Download - GENE REGULATION
GENE REGULATION
Key control mechanism for dictating cell phenotypeand function
Two kinds of genes
• Housekeeping genes Needed for cell metabolism
• Required for nearly all cell types
• Regulated Genes Controls cell phenotype and function
Housekeeping Genes
• Pol I transcripts Ribosomal RNA genes (18S, 5.8S, and 28s rRNAs)
• Some Pol II transcripts e.g. Structural Proteins such as Actin
• Pol III transcripts 5S rRNA (ribosomal RNA) tRNAs (translation) snRNA (splicing)
Regulated Genes
• Pol II transcripts For e.g.
• Transcription factors• Cytokines• Kinases• Phosphatases• Ubiquitinases• etc., etc., etc.
• Pol III transcripts• miRNAs (siRNA like molecules that inhibit specific gene
expression)
Multiple Mechanisms of Gene Regulation
• Transcription• Initiation• Elongation
• Post-transcription RNA level
• RNA processing (alternative splicing, polyadenylation)• RNA transport• mRNA stability
Protein level• Translation initiation• Protein transport• Protein stability• Protein processing
• Epigenetic
Transcription
• Housekeeping Pol I transcription
• Ribosomal RNA genes (18S, 5.8S, and 28s rRNAs) Pol III transcription
• 5S rRNA (ribosomal RNA)• tRNAs (translation)• snRNA (splicing)• miRNAs (control of gene regulation)
• Regulated Pol II transcription
• Protein encoding transcripts
Pol I Transcription
• 18S, 5.8S, and 28S RNA genes transcribed as one 13 kb transcript.
• This transcript is subsequently processed (cleaved) to give individual 18S, 5.8S and 28S rRNAs.
• On chromosome, 13 kb transcription unit (along with a 27kb intergenic region) is repeated 30-40 times Helps provide higher expression of these
housekeeping gene products.
Pol I Transcription
Pol I Promoter Function
Pol III Transcription
Pol II Transcription
• Three types of cis elements: Core promoter elements (-45 to +40)
• Binds basal factors required for initiation and elongation.
Proximal promoter elements (-1kb to +200)• Binds regulatory transcription factors involved in activating or
suppressing basal transcription
Enhancers/Silencers (far up or downstream)• Binds regulatory transcription factors involved in activating or
suppressing basal transcription
Pol II Transcription
Core promoter function - facilitates transcription initiation and elongation- Pol II - Catalyzes RNA synthesis- TFIID - Provides scaffold for general transcription factors (TBP is at core of this complex and is associated with TAFs (TBP Associated Factors)- TFIIB - Binds TBP, selects start site and recruits Pol II- TFIIA - Stabilizes binding of TFIIB and TBP to promoter- TFIIF - Binds TFIIB and Pol II- TFIIE - Recruits TFIIH- TFIIH - Helicase and kinase (Unwinds DNA phosphorylates C-terminus of Pol II)
Pol II Transcription
Proximal promoter function - regulates core promoter functionProximal promoter binding factors activate transcription through multiple mechanisms:
- Recruit basal factors- Recruit coactivators and mediators (for example, CBP, p300, p/caf, etc)
- helps recruit basal factors- contain or recruit histone acetyl-transferases- recruit histone methyl-transferases- contain or recruit ATP dependent chromatin remodeling enzymes- helps form stable complexes between multiple proximal transcription factors
Regulation of promoter function by proximal promoter factors and enhancer/silencers
• Recruitment of basal factors*
• Recruitment of histone acetylases
• Recruitment of histone methylases
• Recruitment of ATP dependent chromatin remodeling complexes*
Histone modification
- Histone acetylation - generally associated with promoter activation (histone deacetyleses (HDACs) inhibit transcription
- Neutralizes basic charges on lysines and arginine residues - relaxes nucleosome- Allows direct binding of activating proteins to promoter bound histones
- Histone methylation- Arginine methylation associated with promoter activation- Lysine methylation associated with promoter inactivation
Promoter Elements Function in Either Orientation
Pol II Promoters Contain Multiple Transcription Factor Binding Sites
Human Insulin Promoter - red, specific for pancreatic beta cells
Reasons?- Coactivator interactions stabilized by binding to multiple transcription factors at the same time- Some factors cannot carry out all steps required for promoter activation (SP1)- Some elements play a role in signaling activation by different effectors
Solved DNA Interaction Motifs
DNA Recognition
Regulation of Transcription factor function
• Tissue specific expression of transcription factors
• Translocation of transcription factor to nucleus
• Post-transcriptional modification of transcription factors
Steroid Hormone Receptors
- Zinc fingers- Bind as dimers
Regulation of Steroid Hormone Receptors
Regulation of CREB
NF-kB Regulation
Other Mechanisms for Regulating Gene Expression
• Regulation of translation
• Regulation of mRNA stability
• Alternative promoter usage
• Alternative Splicing
• Alternative polyadenylation
Translational Control and RNA Stability Control
Tissue Specific Promoter Usage
Dystrophin GeneC - CoricalM - MuscleP - PurkinjeR - RetinalCNS - Central Nervous SystemS - Schwann cellG - General
Alternative Splicing
Alternative Splicing - Examples