* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Transcription Biology Review
Cre-Lox recombination wikipedia , lookup
Genetic code wikipedia , lookup
Biochemistry wikipedia , lookup
Molecular evolution wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Gene regulatory network wikipedia , lookup
RNA interference wikipedia , lookup
List of types of proteins wikipedia , lookup
Histone acetylation and deacetylation wikipedia , lookup
Transcription factor wikipedia , lookup
Biosynthesis wikipedia , lookup
Non-coding DNA wikipedia , lookup
Two-hybrid screening wikipedia , lookup
Messenger RNA wikipedia , lookup
Polyadenylation wikipedia , lookup
Promoter (genetics) wikipedia , lookup
RNA silencing wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Silencer (genetics) wikipedia , lookup
Non-coding RNA wikipedia , lookup
Eukaryotic transcription wikipedia , lookup
Gene expression wikipedia , lookup
RNA polymerase II holoenzyme wikipedia , lookup
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 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 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’ 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 DNA Packaging & Nucleosomes Gene Structure – Exons & Introns Exon Size distribution 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 Histones and Modifications DNA contacts histones on their tails Histone tails can be modified Histones can stay loose or assemble tightly Proteins Modify Histones DNA Methylation Adding a Methyl to Cytosine Cytosine methylation is passed on to daughter cells Controlling Transcription 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 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 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 cofactor to stimulate transcription • If Max is coupled with Mad instead, the genes are repressed Kick-starting Pol II & Elongation • Mediator protein bridges TF proteins and RNA Pol II • Contains kinase domains – may phosphorylate CTD of RNA Pol II Initiating Transcription TBP on a TATA Box RNA Polymerase II RNA Polymerase II Structure RNA (red) copied from DNA (blue) by RNA Polymerase II The cycle of adding nucleotides Terminating Transcription RNA Processing RNA Processing Steps • Nucleus – – – – capped, spliced, cleaved, polyadenylated • Exported • Cytoplasm – stored – translated – degraded Capping mRNA The RNA factory RNA Splicing Poly-adenylating RNA •Poly-A Polymerase adds ~100150 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 RNA Export • RNA has to be passed through nuclear pores to show up in the cytoplasm (where we measure it) Micro RNA’s P-Bodies • Loci where RNA accumulates and is degraded • Have their own structural proteins 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