Download - Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters
![Page 1: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/1.jpg)
Gene regulation overviewand
Saccharomyces cerevisiae cell-type specific mating type promoters
Nate Sotuyo
Allison Suarez
![Page 2: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/2.jpg)
Transcription
Prokaryotes
![Page 3: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/3.jpg)
Overview
• (RNA)n + ribonucleoside triphosphate ⇌ (RNA)n+1 +PPi– Divalent metal ion required (Mg2+ orMn2+)
• Cytoplasm, mRNA isnot modified• 5 Steps
– Pre-initiation– Initiation– Promoter clearance– Elongation– termination
![Page 4: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/4.jpg)
DNA Synthesis comparisonSimilarities• 5’ 3’• Nucleophilic attack by 3’ OH on phosphate• Driven by hydrolysis or pyrophosphate
– Pyrophosphate orthophosphate
Differences• No Primer required• Error rate higher
![Page 5: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/5.jpg)
Pre-initiation
• RNA holoenzyme α2ββ'σω binds DNA– “slides” along double
helix
• Unwinds the DNA to form initiation bubble
![Page 6: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/6.jpg)
Initiation and promoter clearance
Initiation• RNA polymerase binds promoter (with sigma
factor)– Prinow box (-10), -35 region
• First phosphodiester bond formedPromoter clearance• Abortive initiation• CTD phosphorylation by TFIIH
![Page 7: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/7.jpg)
Elongation and Termination
Elongation• 5’3’, TU• σ factor released • TopoisomeraseII feedbackTermination• Rho-independent
– G-C hairpin followed by string of U’s
• Rho-dependent– ρ destabilizes mRNA-template interaction
![Page 8: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/8.jpg)
Review: Gene Regulation and Transcription in Eukaryotes
• Similar to gene regulation in prokaryotes, except more complex: more types of regulatory proteins and interactions with regulatory regions in DNA
• Both prokaryotes and eukaryotes have promoters– Region of DNA that is the RNA polymerase’s transcription initiation site
• Important differences in eukaryotes:• Nucleosomes, chromatin
– Chromatin remodeling
• 3 types of RNA polymerases• RNA modification
– Transcription occurs in the nucleus– Translation occurs in the cytoplasm
• Binding of DNA-binding proteins outside the promoter region
![Page 9: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/9.jpg)
Example of chromatin remodeling
• Chromatin remodeling is the changing of nucleosome position• Histones
– Core octamer, amino-terminal ends
– Covalent modification termed “histone code”
• Acetylation, deacetylation, and gene expression– Acetylation of certain histone residues can cause the histone to
slide along the DNA, no longer inhibiting a promoter region or other important DNA-protein binding sites necessary for transcription
![Page 10: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/10.jpg)
http://www1.ci.uc.pt/yss/Material/pdf_RNA%20Regulation/figurea6.jpg
Overview of transcription translation in eukaryotes
![Page 11: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/11.jpg)
Genomic Footprinting of the Promoter Regions of STE2 and
STE3 genes in the Yeast Saccharomyces cerevisiae
Brigitte Ganter, Song Tan and Timothy J. Richmond
![Page 12: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/12.jpg)
Overview
Overall goal– Develop high resolution map of the
promoter regions of STE2 and STE3 – Analyze the chromatin structure in the
promoter regions using DMS methylation, micrococcal nuclease and DNase I.
![Page 13: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/13.jpg)
Mating types review
• Three cell types– Haploid: a,α– Diploid: a/α
• Specific gene expression determined by MATa or MATα
• Three transcription regulators expressed– MATa1,MATα1,MATα2
• Other key transcription factors– MCM1, STE12, SSN6, TUP1
![Page 14: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/14.jpg)
Transcription factors
• MCM1– Activates both a and alpha– Purified vs. crude extracts (Q factors?)– a-specific genes conformational change
• STE12– Component of pheromone response pathway– Binds PRE signaling cascade
• Poor interaction unless MCM1 present
• MATα2 – Precise positioning of nucleosomes downstream STE2 UAS
elements in α cells
![Page 15: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/15.jpg)
Transcription factors cont.
• SSN6 and TUP1– Required for full repression of a-genes in
alpha cells– Mutated ssn6 resulted in alpha cells that
could mate with other alpha cells (Though not efficiently)
![Page 16: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/16.jpg)
Haploid Mating overview
STE2
STE3
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=p-box&rid=mcb.section.3752#3756
![Page 17: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/17.jpg)
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=p-box&rid=mcb.section.3752#3756
![Page 18: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/18.jpg)
Diploid Mating overview
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=p-box&rid=mcb.section.3752#3756
![Page 19: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/19.jpg)
Significant nucleosome positioning
• Contribute to transcription regulation
• Stably positioned nucleosomes STE2/ α cells– Only MCM1 bound no
stable array– TFIID binding site is
protected
• a-cells only protected in TATA region– Due to TFII binding, not
nucleosome
![Page 20: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/20.jpg)
Nucleosomal protection cont.
• STE 3 more complicated– a-cells
• MCM1 binding to P’-box on coding strand only in vitro– in vivo result consistent with each other
– alpha-cells• Concerted binding of MCM1 and MAT-alpha1
– Additional protection not detected in vitro observed on Q-box side
• Possible other factors that bind to these regions
![Page 21: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/21.jpg)
Genomic Footprinting Techniques
![Page 22: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/22.jpg)
“Conventional PCR is not immediately applicable to sequencing or footprinting because it requires two defined ends. A sequence or footprint ladder is composed of a population of related nucleic acid fragments. One end of each fragment is fixed by a primer or restriction cut and is therefore the same for all, whereas the other end is determined by variable chemical cleavage or chain termination and is therefore unique for each fragment. To apply PCR to a sequence ladder, [Mueller and Wold] introduced a simple ligation step that adds a common oligonucleotide sequence to the unique end of each member. A primer complementary to this new common sequence is then used, together with a primer complementary to the original fixed end, for simultaneous exponential amplification of all members of the sequence ladder. The procedure has high selectivity and specificity that are derived from the design of the ligation step and choice of primers. It also has high fidelity; a footprint consists of subtle differences in the starting concentrations of particular members of a sequence a sequence ladder, and these differences are reproducibly retained through amplification.”
Mueller, P.R. and Wold, B. (1989). In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science, 246, 280-286
Ligation Mediated PCR
![Page 23: Gene regulation overview and Saccharomyces cerevisiae cell-type specific mating type promoters](https://reader035.vdocument.in/reader035/viewer/2022070403/568139a1550346895da13e28/html5/thumbnails/23.jpg)
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Mueller, P.R. and Wold, B. (1989). In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science, 246, 280-286