MODULE 3: TRANSCRIPTION PART II

Lesson Plan: Title Transcription Part II: What happens to the initial (premRNA) transcript made by RNA pol II? Objectives  Explain how the transcript generated by RNA polymerase II (the pre-mRNA) is processed to become mature mRNA, using the sequence signals identified in Module 2.  Use the genome browser to analyze the relationships among: 1. pre-mRNA 2. 5’ capping 3. 3’ polyadenylation 4. splicing 5. mRNA Pre-requisites  Modules 1 and 2  Define pre-mRNA as the RNA that results from the process of transcription; this initial transcript includes exons and introns Order  Warm Up Discussion  Investigation Homework None Class instruction  Discuss the question: What happens to the initial (premRNA) transcript made by RNA pol II? Does it leave the nucleus ‘as is’? Or do changes have to occur? (Hint: introns vs. exons) (Discuss with a partner then as a class).  Mini-presentation illustrating that during pre-mRNA processing, three events occur: 1. 5’ capping, 6. 3’ polyadenylation 7. splicing out of introns  Work through the genome browser investigation, with pauses to discuss the answers to the questions.  Conclude with emphasis on main points:  Pre-mRNA is processed using 3 steps: 1. 5’ capping, 8. 3’ polyadenylation, 9. removal of introns through splicing (via spliceosome) INTRODUCTION Module Three: Transcription Part Two – BIO Genetics Online School Due to COVID-19 UNC Spring 2020 1 Last update: 07/28/2019 In Module 2, you identified the transcription start site (TSS) for the A isoform of the tra gene (tra-RA). In this module, we will explore each of the three steps of pre-mRNA processing. SETTING UP OUR BROWSER PAGE (REVIEW): 1. Open a new web browser window and go to the UCSC Genome Brower Mirror site at contig1 project in the D. melanogaster "July 2014 (Gene)" assembly. 1. As you may remember from Module 1, contig1 is derived from chr3L in the D. melanogaster genome. This contig contains three different genes (CG32165, spd-2, and tra). Enter "contig1:9,500-11,000" into the "enter position or search terms" textbox and then click on the "go” button to navigate to the genomic region surrounding the tra gene. 2. Because the Genome Browser remembers your previous display settings, you should click on the "default tracks" button to reset the display to the default settings. Change the display mode for the "Base Position" track to "full" and verify that the "FlyBase Genes" track is set to "pack". Click on the "refresh" button. 3. Scroll down to the "RNA Seq Tracks" section and then click on the "RNA-Seq Coverage" link. Change the track display settings to the following, as we did in Module 2: 4. Change the "Display mode" field to "full" 5. Select the "Data view scaling" field to "use vertical viewing range setting" 6. Change the "max" field under "Vertical viewing range" to 37 7. Under the "List subtracks" section, select BOTH the "Adult Females" and the “Adult Males” (Select the check box next to subtrack to turn the subtrack on.) 8. Click on the "Submit" button. Verify that the RNA-Seq Coverage track on the browser page is set to “full.” INVESTIGATION: MRNA PROCESSING The processing of pre-mRNA into mRNA involves three key steps (Figure 1):  The addition of a 5’ cap  The addition of a 3’ poly(A) tail  The removal of introns through splicing Removal of the introns during this process results in adjacent exons being brought together in the final mRNA message. Module Three: Transcription Part Two – BIO Genetics Online School Due to COVID-19