transcription biology review
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Transcription Biology Review. Bios 691 – Systems Biology January 2008. Outline. Gene structure Chromatin structure & modifications Transcription apparatus Transcription factors and cofactors Elongation and termination RNA capping, splicing, and adenylation RNA processing and miRNA’s. - PowerPoint PPT PresentationTRANSCRIPT
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Transcription Biology Review
Bios 691 – Systems Biology
January 2008
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Outline
• Gene structure
• Chromatin structure & modifications
• Transcription apparatus
• Transcription factors and cofactors
• Elongation and termination
• RNA capping, splicing, and adenylation
• RNA processing and miRNA’s
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Chromosome Organization
• Mammalian chromosomes tend to fill discrete regions within the nucleus
• An elaborate network of fibrils maintains these arrangements
• RNA ‘factories’ at distinct locations do most of the transcription work
• Nucleoli are factories for rRNA
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Chromatin Structure
• Protein scaffolds anchor the DNA
• Within the scaffold there are loops
• Most transcription happens on the loops
• Much chromatin is wrapped in 30nm ‘heterochromatin’
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Fine Structure of Chromatin
• Heterochromatin – inaccessible– Bound with many proteins– Centromeres; telomeres; some other areas
• Euchromatin – accessible– Still needs to be opened
Telomeric Heterochromatin and Sirtuins Euchromatin: 30 nm & open
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DNA Packaging & Nucleosomes
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Gene Structure – Exons & Introns
Exon Size distribution
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Gene Structure – Initiation Sites
• Most (~2/3) genes have multiple promoters
• Most promoters are either ‘sharp’:– Very narrow range– Usually TATA + Inr– Often tissue specific
• or ‘broad’:– Typically 70 bp range– Rarely TATA / Inr– Often widespread
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Histones and Modifications
DNA contacts histones on their tails Histone tails can be modified
Histones can stay loose or assemble tightly
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Proteins Modify Histones
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DNA Methylation
Adding a Methyl to Cytosine
Cytosine methylation is passed on to daughter cells
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Controlling Transcription
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DNA-Binding Proteins• All proteins interact weakly
with DNA• Proteins with projecting
amino acids interact with the DNA major groove
• Hydrogen bonds stabilize position of proteins on DNA
• Proteins that line up several amino acid contacts bind strongly to specific DNA sequences
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Transcription Factor Families
• Several structures line up amino acids– Helix-turn-Helix
(Homeodomain)– Helix-loop-helix– Zinc Finger
• Mostly dimers• These families have
proliferated because of their role in attracting transcription apparatus
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Cofactors
• Frequently the effect of DNA-binding proteins depends on co-factors
• E.g. ER sits on the DNA but requires estrogen as a co-factor to function
• Myc requires Max as a co-factor to stimulate transcription
• If Max is coupled with Mad instead, the genes are repressed
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Kick-starting Pol II & Elongation• Mediator protein
bridges TF proteins and RNA Pol II
• Contains kinase domains – may phosphorylate CTD of RNA Pol II
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Initiating Transcription
TBP on a TATA Box
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RNA Polymerase II
RNA (red) copied from DNA (blue) by RNA Polymerase II
RNA Polymerase II Structure The cycle of adding nucleotides
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Terminating Transcription
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RNA Processing
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RNA Processing Steps
• Nucleus– capped, – spliced, – cleaved, – polyadenylated
• Exported• Cytoplasm
– stored– translated– degraded
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Capping mRNA
The RNA factory
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RNA Splicing
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Poly-adenylating RNA
•Poly-A Polymerase adds ~100-150 Adenines to 3’ end•After export to cytoplasm, nucleases chop off ~10-20 A’s at a bite•Nucleases compete with ribosomes for mRNA’s•When ~30 A’s left degradation speeds up
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RNA Export
• RNA has to be passed through nuclear pores to show up in the cytoplasm (where we measure it)
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Micro RNA’s
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P-Bodies• Loci where RNA accumulates and is degraded• Have their own structural proteins
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Implications for Systems Biology
• Levels of TF’s on a promoter may not predict levels of transcripts
• Rate of transcription may not predict level of mRNA in the cytoplasm
• Levels of mRNA in cytoplasm may not predict levels of protein