Module 6 Instructor Resources =============================== .. rubric:: Instructor Resources for Module 6: Alternative splicing :class: header1 Cover Page ------------------------------- Submission Details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Submitter: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ | Submission timestamp: | 2019/12/16 3:40:05 PM CST | +-----------------------------------+-----------------------------------+ | Author: | Leocadia Paliulis, | | | Bucknell University | +-----------------------------------+-----------------------------------+ | Corresponding author: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ Lesson Overview ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Lesson abstract: | Many genes have exons that can be | | | linked together in more than one | | | way to produce a variety of | | | different (though related) | | | transcripts. In this lesson, | | | students will examine how | | | alternative splicing of a gene | | | can lead to different mRNAs | | | and how alternative splicing | | | can lead to the production | | | of different polypeptides | | | and result in drastic changes | | | in phenotype. | +-----------------------------------+-----------------------------------+ | Lesson keywords: | - Alternative Splicing | | | | | | - Exon | | | | | | - Intron | | | | | | - Messenger RNA | | | | +-----------------------------------+-----------------------------------+ | Organism(s) that are the focus of | None | | this lesson: | | +-----------------------------------+-----------------------------------+ | Type(s) of student learning | Short answer formative questions | | assessments: | | +-----------------------------------+-----------------------------------+ | 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: | - Genetics | | | | | | - Genomics | | | | | | - Molecular Biology | +-----------------------------------+-----------------------------------+ | Topics in mathematics or | - None | | statistics: | | +-----------------------------------+-----------------------------------+ | Topics in bioinformatics or | - Similarity searches (BLAST, | | data science: | Multiple Sequence Alignment) | | | | | | - Data visualization | +-----------------------------------+-----------------------------------+ 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: | More than 50 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: Alternative Splicing, Exon, Intron, Messenger RNA Lesson Plan ------------------------------- Title ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Alternative splicing Objectives ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Demonstrate how alternative splicing of a gene can lead to different mRNAs. - Show how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype. - Identify how alternative splicing of a gene can lead to different mRNAs (:ref:`Investigation 1`). - Identify how alternative splicing can lead to the production of different polypeptides (:ref:`Investigation 1`). - Describe how alternative splicing producing different polypeptides might result in changes in phenotype (:ref:`Investigation 2`). Pre-requisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`module1/module1_exercise:Module 1` - :ref:`module2/module2_exercise:Module 2` - :ref:`module3/module3_exercise:Module 3` - :ref:`module4/module4_exercise:Module 4` - :ref:`module5/module5_exercise:Module 5` Order ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Introduce students to tra-RB, a second isoform of *tra*. - Investigation 1 - Investigation 2 - Discussion Homework ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - None included. Students could analyze a second gene on the browser using the work they have done on *tra* as a template. Class Instruction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Introduce tra-RB - Discuss differences between tra-RB and tra-RA. Reinforce concept of isoform. - Investigation 1: How can there be different mRNAs encoded in the same gene? - Investigation 2: Examine the *tra* polypeptides by looking at the three possible reading frames. Review concept of reading frame and introduce phase if not previously introduced. Students will construct a gene model for tra-RB, using sequence information, and RNA-Seq data as evidence. - Discussion of gene models/wrap-up Associated Videos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - `Genes and Isoforms video `_ - `Splicing and Phase video `_ - `RNA Seq and TopHat video `_