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Feedback assignment #1 due Monday, 5 p.m. Did anybody call home? Please pick a trait and “survey” your biological family [this is NOT to be turned in; nor will I CALL ON anyone to share!] CALL YOUR RELATIVES!! Cleft chin Straight hair line or “Widow’s Peak” Attached or unattached ea...

Feedback assignment #1 due Monday, 5 p.m. Did anybody call home? Please pick a trait and “survey” your biological family [this is NOT to be turned in; nor will I CALL ON anyone to share!] CALL YOUR RELATIVES!! Cleft chin Straight hair line or “Widow’s Peak” Attached or unattached earlobe ANYTHING ELSE that’s distinctive about you. CASE #1: IN CLASS Welcome to Genetics! Let’s have a look at the incredible molecular machines that “read” DNA https://youtu.be/7Hk9jct2ozY?si=CWPOKRDBHy2Kxg0S Eukaryotic gene regulation Transcription and translation eukaryotes vs prokaryotes The Central Dogma applies to both We’ll focus on Pol2, in eukaryotes How genes are represented by convention Consensus sequence maps  TATAAA box: 6-10 nuc sequence, binding initiating protein TATA Binding Protein (TBP) Assembly of RNA pol II on the core promoter TFIID complex, includes TATA BINDING PROTEIN (TBP) Genes that are highly regulated show RNApol II pausing : the complex await some signal before starting to run  TRANSCRIPTI ON SPECIFICITY Transcr Activator Enhancer (cis) (trans) Most genes have TATA boxes, that bind to “basal transcription factors”. So what makes them specific? Transcription in eukaryotes: https://youtu.be/SMtWvDbfHLo?si=dCOtQeDZhRDW9Y5R  C. elegans: 13 TF regulating the eat- 4 gene: Combinatorial regulation TF bind to “enhancers” and “silencers” in the “cis-regulatory module”. At least 13 enhancers/silencers Data suggests genes in mammals have an average of 50 regulatory elements We are incredibly complex critters, requiring incredibly complex gene regulation! Estimate is 50 regulatory elements (Enhancers/Silencers mostly) per gene, or a million total!) We’ll go back to this point throught the course…. It’s amazing!  Genes have a modular structure! Reporter genes! GFP CRM (cis-regulatory module): Enhancers  GFP LUCIFERASE lacZ  Altering cis-regulatory- module Orthologs in 3 different species Functional genomics: Mess with the regulatory regions! Dramatic changes when CRM of hox genes are altered “Gain of function” mutation Expressing gene for ‘leg’ where The antenna are normally made! Pattern formation  Altered expression driving evolutionary change Hox-C6 in vertebrates stimulates Thoracic vertebrae, which have have ribs What would you see in a mouse that overexpresses Hox- C6, more anteriorly, in vertebrae? Eliminates? TFs have at least 2 domains: Activation/interaction (typically have hydrophobic and negatively charged areas), and DNA binding 3 Modifications to create mRNA Promoter 5’UTR  RNA Processing 5’ CAP: Guanosine, with a 5’-5’ linkage Added even before transcription finished. Protects 5’ end; transport; binds ribosomes. Polyadenylation/Termination site: AAUAAA sequence; 10-35 N afterwards, cleaved. Poly A tail: 3’; up to 250 A nucleotides post-transcriptionally https://en.wikipedia.org/wiki/Five-prime_cap#/ media/File:5%27_cap_structure.png In absence, transcripts quickly degraded. Initial transcript is much larger than the final mRNA: “pre-mRNA” Collection of “pre-mRNA” or “heterogeneous nuclear RNA” [hnRNA] Alternative splicing 85% of mammalian genes have alternative splicing!  Consencus Sequence: Within Introns: GU on 5’ end of intron; AG on 3’ Spliceosome has protein and snRNA components * Actual mechanism not important for us. Spliceosome 60S; about the size of a ribosome subunit! Uses snRNAs: 100-200 bp, assist in splicing snRNPs Noncoding RNAs Exome 2% of genome that is protein coding 85% of mutations that affect our health Questions you should be able to answer 12.1-3, 4a, 5, 6, 9-13, 18a,b, 19