Module 2 Instructor Resources =============================== .. rubric:: Instructor Resources for Module 2: Transcription Part I: From DNA sequence to transcription unit :class: header1 Cover Page ------------------------------- Submission Details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Submitter: | Alexa Sawa | | | (asawa@collegeofthedesert.edu) | +-----------------------------------+-----------------------------------+ | Submission timestamp: | 2019/07/31 1:35:52 PM EST | +-----------------------------------+-----------------------------------+ | Authors: | - Maria S. Santisteban, | | | University of North Carolina - | | | Pembroke | | | | | | - Alexa Sawa, College of the | | | Desert | +-----------------------------------+-----------------------------------+ | Corresponding author: | Alexa Sawa | | | (asawa@collegeofthedesert.edu) | +-----------------------------------+-----------------------------------+ Lesson Overview ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Lesson abstract: | This module will introduce you to | | | the use of the Genome Browser to | | | illustrate the process of | | | transcription and help you | | | identify regulatory elements, | | | using the *Drosophila | | | melanogaster* *transformer* | | | (*tra*) gene as an example. You | | | will use the UCSC Genome Browser | | | Mirror developed by the Genome | | | Education Partnership (GEP), | | | which contains RNA expression | | | data, to identify the different | | | parts of the gene that give rise | | | to pre-mRNA through | | | transcription. | +-----------------------------------+-----------------------------------+ | Lesson keywords: | - Genome Browser | | | | | | - Transcription Initiation | | | | | | - Transcription Start Site | | | | | | - Transcription Termination | | | Signal | +-----------------------------------+-----------------------------------+ | Organism(s) that are the focus of | *Drosophila melanogaster* | | this lesson: | | +-----------------------------------+-----------------------------------+ | Type(s) of student learning | Short answer formative and | | assessments: | summative questions | +-----------------------------------+-----------------------------------+ | Websites and online databases | GEP UCSC Genome Browser | | used: | (http://gander.wustl.edu) | +-----------------------------------+-----------------------------------+ | Resources in addition to the | YouTube videos | | lesson instructions | | +-----------------------------------+-----------------------------------+ Learning Topics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Topics in scientific fields: | - Bioinformatics | | | | | | - Genomics | | | | | | - Molecular Biology | +-----------------------------------+-----------------------------------+ | Topics in mathematics or | - None | | statistics: | | +-----------------------------------+-----------------------------------+ | Topics in bioinformatics or | - Data visualization | | data science: | | +-----------------------------------+-----------------------------------+ Student Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Recommended prior course work: | - High school level biology | +-----------------------------------+-----------------------------------+ | Recommended computer skills: | Basic: Familiarity with web | | | browsers, word processing | +-----------------------------------+-----------------------------------+ Instructor Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Recommended computer skills: | Basic: Familiarity with web | | | browsers, word processing | +-----------------------------------+-----------------------------------+ | Instructional requirements: | Basic Computer Lab (Access to | | | laptops/desktops, no large memory | | | or CPU requirements) | +-----------------------------------+-----------------------------------+ Implementation Recommendations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Instructional time required: | 1 class period or less | +-----------------------------------+-----------------------------------+ | Students work as individuals or | Either individual or team work is | | teams? | possible | +-----------------------------------+-----------------------------------+ | Number of students in a class: | 10-25 students (assume no TAs and | | | one computer for each student) | +-----------------------------------+-----------------------------------+ Accessibility ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Available languages: | English | +-----------------------------------+-----------------------------------+ | Additional materials for students | None | | with disabilities: | | +-----------------------------------+-----------------------------------+ .. meta:: :keywords: Genome Browser, Transcription Initiation, Transcription Start Site, Transcription Termination Signal Lesson Plan ------------------------------- Title ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Transcription Part I: From DNA sequence to transcription unit Objectives ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Describe how a primary transcript (pre-mRNA) can be synthesized using a DNA molecule as the template. - Explain the importance of the 5' and 3' regions of the gene for initiation and termination of transcription by RNA polymerase II. - Identify the beginning and end of a transcript using the capabilities of the genome browser (RNA-Seq, Short Match). - Use the genome browser to visualize a given transcriptional unit (:ref:`Investigation 1`). - Predict the locations of exons and introns using RNA seq reads (:ref:`Investigation 1`). - Predict TSS regions using RNA-Seq data (:ref:`Investigation 2`). - Identify putative TSS sites using modENCODE data (:ref:`Investigation 2`). - Determine the most likely TSS coordinate by evaluating multiple lines of evidence in the genome browser (:ref:`Investigation 2`). - Predict the approximate end of a transcription unit using RNA-seq data (:ref:`Investigation 3`). - Identify the most likely termination signal using the genome browser (:ref:`Investigation 3`). Pre-requisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Structure of a gene (:ref:`module1/module1_exercise:Module 1`) Order ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Describe regulatory signals: Transcription Start Site (TSS), and AATAAA sequence (site of transcript cleavage for termination) - Investigation 1: Students find the transcript for tra-RA using the genome browser and identify the transcription unit - Investigation 2: Students map the 5' end of the transcript - Investigation 3: Students map the 3' end of the transcript - Review pairing of DNA bases Homework ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - None Class Instruction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Discuss the questions: What is transcription? What cellular proteins are required for transcription? How does it work mechanistically? What is/are the products of transcription? (students discuss in pairs, then as a class) - Work through the genome browser investigation, then identify where transcription starts and ends for the *tra* gene. How long is the pre-mRNA? - Conclude by challenging students to think about these questions: - How important is it for RNA polymerase II to recognize the promoter sequence? - Do you think it is possible for a gene to have more than one transcription start site? How would RNA polymerase II know which one to choose? When would it make a difference in the protein product, and when not? Associated Videos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - `RNA Seq and TopHat video `_ - `Short Match video `_