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 (asawa@collegeofthedesert.edu) |
| Submission timestamp: | 2019/07/31 1:35:52 PM EST |
| Authors: |
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| Corresponding author: | Alexa Sawa (asawa@collegeofthedesert.edu) |
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. |
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| 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 (http://gander.wustl.edu) |
| Resources in addition to the lesson instructions | YouTube videos |
Learning Topics¶
| Topics in scientific fields: |
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| Topics in mathematics or statistics: |
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| Topics in bioinformatics or data science: |
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Student Prerequisites¶
| Recommended prior course work: |
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| 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) |
Accessibility¶
| Available languages: | English |
| Additional materials for students with disabilities: | None |
Lesson Plan¶
Title¶
- Transcription Part I: From DNA sequence to transcription unit
Objectives¶
- 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).
Order¶
- 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
Homework¶
- 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?