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Transcription Start Sites (TSS)

The Transcription Start Sites (TSS) modules illustrate how empirical data (e.g., CAGE, RAMPAGE, DNase I Hypersensitive Sites, RNA-Seq data) and computational results (chromatin states, pairwise and multiple sequence alignments) can be used to define the transcription start site positions, TSS search regions, and the shape of the promoter for each isoform of a gene in Drosophila.

Faculty Resources

All of the modules listed below are available with answer keys in a single package (automatic download) that uses members’ individual login credentials for the Project Management System. Also note that there is a new item of Pilot Curriculum associated with TSS—Understanding Promoter Architecture.

Module TSS2: Using Sequence Alignment to Identify a TSS

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

Module TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq

This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster.

Searching for Transcription Start Sites in Drosophila

This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.

TSS Annotation Workflow

This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.

Pilot Curriculum

The Understanding Promoter Architecture mini-modules aim to familiarize students with the process of defining transcription start sites and characterizing the shape of the promoter for each isoform of a gene. Using the GEP UCSC Genome Browser, students can investigate DNase Hypersensitive Sites, Promoter Motifs, CAGE and RAMPAGE, Chromatin State, and Promoter Shape.

Last Updated
AuthorsJamie Siders, Meg Laakso, Le Paliulis, and Wilson Leung
Curriculum TypeLesson with Exercises
Topics CoveredPromoter Structure, CAGE, RAMPAGE, Chromatin State, DHS, Motif Finding
Tools CoveredGEP UCSC Genome Browser
Target AudienceAdvanced Student
Research Project
SpeciesDrosophila melanogaster
Feedback SurveyQualtrics Form
ResourceBox Folder


The TSS modules were developed by Margaret Laakso, Jamie Siders, and Michael Foulk. We would like to thank additional members of the GEP who helped to review and revise these modules.