gene regulation
DESCRIPTION
GENE REGULATION. Key control mechanism for dictating cell phenotype and 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 - PowerPoint PPT PresentationTRANSCRIPT
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GENE REGULATION
Key control mechanism for dictating cell phenotypeand function
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Two kinds of genes
• Housekeeping genes Needed for cell metabolism
• Required for nearly all cell types
• Regulated Genes Controls cell phenotype and function
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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)
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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)
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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
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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
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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.
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Pol I Transcription
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Pol I Promoter Function
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Pol III Transcription
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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
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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)
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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
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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*
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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
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Promoter Elements Function in Either Orientation
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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
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Solved DNA Interaction Motifs
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DNA Recognition
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Regulation of Transcription factor function
• Tissue specific expression of transcription factors
• Translocation of transcription factor to nucleus
• Post-transcriptional modification of transcription factors
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Steroid Hormone Receptors
- Zinc fingers- Bind as dimers
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Regulation of Steroid Hormone Receptors
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Regulation of CREB
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NF-kB Regulation
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Other Mechanisms for Regulating Gene Expression
• Regulation of translation
• Regulation of mRNA stability
• Alternative promoter usage
• Alternative Splicing
• Alternative polyadenylation
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Translational Control and RNA Stability Control
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Tissue Specific Promoter Usage
Dystrophin GeneC - CoricalM - MuscleP - PurkinjeR - RetinalCNS - Central Nervous SystemS - Schwann cellG - General
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Alternative Splicing
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Alternative Splicing - Examples