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Lecture

Long-Read Sequencing Technology

This lecture on Long-Read Sequencing Technology was created by Katie Sandlin for the 2024 National GEP Faculty Workshop. The lecture covers four major topics: 1) Review of RNA-Seq Short-read Sequencing, 2) Overview and benefits of Long-read Sequencing, 3) Oxford Nanopore Sequencing, and 4) Pacific Biosciences Sequencing. Each slide is scripted in the Notes section for reference.

Pathways Project Primer

This PowerPoint presentation provides a primer on the recommended annotation strategy for the Pathways Project. The presentation provides an overview of the goals of the Pathways Project annotations, an introduction to RNA-Seq, web databases, and a discussion on the phases of the splice donor and acceptor sites.

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.

Introduction to Motifs and Motif Finding

This document contains the notes from a lecture on motif finding given by Dr. Jeremy Buhler in the Bio 4342 course at WU. The lecture covers the different approaches used to represent sequence motifs and to search for sequence motifs in a genome.

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.

RNA Quantitation from RNA-Seq Data

Developed by Dr. Jeremy Buhler, this PowerPoint presentation provides an overview of the approaches for quantifying transcript abundance based on RNA-Seq data. The presentation includes a discussion on the benefits and limitations of the two approaches commonly used for RNA quantitation – RPKM and TPM.