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Nature vs. Nurture: Epigenetics on AnVIL

Analysis, Visualization, and Informatics Lab-space

Ava Hoffman

21 September 2023

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Terms of Use

Except where otherwise indicated, The contents of this slide presentation are available for use under the Creative Commons Attribution 4.0 license.

You are free to adapt and share the work, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.

Sample attribution: [Title of work] by Johns Hopkins Data Science Lab. CC-BY 4.0

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Epigenetics on AnVIL

Background
DEMO: Starting with data: Visualizing narrowPeak results in RStudio on AnVIL
Starting from scratch: Using other AnVIL tools, from fastq to narrowPeak
Starting from scratch: UCSC Genome Browser

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Epigenetics on AnVIL

Background
DEMO: Starting with data: Visualizing narrowPeak results in RStudio on AnVIL
Starting from scratch: Using other AnVIL tools, from fastq to narrowPeak
Starting from scratch: UCSC Genome Browser

CC-BY hutchdatascience.org

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“The new science of epigenetics reveals how the choices you make can change your genes- and those of your kids”

John Cloud, Time Magazine, January 2010. https://content.time.com/time/subscriber/article/0,33009,1952313,00.html

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“The new science of epigenetics reveals how the choices you make can change your genes- and those of your kids”

John Cloud, Time Magazine, January 2010. https://content.time.com/time/subscriber/article/0,33009,1952313,00.html

Epidermis

Epidemic

Epicenter

Epiphyte

Epigenetics / epigenomics…

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Exposure and the Exposome

Vermeulen et al. (2020) Science 367, 392-396

“The exposome is an integrated function of exposure on our body, including what we eat and do, our experiences, and where we live and work.”

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DNA is packaged into chromosomes

Image Source: By BaraahAltarayra, via Wikimedia Commons

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DNA + protein

Protein-Nucleic Acid Interactions

Negatively charged nucleic acids that make up DNA bind to the positively charged ends of histone proteins.
The interactions made with nucleic acids are key to DNA packaging

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Histones → chromatin

Open Chromatin

Condensed Chromatin

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Experimental Approaches

ChIP-Seq (Chromatin Immunoprecipitation Sequencing) involves immunoprecipitating protein-DNA complexes, and then sequencing the enriched DNA fragments.
RNA-Seq (RNA Sequencing) helps identify genes that are differentially expressed due to epigenetic changes
ATAC-Seq (Assay for Transposase-Accessible Chromatin Sequencing) identifies open chromatin regions, which are accessible for transcription factors and other regulatory proteins
Epigenome Editing with CRISPR-Cas9 can validate causal relationships between epigenetic modifications and gene expression

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ChIP-Seq (Chromatin Immunoprecipitation Sequencing):

ChIP-Seq is used to identify DNA regions associated with specific histone modifications or DNA-binding proteins.

It involves cross-linking proteins to DNA, immunoprecipitating the protein-DNA complexes, and then sequencing the enriched DNA fragments.

This method allows researchers to map the distribution of histone marks or protein binding sites across the genome.

RNA-Seq (RNA Sequencing):

RNA-Seq is used to study the impact of epigenetic modifications on gene expression.

Researchers can analyze changes in gene expression profiles by sequencing and quantifying RNA transcripts in a sample.

Epigenetic modifications, such as DNA methylation and histone modifications, can influence gene transcription, and RNA-Seq helps identify genes that are differentially expressed due to epigenetic changes.

ATAC-Seq (Assay for Transposase-Accessible Chromatin Sequencing):

ATAC-Seq is used to identify open chromatin regions, which are accessible for transcription factors and other regulatory proteins.

It involves enzymatic cleavage and sequencing of regions of open chromatin using a transposase enzyme.

ATAC-Seq can help identify regions that are likely to be involved in gene regulation and epigenetic control.

Epigenome Editing:

Researchers can use CRISPR-Cas9 or other genome editing tools to manipulate epigenetic marks at specific genomic loci.

This allows for the study of causal relationships between epigenetic modifications and gene expression.

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ChIP-seq signals

https://www.nature.com/articles/s41467-019-13753-7/figures/7

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Epigenetics on AnVIL

Background
DEMO: Starting with data: Visualizing narrowPeak results in RStudio on AnVIL
Starting from scratch: Using other AnVIL tools, from fastq to narrowPeak
Starting from scratch: UCSC Genome Browser

CC-BY hutchdatascience.org

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CTCF binding and depletion

CTCF protein helps shape chromatin structure.
Khoury et al. (2020) find that certain binding sites of CTCF are especially resistant to depletion.
These 'persistent' sites are commonly found at key structural regions of DNA.

https://www.nature.com/articles/s41467-019-13753-7

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The Study: Khoury et al.

https://www.nature.com/articles/s41467-019-13753-7

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Kallikrein (KLK) locus

https://www.nature.com/articles/s41467-019-13753-7/figures/5

Some KLKs, especially KLK3 (or Prostate-Specific Antigen – PSA), have been used as biomarkers for cancer, particularly prostate cancer.

