MODULE: MODULE NUMBER: JACS CODE: STAGE / YEAR: CREDITS: ORGANISER: PROGRAMME COMMITTEE: VERSION: TERMS TAUGHT: PREREQUISITES: RECOMMENDATIONS:
Eukaryotic gene expression BIO00042I C440 2 10 Prof Bob White BCH October 2014 Spring/Summer 2016 BIO00007C Genetics tba SUMMARY: This module will examine the molecular processes involved in expression of genetic information in eukaryotic cells and how these processes are regulated, including transcription, splicing, translation and subsequent events such as post­translational modification that control the activity of the fully functional gene product. The module will also feature the global analysis of gene expression at the level of RNA (transcriptomics) and protein (proteomics). LEARNING OUTCOMES: · How core methods are used for analysing gene expression and function · An understanding of how eukaryotic gene expression is regulated at many different levels · The importance of chromatin structure and chromatin modifications in control of transcription · How transcription initiation is controlled by cis­ and trans­acting factors · The role that RNA processing plays in modulating gene expression · The role of non­coding RNAs in controlling gene expression · The generation of protein diversity through alternative splicing and RNA editing · How mRNAs are exported from the nucleus and localized in the cytoplasm · How proteins are generated by translation and subsequently modified for biological activity. · The importance of mRNA and protein stability in gene expression and how these macromolecules are degraded SYNOPSIS OF TEACHING: Event Durati
on (Hrs) Topic Staff Room type Timin
g Lecture 1 1 DNA to RNA to Protein. How is genetic information transformed into functional Bob White Lecture room First lecture information in eukaryotic cells and how does this compare with prokaryotes. An introductory overview of the multiple control points of eukaryotic gene expression. of Spring Term Lecture 2 1 Chromatin structure. How is naked DNA packaged into chromosomes? The role of histones in this process and the effect of histone modifications on chromatin structure and template accessibility. An introduction to chromatin assembly and the importance of chromatin re­modeling enzymes. Set Chong Lecture room Lecture 3 1 Transcription Initiation 1. Exploring the structure, composition and role of RNA polymerases in transcription of eukaryotic genes with emphasis on RNA polymerase II (RNAPII). How does RNAPII initiate transcription and what are basal transcription factors? Introduction to some basic techniques used in studying transcription and transcription factors using some classic examples. Set Chong Lecture room Lecture 4 1 Transcription Initiation 2. What is the difference between basal and regulated transcription? How are promoters modular? How is initiation of transcription from some RNAPII promoters regulated? Further explanation of some basic techniques used in studying regulation of transcription and transcription factors using some classic examples. Set Chong Lecture room Lecture 5 1 Transcription Initiation 3, Elongation and Termination. More on transcription initiation. Brief summary of how RNAP processes and elongates nascent RNA and how it terminates transcription to result in the correct message. What are some of the factors involved? Set Chong Lecture room Lecture 6 1 Nuclear Processing Events. The mechanism of co­transcriptional RNA Louise Jones Lecture room modifications: capping, polyadenylation and splicing. Splice site choice. Lecture 7 1 Alternative splicing and RNA editing. Processes that can increase the protein coding capacity of eukaryotic cells. Mechanism of alternative splicing using specific examples. Mechanism of RNA editing with specific examples. Louise Jones Lecture room Lecture 8 1 Nuclear export, cytoplasmic localisation Louise and RNA decay. How is mRNA exported Jones from the nucleus. Mechanism and significance of specific mRNA localisation in the cytoplasm. Pathways of mRNA decay with an emphasis on quality control mechanisms. Lecture room Lecture 9 1 Non­coding regulatory RNAs. How RNAs can regulate gene expression by directing mRNA cleavage, inhibition of translation or chromatin modifications. Louise Jones Lecture room Lecture 10 1 Translation in eukaryotes. The ribosome, translation factors and their function. Bob White Lecture room Lecture 11 1 Translation –regulation. What are the cis­ and trans­acting factors that regulate eukaryotic translation? A range of examples will be discussed. Bob White Lecture room Lecture 12 1 Post­translational modifications, protein secretion and degradation. How are proteins modified after synthesis and how are these processes regulated? Bob White Lecture room Lecture 13 1 The big picture: genes to proteins. How do the complexities of gene expression determine the global expression patterns of RNA and proteins. Use of transcriptomics and proteomics, specific examples and applications. Bob White Lecture room Practical 1a 3 Nuclear Extraction from HeLa Cells Set Chong, White Biolab 1 Spring term after Extraction of histones and analysis by protein gel electrophoresis. Use of micrococcal nuclease to reveal nucleosome spacing Nuclear Extraction from HeLa Cells (requires fume hoods) lecture 1 Set Chong, White Biolab 1 (requires fume hoods) After Practi
cal 1a same day Practical 1b 3 Workshop 1 3 Data analysis and feedback session on Practicals 1 Set Chong, Bob White Biolabs After Practi
cal 1 Workshop 2 2 Supported learning problem solving workshop Set Chong Biolabs After works
hop 1 Workshop 3 2 Supported learning problem solving workshop Louise Jones Biolabs Summ
er term Workshop 4 2 Supported learning problem solving workshop Set Chong, Louise Jones, Bob White Biolabs Summ
er term Extraction of histones and analysis by protein gel electrophoresis. Use of micrococcal nuclease to reveal nucleosome spacing continued.** KEY TEXTS​
: These are available in EARL which is accessible through the VLE module site. ASSESSMENT​
: Formative: Workshops. Past papers available for self­assessment. Formative questions on the VLE. Summative:​
Practical assessment 2 – laboratory report submitted spring term, weighted 20% of module mark 1 hour closed examination in summer assessment period, weighted 80% of module mark. Short answer and problem questions. Re­assessment:​
1 hour closed examination in August resit period Practical work is not re­assessable if you missed the practical sessions. DEMONSTRATING REQUIREMENTS: ​
Demonstrators will need to attend both practicals and workshop1 (data analysis for practicals). MAXIMUM NUMBERS:​
to capacity of Lecture theatre, biolabs STUDENT WORKLOAD:​
students’ ​
workload totalling 100 hours per 10 credit module Lectures: 13 Workshops: 3 Supported learning sessions
6 Practicals: 6 Tutorials Total Contact hours: 28 Assessments (formative and summative): 1 Private study: 71