Lecture 17 Gene Regulation II Biology 2024 PDF

BIOL 23373 – General Genetics Fall 2024 Lecture 17 Gene Regulation II Announcements Exam 2 is in class on Wed., Oct. 9. Exam prep resources will be posted to Bb this week. Those with CEA accommodations need to make their appointment to take exam...

BIOL 23373 – General Genetics Fall 2024 Lecture 17 Gene Regulation II Announcements Exam 2 is in class on Wed., Oct. 9. Exam prep resources will be posted to Bb this week. Those with CEA accommodations need to make their appointment to take exam at testing center. Tutoring Tutoring @ the CORD offers 1-on-1 and small group assistance in over 100 U of A courses. Students can meet with tutors in person or online by scheduling an appointment or accessing drop-in services. Learn more about Tutoring services and book an appointment at: https://success.uark.edu/academic-initia tives/tutoring.php Corresponding Readings Chapter sections: 17.1-17.5, 18.2-18.3, 18.5 Gene Regulation in Eukaryotes Eukaryotes have some of same regulatory mechanisms as prokaryotes Activator and repressor proteins influence ability of RNA polymerase to initiate transcription Many are regulated by small effector molecules Many important differences compared to prokaryotes Genes almost always regulated individually Regulation is more complex and involves a combination of mechanisms Gene Regulation in Eukaryotes - Overview 6 Features of Most Eukaryotic Promoters TATA box (5’ – TATAAAA – 3‘) -25 bp upstream from transcriptional start site Transcriptional start site Where transcription begins (+1) +1 site with TATA box forms core promoter Proximal promoter elements Usually upstream of TATA box Recognized by regulatory proteins (TFs) that control initiation of transcription TATA box Transcriptional 5′ start site 3′ Coding-strand sequences: TATAAA Py2C A Py5 –100 –50 –25 +1 Structural gene Common location for Core promoter Transcription regulatory elements Transcription Initiation - Eukaryotes Three things are needed to initiate transcription: 1. An RNA polymerase II 2. 5 general transcription factors (GTFs) 3. Large protein complex called mediator GTFs TATA box Preinitiation complex Transcriptional start site RNA polymerase II Regulation of Transcription Initiation GTFs and RNA polymerase II must come together at core promoter (TATA box) before transcription can be initiated Mediator is composed of several proteins Partially wraps around GTFs and RNA polymerase II Mediates interactions with activators or repressors that bind to enhancers or silencers in regulatory regions of DNA Controls rate at which RNA polymerase begins transcription Enhancer Mediator Preinitiation complex Regulation of Transcription Initiation Activators – proteins that bind to regulatory DNA regions and activate transcription Repressors – proteins that bind to regulatory DNA regions and repress transcription Regulate rate of transcription of a gene sometimes nearby (proximal promoter elements) and sometimes far away (enhancers and silencers) Most do not interact directly with RNA polymerase II, but interact with proteins bound to promoter and/or induce bends in DNA Regulation of Transcription Initiation Three ways to control RNA polymerase II: 1. Activators and repressors regulate RNA polymerase II by binding to regulatory regions 2. Regulate RNA polymerase II via mediator 3. Recruit proteins that influence DNA compaction Regulation of Transcription Initiation Activators and repressors regulate RNA polymerase 1 An activator binds to a proximal promoter element. II by binding to regulatory Activator regions Activators bind enhancers Proximal promoter element and proximal promoter 2 The activator enhances the elements and interact with ability of a GTF called TFIID to bind to the TATA box. TFs bound to gene promoters, enhancing TFIID transcription (+ control) TATA box Repressors bind silencer 3 TFIID promotes the assembly of the preinitiation region that induces bends complex. in DNA that interfere with TFIID TF assembly, silencing Preinitiation complex transcription (- control) TATA box Regulation of Transcription Initiation Regulate RNA Enhancer polymerase II via mediator Mediator Preinitiation complex Activators stimulate mediator by allowing faster initiation Repressors inhibit mediator so RNA polymerase II cannot Coactivator progress to elongation Enhancer Activator Regulation of Transcription Initiation Insulators prevent enhancer activity and can redirect enhancer to a different gene promoter Regulation of Transcription Initiation Recruit proteins that influence DNA compaction Chromatin condensation plays a role in regulating gene expression by controlling access to DNA Access to the DNA is allowed in the loosely packed open conformation (euchromatin) Transcription is difficult or impossible in the closed conformation of tightly packed chromatin (heterochromatin) Histone Modification Different amino acids in the amino (N) terminal ac tails of histone proteins Lys 5 ac Amino terminal tail p Lys p ac Ser 15 ac are subject to several Ser ac ac 10 Lys 20 Lys types of covalent Lys Lys 15 5 10 20 H2B modification Globular domain H2A Addition of acetyl, methyl, phosphate groups are p ac Lys 10 Lys ac common Arg m Ser m ac Arg Lys 5 15 Lys ac m Pattern of modifications m m Lys Lys ac ac 20 Arg Lys H4 5 m Lys 15 (histone code) affects ac p 20 Lys Ser H3 degree of chromatin 10 compaction Histone Modification cont. Histone acetyltransferase attaches acetyl groups to histone proteins so they don’t bind DNA as tightly Histone deacetylases remove acetyl groups so histones bind DNA more tightly Chromatin Remodeling ATP-dependent (a) Change in nucleosome position chromatin remodeling or enzymes also loosen DNA compaction Chromatin-remodeling complex Changes the spacing (not shown) changes the relative or of nucleosomes over a positions of a few nucleosomes. long distance. Change position of (b) Histone eviction nucleosome or spacing between Remove some histones Histone octamers are removed by a chromatin-remodeling complex. Replace standard histones (c) Replacement with variant histones with variant histones Standard histones are replaced with variant histones by a chromatin-remodeling complex. DNA Methylation DNA methylase attaches methyl (-CH ) groups to cytosine 3 Usually inhibits transcription Common in some eukaryotes but not all In mammals, 5% of DNA is methylated CpG islands near promoters in vertebrates and plants Cytosine and guanine connected by phosphodiester bonds Unmethylated CpG islands are correlated with active genes Repressed genes contain methylated CpG islands Gene Regulation in Eukaryotes Methylation can inhibit transcription two ways: 1. Methylation of CpG islands may prevent an activator from binding to an enhancer element 2. Converting chromatin from an open to a closed conformation Methyl-CpG-binding proteins bind to methylated sequences and recruit proteins that condense the chromatin Micro RNAs & small interfering RNA miRNAs and siRNAs are small RNA molecules that silence the expression of mRNAs (i.e., prevent from being translated) Widely found in animals and plants Important mechanism of mRNA silencing, also called RNA interference (RNAi) mRNA Silencing Synthesized as pre-miRNA Pre-miRNA 5′ or pre-siRNA 3′ 1 The double-stranded region of Cut by RNA endonuclease a pre-miRNA (shown here) or a pre-siRNA (not shown) is cut by dicer and releases a 22-bp RNA. called dicer to release 5′ miRNA or siRNA 3′ Associates with cellular 2 The double-stranded miRNA or siRNA associates with proteins to form RISC. One of the RNA strands is degraded. proteins to become 3′ RNA-induced silencing 5′ RISC complex (RISC) 3 RISC binds to a cellular mRNA Upon binding mRNA, either due to complementarity with the miRNA or siRNA within RISC. Cellular mRNA mRNA is degraded, or 5′ 3′ RISC RISC inhibits translation OR siRNA miRNA Either way, mRNA is silenced The mRNA is Translation is degraded (high inhibited (low complementarity complementarity of bases). of bases). X