Module 2 Instructor Resources

Instructor Resources for Module 2: Transcription Part I: From DNA sequence to transcription unit

Cover Page

Submission Details

Submitter: Alexa Sawa (
Submission timestamp: 2019/07/31 1:35:52 PM EST
  • Maria S. Santisteban, University of North Carolina - Pembroke
  • Alexa Sawa, College of the Desert
Corresponding author: Alexa Sawa (

Lesson Overview

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 this lesson: Drosophila melanogaster
Type(s) of student learning assessments: Short answer formative and summative questions
Websites and online databases used: GEP UCSC Genome Browser (
Resources in addition to the lesson instructions YouTube videos

Learning Topics

Topics in scientific fields:
  • Bioinformatics
  • Genomics
  • Molecular Biology
Topics in mathematics or statistics:
  • None
Topics in bioinformatics or data science:
  • 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 or less
Students work as individuals or teams? Either individual or team work is possible
Number of students in a class: 10-25 students (assume no TAs and one computer for each student)


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

Lesson Plan


  • Transcription Part I: From DNA sequence to transcription unit


  • 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 (Investigation 1).
  • Predict the locations of exons and introns using RNA seq reads (Investigation 1).
  • Predict TSS regions using RNA-Seq data (Investigation 2).
  • Identify putative TSS sites using modENCODE data (Investigation 2).
  • Determine the most likely TSS coordinate by evaluating multiple lines of evidence in the genome browser (Investigation 2).
  • Predict the approximate end of a transcription unit using RNA-seq data (Investigation 3).
  • Identify the most likely termination signal using the genome browser (Investigation 3).



  • 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


  • 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?