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Let’s take a look at their data comparing control and depleted samples!

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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125641

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https://www.nature.com/articles/s41467-019-13753-7

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Check out the vignettes for the trackViewer package : https://bioconductor.org/packages/release/bioc/html/trackViewer.html

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Epigenetics on AnVIL

Background
DEMO: Starting with data: Visualizing narrowPeak results in RStudio on AnVIL
Starting from scratch: Using other AnVIL tools, from fastq to narrowPeak
Starting from scratch: UCSC Genome Browser

CC-BY hutchdatascience.org

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Option 1: Automate with Workflows

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Option 2: D-I-Y: Bioconductor

https://compgenomr.github.io/book/chipseq.html

https://hbctraining.github.io/Intro-to-ChIPseq/

https://www.bioconductor.org/help/course-materials/2017/BioC2017/Day2/Workshops/ChIP-seq/doc/workflow.html

https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

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Option 3: D-I-Y: Galaxy

https://galaxyproject.org/tutorials/chip/

https://www.msi.umn.edu/sites/default/files/Analyzing%20ChIP%20using%20Galaxy.pdf

https://generegulation.org/teaching/Proficio_Practical_ChIP-seq_analysis_Galaxy_2020.pdf

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Galaxy: Mapping to T2T

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Epigenetics on AnVIL

Background
DEMO: Starting with data: Visualizing narrowPeak results in RStudio on AnVIL
Starting from scratch: Using other AnVIL tools, from fastq to narrowPeak
Starting from scratch: UCSC Genome Browser

CC-BY hutchdatascience.org

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https://hutchdatascience.org/AnVIL_Book_Epigenetics_Intro/index.html

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Wrap up

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We Appreciate Feedback!

https://tinyurl.com/mtxd79wm

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AnVIL in 2 minutes!

youtube.com/@anvilproject1223

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Questions? Let’s Talk at help.anvilproject.org!

help.anvilproject.org

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anvilproject.org

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AnVIL Team

Broad Institute�Anthony Philippakis, Rachel Liao, Kate Balaconis, Alex Bauman, Adrian Sharma, David Bernick, Jonathan Lawson, Kristian Cibulskis, Namrata Gupta, Rob Title, Eric Banks, Alessandro Culotti

University of Chicago�Robert Grossman, Radhika Reddy, Alex Van Tol, Fantix King

University of California Santa Cruz�Benedict Paten, Ben Vizzier, Denis Yuen, Charles Overbeck, Louise Cabansay, Natalie Perez, Ash O’Farrell, Beth Sheets, Walt Shands

Washington University�Adam Coffman, Allison Reieir, Haley Abel, Jason Walker

Carnegie Institution for Science

Frederick Tan

Johns Hopkins University�Michael Schatz, Kasper Hansen, Enis Afgan, Alex Ostrovsky, John Davis, Jenn Vessio, Stephen Mosher, Natalie Kucher, Dannon Baker, Aysam Guerler, Katie Cox, Benjamin Harvey, Kai Hammers, Keith Suderman, Ahmed Awan, Michelle Savage, Tyler Collins, Samantha Zarate, Bohan Ni, Ifeoma Nwigwe

Fred Hutchinson Cancer Center

Jeff Leek, Ava Hoffman, Elizabeth Humphries

Penn State University�Anton Nekrutenko, John Chilton, Nate Coraor, Marten Cech, Emil Bouvier, Nicholas Stoler, Jennifer Jackson, Assunta Desanto, Delphine Lariviere

Oregon Health & Sciences University�Jeremy Goecks, Kyle Ellrott, Brian Walsh, Luke Sargent, Vahid Jalili, Qiange Gu

Roswell Park Cancer Institute�Martin Morgan, Jiefei Wang, Lori Kern, Kayla Interdonato

�

Vanderbilt University Medical Center�Robert Carroll, Jodie Jackson, Peter Embi, Alex Bick, Josh Peterson, Queenie Ho, Sofia Labrecque, Sophie Forman

Massachusetts General Hospital�Jeff Klann, Shawn Murphy, Victor Castro, Heidi Rehm

Brigham and Women’s Hospital�Matt Lebo, Cheryl Clark, Sandy Aronson

American Heart Association�Jen Hall

Harvard Medical School�Vincent Carey, Alexandru Mahmoud, Shweta Gopaulakrishnan, BJ Stubbs

City University of New York�Levi Waldron, Sehyun Oh, Ludwig Geistlinger

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