Transcriptional Control of Gene Expression Notes

Regulatory DNA Elements in Eukaryotes

  • Core promoter elements: Minimal sequence required for transcription initiation.
    • TATA box
    • Initiator element
    • Downstream Promoter Element (DPE)
  • Promoter-proximal elements:
    • Often gene- or cell type-specific
  • Enhancers/Silencers
    • Often gene- or cell type-specific
    • Can work from a distance
    • Orientation-independent modulation of transcription

Regulatory Regions in Eukaryotes

  • (a) Mammalian gene with a TATA box
    • Regulatory elements can be up to -50 kb or more away from the transcription start site (+1).
  • (b) Mammalian CpG-island promoter gene
    • Regulatory elements can be located between -200 and +5, or +10 to +50 kb or more away from the transcription start site (+1).

Transcription Initiation and Holo-enzyme Complex

  • Holo-enzyme complex
    • Pre-assembled, not bound to DNA
    • Lacking TFIID + Mediator-proteins
    • Holo-enzyme complex ≠ PIC (Pre-initiation complex)

Transcription Factors: Modular Structure

  • Transcription factors have a modular structure.
    • DNA-binding and transcription modulating activity reside in separate domains.
  • WT1
    • Repression domain
  • Repressors
    • The functional converse of activators.

Combinatorial Action of Transcription Factors

  • The identity of floral organs is defined by the combinatorial action of MADS box transcription factors.

Overview: Transcriptional Control of Gene Expression

  • Basics of transcriptional regulation (Prokaryotes and Eukaryotes)
  • RNA polymerases
  • Eukaryotic gene control elements and associated transcription factors
  • Regulation of gene expression
  • Chromatin and gene regulation

Gene Expression Response to Environmental Cues

  • How gene expression responds to environmental clues.
  • How gene expression controls development/differentiation and homeostasis.

Nuclear Hormone Receptors

  • Receptors for lipid-soluble hormones within the cell.
  • Examples:
    • Estrogen (agonist)
    • Tamoxifen (antagonist)
    • Cortisol
    • Retinoic acid
    • Thyroxine

Nuclear Hormone Receptors: Two Main Types

  • Two major types with distinct mechanisms:
    • Type 1: e.g., Estrogen receptor (ER), Progesterone receptor (PR), Glucocorticoid receptor (GR)
    • Type 2: e.g., Thyroxine receptor (TR), Retinoic acid receptor (RAR)
  • General primary structure:
    • Variable N-terminal region
    • DNA-binding domain (68 amino acids)
    • Ligand-binding domain (225-285 amino acids, 100-500 aa)
  • Amino acid identity:
    • DNA-binding domain: 42-94%
    • Ligand-binding domain: 15-57%

Type 1 Nuclear Hormone Receptors

  • Glucocorticoid receptor (Type 1) migrates to the nucleus upon ligand binding and activates anti-inflammatory genes.
  • NHRs most commonly bind as a dimer to an inverted repeat sequence.
  • Heat-shock proteins “anchor” GR in the cytoplasm.

Glucocorticoid Receptor and Gene Repression

  • Glucocorticoid receptor (Type 1) can also repress pro-inflammatory genes.
  • Binding of GR to other transcription factors (AP1, NF kappa-beta) has an inhibitory effect and results in repression of pro-inflammatory genes.

Type 2 Nuclear Hormone Receptors

  • Heterodimeric nuclear receptors always localize to the nucleus (Type 2).
  • Example: TR/RXR and RAR/RXR
  • Absence of ligand:
    • Recruitment of HDAC to target promoters.
    • Repression of transcription.
  • Presence of ligand:
    • Conformational change of hormone-binding domain.
    • Loss of interaction with HDACs and associated proteins.
    • Recruitment of HAT-containing co-activators.
    • Activation of transcription.

Signal Transduction Pathways

  • Most signal transduction pathways regulate transcription factors.
  • Example:
    • Cytokine receptor
    • Janus kinase
    • Signal Transducer and Activator of Transcription

Posttranslational Modifications

  • Posttranslational modifications on transcription factors are a major regulatory step.
  • Examples:
    • Phosphorylation (serine, threonine)
    • Acetylation (lysine)
    • Ubiquitination (lysine)
    • Glycosylation (serine, threonine)

Heat Shock Response

  • Regulatory feedback loop: the expression of heat shock proteins is regulated by the heat shock factors (HSF).
  • HSF is kept as a monomer in the cytoplasm by heat shock proteins, preventing their own expression.
  • Upon stress, when heat shock proteins are engaged in chaperoning other proteins, HSF1 is released from the chaperone complex and trimerizes.
  • HSF1 is then transported into the nucleus where it is hyperphosphorylated and binds to the promoter of heat shock genes.

RNA Polymerase II Pausing

  • a, Prior to heat-shock: paused Pol II, which is partially phosphorylated at Ser 5 residues of the carboxy-terminal domain, is in a complex with DSIF and NELF complexes and occupies a region between 20–40 base pairs downstream of the start site.
  • b, HSF binds to its DNA elements in response to heat shock. P-TEFb is the kinase that is critical for the maturation of paused Pol II into a productive elongation product, and it phosphorylates DSIF, NELF and the Ser 2 residues of the CTD

RNA Polymerase II Pausing: Significance

  • Heat shock loci
    • Elongation is the most important level of regulation
    • Function: Rapid response
  • Developmentally regulated genes (Drosophila)
    • Both initiation and elongation regulated
    • Function: Coordinated gene expression
  • More common than presumed for a long time
  • Not always regulated but constitutive (house-keeping genes)

Regulation of Eukaryotic Gene Expression: Summary

  • Nuclear hormone receptors represent a specific class of zinc-finger transcription factors whose activity is regulated by lipid-soluble hormones.
  • Hormone binding to nuclear receptors induces conformational changes and modifies their interaction with other proteins.
  • Inactive Type 1 nuclear hormone receptors are