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Gene Annotation

Pathways Project: Annotation Form

This “Annotation Form” merged the “Annotation Report” and “Annotation Notebook” into a single document and the latter two items were archived.

The “Annotation Form” kept many of the Checks for Understanding type questions that were previously in the “Annotation Notebook.” However, given that not all faculty want their students to answer those questions, we marked any question that is NOT required for submission to the GEP as “OPTIONAL.” Currently the optional questions are organized as letters rather than numbers, which we hope will make it easy to quickly select and delete the OPTIONAL questions that faculty don’t wish to include. Again, all numbered questions are required for submission to the GEP for reconciliation.

Items that were previously asked for in the “Project Details” table of the “Annotation Report” are now available on the Genome Browser Gateway page for each species. Therefore, the “Project Details Table” instructions document is no longer needed.

Design and Use of RepeatMasker

Similar to the lecture notes on Repetitious DNA, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of RepeatMasker, as well as limitations of the program that students should be aware of.

4. Characteristics of the F Element

This lecture uses the themes from Slide Sets 1-3, of the “F Element Project: Annotated Lecture Slides” sequence, in describing what we have learned about the F element—combining wet-bench work in the Elgin lab, results of chromatin mapping by the modENCODE consortium, and the bioinformatics efforts of the faculty and students of the GEP. This includes the following:

  • characterization of the F element as a heterochromatic domain, high in repeated DNA but nonetheless having genes expressed at normal levels (7 slides);
  • mapping the chromatin state in relationship to the genes and to reporter transgenes inserted into the F (9 slides);
  • exploring the TSS and searching for unique factors or motifs associated with the TSSs of F element genes (6 slides);
  • introducing the “expanded F” project, describing some of the finds made looking at the F of D. ananassae, and summarizing the ongoing challenges and questions (9 slides)

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.