This primer includes some biological concepts that may be helpful to review prior to working with the four TSS Modules, including: a brief review of gene transcription, mRNA processing, promoter structure, and chromatin.
This module describes how Celniker TSS annotations, DNase I hypersensitive sites, and the 9-state chromatin models can be used in the classification of promoter shape for the Antp gene.
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.
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.
This module illustrates the use of computational (e.g., blastn) and experimental (e.g., RAMPAGE, CAGE, RNA PolII ChIP-Seq) data to define the narrow and wide TSS search regions for genes with broad promoters.
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.
This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.
This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.
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 | 02/05/2023 |
| Authors | Jamie Siders, Meg Laakso, Le Paliulis, and Wilson Leung |
| Curriculum Type | Lesson with Exercises |
| Topics Covered | Promoter Structure, CAGE, RAMPAGE, Chromatin State, DHS, Motif Finding |
| Tools Covered | GEP UCSC Genome Browser |
| Target Audience | Advanced Student |
| Research Project | — |
| Species | Drosophila melanogaster |
| Feedback Survey | Qualtrics Form |
| Resource | Box 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.
