Skip to content
Search
Close this search box.
Genomics Education Partnership logo
Contact Us
Genomics Education Partnership logo
Contact Us
Home » Gene Annotation » Page 2

Gene Annotation

3. The Dilemma of Transposable Elements: Can’t Live with Them, Can’t Evolve without Them!

This lecture introduces students to the analysis of repetitious elements in the genome. It can be used as a stand-alone lecture, or since the content is also important to our thinking about the relationship of transposable elements to eukaryotic genomes which is a key issue in our study of the expanded F element, it can be included in the “F Element Project: Annotated Lecture Slides” sequence.

The slides provide each of the following:

  • an introduction to transposable elements (TEs), particularly in the human genome (5 slides),
  • examples showing how transposition, resulting in new insertion sites or new rearrangements, creates harmful mutations and/or stimulates inflammation (7 slides);
  • how mechanisms for silencing generate more options for gene regulation (4 slides);
  • how transposable elements have rewired the genome, contributed to novel regulatory proteins, helped build centromeres and telomeres, marked sex chromosomes, and might drive evolution during times of stress (7 slides)


Without our TEs and histones, we would be bacteria!

2. Heterochromatin Formation — It’s all about silencing!

This lecture develops the relationship between chromatin packaging and control of gene expression, a significant epigenetic system that allows the genome to respond to changes in environment, both the external environment and physiological cues (e.g., hormone responses). There are 7 slides developing the importance of epigenetic regulation, particularly the silencing of repeats by heterochromatin packaging; 6 slides on histone post-translational modification; 9 slides on the discovery of Heterochromatin Protein 1a and its validation using Position Effect Variegation (in Drosophila), including the model for spreading of heterochromatin; 8 slides on HOW heterochromatin packaging can lead to silencing; 3 slides on the inheritance and manipulation of the heterochromatic state; and 4 slides on mapping chromatin states across the fly genome.

1. Eukaryotic Genomes and Chromatin Structure

This lecture introduces the following topics:

  • C-value paradox (2 slides)
  • explains how we first recognized that eukaryotic genomes are full of repetitious sequences by using Cot curves (11 slides; allows you to remind students about second order rate equations they learned in freshman chemistry!);
  • repeat characteristics of eukaryotic genomes (5 slides);
  • the need to package all that DNA to get it into a nucleus (3 slides);
  • the development of the nucleosome model (11 slides);
  • the relationship between nucleosome arrays and gene expression (4 slides).

Development of the nucleosome model represents a paradigm shift in our thinking about chromosomes, and slides are included pointing out how this model was initially rejected, but subsequently achieved widespread support in the scientific community.

Why Study the F Element?

This video provides a 50-minute talk on our motivation and progress for the F Element “expansion” Project. The talk briefly introduces the

  • C-value paradox (2 slides);
  • the need to silence repeats (3 slides);
  • basic chromatin structure (3 slides);
  • heterochromatin and the F Element (6 slides);
  • mapping the F Element in D. melanogaster for repeats and heterochromatin structure (10 slides);
  • examining the Transcription Start Site, looking for regulatory motifs (6 slides);
  • describing the “F Element expansion” project and our initial findings (8 slides).

The slide set used in the video is provided as a PowerPoint (automatic download) and a PDF Handout using the buttons below.

Parasitoid Wasps Project: Annotation Workbook

For the Parasitoid Wasps Project gene annotation, project submission will consist of a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein. This Annotation Workbook is an Excel file with space to fill out all the necessary information for the gene annotation.

If it is done correctly, filling out the workbook will also auto-populate a GFF file that can be used for testing the accuracy of gene models (described in the “Checking Accuracy of the Gene Model (Alternative to Gene Model Checker)” section of the “Annotation Workbook Directions“). Please note that everything should be filled out exactly as described: the vocabulary and formatting need to be very precise to make a functional GFF file.

The “Example” sheet has been completed for you to reference while completing the “Transcript” sheet.

Parasitoid Wasps Project: Annotation Workbook Directions

This document provides directions for how to complete and obtain the items needed to submit a Parasitoid Wasps Project annotation—a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein.

Parasitoid Wasps Project: Annotation Walkthrough

This exercise will walkthrough an example of annotating a wasp venom gene for the Parasitoid Wasps Project. It will discuss wasp versions of common GEP annotation tools—Genome Browser, Gene Record Finder, and Gene Model Checker—and provide background for the interpretation of data tracks that are unique to the Parasitoid Wasps Project.

Pathways Project: Annotation Workflow

The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.

Pathways Project: Annotation Report

GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report.