Module 4 Instructor Resources

Instructor Resources for Module 4: Removal of introns from pre-mRNA by splicing

Cover Page

Submission Details

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

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 this lesson: None
Type(s) of student learning assessments: Short answer formative questions
Websites and online databases used: GEP UCSC Genome Browser (http://gander.wustl.edu)
Resources in addition to the lesson instructions YouTube videos

Learning Topics

Topics in scientific fields:
  • Genetics
  • Genomics
  • Molecular Biology
Topics in mathematics or statistics:
  • None
Topics in bioinformatics or data science:
  • Similarity searches (BLAST, Multiple Sequence Alignment)
  • Data visualization

Student Prerequisites

Recommended prior course work:
  • High school level biology
Recommended computer skills: Basic: Familiarity with web browsers, word processing

Instructor Prerequisites

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

Instructional time required: 1 class period
Students work as individuals or teams? Either individual or team work is possible
Number of students in a class: More than 50 students (assume no TAs and one computer for each student)

Accessibility

Available languages: English
Additional materials for students with disabilities: None

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 (Investigation 1).
  • Identify splice donor and acceptor sites using the genome browser (Investigation 2).

Pre-requisites

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 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