Module 1 Instructor Resources

Instructor Resources for Module 1: Introduction to the Genome Browser: What is a gene?

Cover Page

Submission Details

Submitter: Anne Rosenwald (rosenwaa@georgetown.edu)
Submission timestamp: 2019/07/31 4:07:32 PM EST
Authors:
  • Joyce Stamm, University of Evansville
  • Jennifer Kennell, Vassar College
  • Wilson Leung, Washington University in St. Louis
  • Leocadia Paliulis, Bucknell University
  • Srebrenka Robic, Agnes Scott College
Corresponding author: Anne Rosenwald (rosenwaa@georgetown.edu)

Lesson Overview

Lesson abstract: This lesson introduces the University of California Santa Cruz genome browser to students, walking them through some of the key features so that it can be used for analysis of gene structure.
Lesson keywords:
  • Genome Browser
  • Exons
  • Introns
  • Evidence Track
  • Start Codon
  • Stop Codon
Organism(s) that are the focus of this lesson: Drosophila
Type(s) of student learning assessments: Quiz questions
Websites and online databases used: GEP UCSC Genome Browser (http://gander.wustl.edu)
Resources in addition to the lesson instructions: Questions to work through

Learning Topics

Topics in scientific fields:
  • Bioinformatics
  • Genetics
Topics in mathematics or statistics:
  • None
Topics in bioinformatics or data science:
  • Similarity searches (BLAST, Multiple Sequence Alignment)

Student Prerequisites

Recommended prior course work:
  • High school level biology
  • Introductory college biology
  • Genetics
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 or less
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

  • Introduction to the Genome Browser: What is a Gene?

Objectives

  • Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks.
  • Explain the relationships among DNA, pre-mRNA, mRNA, and protein.
  • Use the navigation tools in the genome browser to zoom in and zoom out on a given region and identify the genes in that region (Section 1.1).
  • Determine the orientation, number of exons, and number of introns for any given isoform (Section 1.2).
  • Use the genome browser to visualize the three possible reading frames on each strand (Section 1.3).
  • Locate the start codon and stop codon for any given isoform (Section 1.3).
  • Identify open reading frames using the genome browser (Section 1.4).

Pre-requisites: knowledge of…

  • DNA structure (base composition, anti-parallel double-stranded helix, base-pairing properties)
  • Chromosome structure (a chromosome is a continuous DNA molecule, basic understanding of chromosome arms)
  • Protein structure (proteins are made up of amino acids)

Order

  • Warm Up
  • Investigation
  • Exit

Homework

  • Discuss the question: What is a gene? (Discuss with a partner, then as a class.) Emphasize the function of a gene; consider how the structure of the gene is related to its function.
  • Work through the genome browser investigation, with pauses to discuss the answers to the questions.
  • Conclude with an emphasis on the main points:
  • Genes may run in either direction on a chromosome;
  • Genes are represented on the genome browser as blocks connected by lines;
  • Eukaryotic genes are made up of protein-coding exons (the blocks) connected by introns;
  • Proteins usually begin with a Methionine (M) and end at a stop codon (*)

Module 1 Resources

The evidence tracks in the Genome Browser are grouped into three categories:

  • Mapping and Sequencing Tracks
    Basically these contain the information obtained from sequencing that region of the chromosome. These tracks show the As, Ts, Cs, and Gs (Base Position) and matches to particular sequences of interest (Short Match) or to the cleavage sites for different “Restriction Enzymes”.
  • Genes and Gene Prediction Tracks
    These tracks show the genes as they are reported in the Drosophila Database (FlyBase Genes), and as predicted by a couple of computer programs (Genscan Genes, N-SCAN Genes). It also contains the transcription start site (TSS) annotations (TSS Annotations) and D. melanogaster cDNAs that have been mapped to contig1.
  • RNA Seq Tracks
    These tracks show the results of sequencing mRNAs derived from a particular tissue and developmental time point. Most of the RNA-Seq reads are derived from processed mRNAs (where the introns have been removed). The mRNAs are broken into smaller fragments (e.g. via nebulization) prior to sequencing (usually using the Illumina HiSeq platform). The short reads (~100–125bp) are then mapped against the D. melanogaster genome. The y-axis of the RNA-Seq Coverage track shows the number of reads that has been mapped to each position of the contig (x-axis); this provides an estimate of the expression level. The Exon Junctions track shows the predicted locations of the introns. This track is derived from the subset of RNA-Seq reads that map partially to each of two adjacent exons (i.e. spliced RNA-Seq reads).

Tip

For manipulating tracks, students may need to be reminded to read carefully what is immediately under the displayed tracks: Click on a feature for detail. Click sidebars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to a new position.