have enormous potential for treating degenerative diseases:

  • Haematopoietic stem cell transplants (bone marrow transplants) - used to treat leukaemia, sickle cell disease, thalassaemia
  • Corneal repair - limbal stem cells used to repair corneas damaged by burns or disease
  • Potential future uses: growing replacement heart tissue (for heart failure), neural tissue (for Parkinson's, spinal injury), insulin-producing beta cells (for Type 1 diabetes)

Induced pluripotent stem cells (iPSCs): Yamanaka (2006) showed that adult differentiated cells can be reprogrammed back to a pluripotent state by introducing specific transcription factors (Oct4, Sox2, Klf4, c-Myc). This bypasses ethical concerns about embryo use and allows patient-specific stem cells to be generated (reducing rejection risk).

Ethical issues with embryonic stem cells:

  • Using human embryos raises concerns about the moral status of the embryo
  • Embryos are destroyed in the process
  • iPSCs are seen as a more ethically acceptable alternative but are not yet fully equivalent to ESCs

Cancer and Gene Expression

Cancer arises from uncontrolled cell division - the result of disrupted gene expression at the level of:

Proto-oncogenes: normal genes that promote cell division. When mutated to form oncogenes, they continuously promote division even without a signal. A single mutated allele is enough (dominant effect).

Tumour suppressor genes (e.g. p53, Rb): normally inhibit cell division or trigger apoptosis in damaged cells. Both alleles must be mutated for function to be lost (recessive effect - "two-hit hypothesis"). p53 is mutated in ~50% of all human cancers.

Epigenetic changes in cancer: promoter hypermethylation silencing tumour suppressor genes is common in cancer. This is a target for therapy - demethylating agents can reactivate silenced tumour suppressor genes.

Summary

  • Gene expression: all cells have the same DNA; different cells express different genes → differential gene expression → cell differentiation
  • Transcriptional control: transcription factors (activators/repressors) bind to promoter/enhancer/silencer regions
  • Histone modification: acetylation → euchromatin → active transcription; deacetylation → heterochromatin → silenced
  • DNA methylation: methylation of promoter CpG sites → gene silencing; heritable
  • Epigenetics: heritable changes in expression without DNA sequence change; mechanisms = histone modification + DNA methylation; influenced by environment
  • X-inactivation: random silencing of one X chromosome in female mammals; Barr body; XIST RNA
  • Stem cells: totipotent → pluripotent → multipotent → unipotent (decreasing potency); ESCs = pluripotent; adult stem cells = multipotent; iPSCs = reprogrammed adult cells
  • Cancer: oncogenes (dominant gain-of-function)+tumour suppressor gene loss→uncontrolled division

AQA Exam Tips

  • Epigenetics definition: must include "heritable" and "without change to DNA base sequence." Do not just say "changes gene expression" - state that the changes are heritable.
  • Histone acetylation and transcription: acetylation reduces positive charge on histones → DNA-histone attraction weakens → chromatin uncoils → RNA polymerase can access DNA → transcription occurs. Know the full chain.
  • DNA methylation → silencing: methylation of CpG sites in the promoter prevents transcription factor binding AND recruits proteins that compact chromatin.
  • Stem cell potency hierarchy: totipotent > pluripotent > multipotent. Embryonic stem cells are pluripotent (not totipotent). AQA tests this distinction.
  • iPSC significance: avoids destroying embryos; allows patient-specific cells; Nobel Prize awarded to Yamanaka (2012).
  • Cancer: proto-oncogene (normal) → oncogene (mutated, dominant) causes excess division. Tumour suppressor gene (normal) → both alleles must be lost (recessive). p53 = guardian of the genome; lost in ~50% of cancers.
  • X-inactivation as epigenetics: good example because it shows that epigenetic silencing is heritable (once a cell has inactivated one X, all its descendants inactivate the same X), and that it does not change the DNA sequence.