Gene Control & Cell Differentiation – Lecture Overview

Shared Genome Across Cell Types

• Core idea: Every somatic cell in a multicellular organism contains the same DNA sequence.

  • Illustrated by comparing a retinal neuron’s elaborate dendritic tree with a metabolically focused liver cell (Figure 7-1).

  • Phenotypic divergence arises not from DNA sequence changes but from differential gene expression.

• Historical misconception: Early biologists thought differentiation entailed selective gene loss because the process appeared irreversible.

• Conceptual link: Reinforces the Central Dogma—information flow is regulated after DNA, not by DNA deletion in normal development.

Evidence That Differentiated Cells Retain a Complete Genome

• Frog nuclear-transfer experiments (Figure 7-2A)

  • Nucleus from an adult frog skin cell → enucleated frog egg → normal tadpole.

  • A serial transfer step (broken arrow) gives donor chromatin time to reprogram to an embryonic state.

  • Conclusion: No crucial genomic regions are lost during skin-cell differentiation.

• Plant tissue culture (Figure 7-2B)

  • Many differentiated plant cells can dedifferentiate in vitro → single cell regenerates an entire adult plant (clonal progeny).

• Mammalian cloning (Figure 7-2C)

  • Nucleus from a differentiated cow cell inserted into an enucleated egg → calf.

  • Multiple calves from the same donor nucleus are genetically identical clones.

• Ethical / practical implication: Basis for reproductive cloning, regenerative medicine, and understanding epigenetic reprogramming.

Distinct RNA & Protein Profiles Define Cell Identity

• Every cell transcribes only a subset of its genome, leading to cell-type-specific RNA and protein repertoires.

• Four empirical observations

  1. Universal “house-keeping” gene products (Figure 7-3A)

  • Chromosomal proteins, DNA/RNA polymerases, DNA-repair enzymes, ribosomal RNAs & proteins, central-metabolism enzymes, cytoskeletal proteins such as actin.

  1. Cell-type-restricted molecules (Figure 7-3B)

  • Hemoglobin → red blood cells only.

  • Tyrosine aminotransferase → liver cells; virtually absent elsewhere.

  1. Breadth of gene expression

  • A typical human cell expresses 30-60\% of its \approx 25,000 genes at a meaningful level.

    • \approx 20,000 protein-coding genes.

    • \approx 5000 non-coding RNA genes.

  • Expression levels of almost every gene vary quantitatively among cell types—most differences are subtle; some (e.g., hemoglobin) are dramatic.

  1. Post-transcriptional layers magnify diversity

  • mRNA profiles underestimate final protein output because of regulation at RNA export, translation, protein modification, etc.

  • 2-D gel electrophoresis (Figure 7-4) shows brain vs liver protein spectra—blue (tissue-specific) spots vastly outnumber red (shared) spots.

  • Phosphorylation variants appear as horizontal spot series (charge differences).

  • Modern mass spectrometry supersedes gels, revealing protein ID, modification type & site.

mRNA Repertoires as Molecular Barcodes for Cell Typing

• Single-cell RNA-sequencing (scRNA-seq) enumerates all mRNAs per cell (pp. 537-538).

• Allows unambiguous cell identification—finer than traditional histology.

• Figure 7-5 case study

  • ~4000 mouse neurons activated by a stimulus were isolated and sequenced.

  • Unsupervised clustering organized cells into 7 transcriptionally distinct subtypes.

  • Heat-map: each rectangle = mRNA abundance; red = high, green = low.

  • Cluster plot: spatial proximity reflects transcriptomic similarity (Subtype 1 closer to 4 than to 7).

  • Insight: Neurons that look identical morphologically can differ markedly in mRNA content and, therefore, function.

• Broader impact: Reveals hidden heterogeneity in tissues (e.g., zonation within liver lobules), refines developmental lineages, informs targeted therapies.

External Signals Dynamically Rewire Gene Expression

• Glucocorticoid hormone example

  • Released during starvation / intense exercise.

  • In liver cells → induces protein set for generating energy from amino acids; includes tyrosine aminotransferase.

  • After hormone withdrawal → expression returns to baseline (reversible control).

  • Fat cells respond by reducing tyrosine aminotransferase; some cell types show no response.

• Key principle: Same signal elicits different gene-expression programs in different cell types, overlaying permanent identity with context-dependent modulation.

Multilevel Control Points in the Gene-Expression Pathway (Figure 7-6)

1. Transcriptional control – when/how often a gene is transcribed.

2. RNA-processing control – splicing & other processing of the primary transcript.

3. RNA transport & localization control – which mature mRNAs exit nucleus and where they localize in cytoplasm.

4. Translational control – selecting which cytoplasmic mRNAs are translated by ribosomes.

5. mRNA degradation control – regulated stability vs decay of specific mRNAs.

6. Protein degradation control – selective proteolysis (e.g., ubiquitin-proteasome system).

7. Protein activity control – covalent modifications, allosteric changes, compartmentalization.

• Hierarchy of importance: For many genes, initiation of transcription (Step 1) is the dominant regulatory checkpoint—prevents wasteful synthesis of RNA/protein intermediates.

Conceptual & Real-World Connections

• Epigenetics: Nuclear transfer & dedifferentiation highlight reversible chromatin states rather than irreversible DNA loss.

• Biotechnology: Cloning, induced pluripotent stem cells (iPSC) techniques derive from understanding genomic totipotency.

• Clinical diagnostics: scRNA-seq aids tumor sub-classification, immune-cell profiling, personalized medicine.

• Systems biology: Integration of transcriptomics and proteomics is vital for mapping regulatory networks.

• Ethical considerations: Cloning raises questions of identity, biodiversity, and animal welfare.

Key Terms (expanded)

• Transcriptional control – regulating initiation frequency; involves transcription factors, chromatin state.

• RNA-processing control – alternative splicing, 5′/3′ end formation, RNA editing.

• RNA transport & localization control – nuclear export signals, zipcode sequences in mRNA.

• Translational control – initiation-factor availability, upstream open reading frames, miRNA repression.

• mRNA degradation control – deadenylation, decapping, miRNA-guided slicing.

• Protein degradation control – ubiquitylation chains direct proteins to the 26S proteasome or lysosome.

• Protein activity control – post-translational modifications (phosphorylation, acetylation, ubiquitylation), allosteric ligands, subcellular trafficking.

Synthesis Summary

• A single genome encodes thousands of RNAs & proteins, but cell identity is sculpted by selective expression of a fraction of these genes.

• Differential gene expression is reversible and environment-responsive; regulation can occur at seven points between DNA and active protein.

• For most genes, transcriptional initiation is the pivotal regulatory stage, aligning energy efficiency with precision control.

• Understanding these mechanisms underpins developmental biology, disease pathology, and modern biotechnologies from cloning to single-cell analytics.