Module 4 Instructor Resources =============================== .. rubric:: Instructor Resources for Module 4: Removal of introns from pre-mRNA by splicing :class: header1 Cover Page ------------------------------- Submission Details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Submitter: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ | Submission timestamp: | 2019/12/16 3:29:24 PM CST | +-----------------------------------+-----------------------------------+ | Author: | Meg Laakso, Eastern University | +-----------------------------------+-----------------------------------+ | Corresponding author: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ Lesson Overview ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Lesson abstract: | All RNAs in the cell are | | | collectively known as the | | | "transcriptome," as almost | | | all RNA is produced by | | | transcription from a DNA | | | template. (In some cases, RNA is | | | made from an RNA template.) The | | | transcriptome includes messenger | | | RNAs, ribosomal RNAs, transfer | | | RNAs, and other RNAs that have | | | specialized functions in the | | | cell. Here, we will investigate | | | how mRNA specifically is | | | modified. Students will learn to | | | identify splice donor and | | | acceptor sites that are best | | | supported by RNA-Seq and TopHat | | | splice junction predictions and | | | use the canonical splice donor | | | and splice acceptor sequences to | | | identify intron-exon boundaries. | +-----------------------------------+-----------------------------------+ | Lesson keywords: | - Exon | | | | | | - Intron | | | | | | - Splicing | | | | | | - RNA Maturation | | | | +-----------------------------------+-----------------------------------+ | 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 | +-----------------------------------+-----------------------------------+ | 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: Exon, Intron, Splicing, RNA Maturation Lesson Plan ------------------------------- Title ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Removal of introns from messenger RNA by splicing Objectives ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Identify splice donor and acceptor sites that are best supported by RNA-Seq and TopHat splice junction predictions. - Utilize the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries. - Predict the location of the transcription start site and the number of exons and introns in a gene using RNA Seq evidence tracks (:ref:`Investigation 1`). - Identify splice donor and acceptor sites using the genome browser (:ref:`Investigation 2`). Pre-requisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`module1/module1_exercise:Module 1` - :ref:`module2/module2_exercise:Module 2` - :ref:`module3/module3_exercise:Module 3` Order ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Review mRNA processing; Investigation 1 - Define isoform - Introduce consensus sequences; Investigation 2 - Discuss pre-mRNA vs. mRNA - Explore how to find exon-intron junction using tra-RA as the example; Investigation 3 Homework ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Students will identify intron-exon junctions for spd-2-RA Class Instruction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Review pre-mRNA processing using appropriate figures from the textbook or :ref:`module3/module3_exercise:Module 3` - Investigation 1: Students familiarize themselves with RNA-Seq data - Review consensus sequences for splice donor and splice acceptor sites - Investigation 2: Students find splice donor and acceptor for intron 1 - Review RNA splicing of intron 1 using tra-RA as the example - Investigation 3: Students find remaining splice donor and splice acceptor for intron 2 - Discuss length of pre-mRNA vs. length of spliced mRNA - Identify isoforms with different TSSs, or alternative splicing patterns Associated Videos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - `RNA-Seq and TopHat video `_ - `Genes and Isoforms video `_