Single cell epigenomics | Databio Slides

# Single cell epigenomics

Nathan Sheffield

<span style="font-size:0.6em"><a href="http://www.databio.org/slides">www.databio.org/slides</a></span>

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## What is epigenomics?

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Epigenomics is the study of the physical modifications, associations and conformations of genomic DNA sequences (Schwartzman and Tanay 2015)
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Epigenomics is the study of the chemical modification and physical conformation of cellular DNA and bound proteins
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Rosa and Shaw 2013

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## The epigenome

If we can measure how DNA is packaged,
we can understand what a cell is doing

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<h3>Epigenomics</h3>
the study of the chemical modification and physical conformation of cellular DNA and bound proteins
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<h3>Epigenetics</h3>
???
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## What is epigenetics?

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the causal study of embryological development (Waddington 1957, The strategy of the genes)
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The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence (Riggs et al. 1996)
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a change in the state of expression of a gene that does not involve a mutation, but that is nevertheless inherited in the absence of the signal (or event) that initiated the change. (Ptashne and Gant 2002)
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## What is epigenetics?

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the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. (Bird 2007)
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Epigenetics refers to changes in gene regulation brought about through modifications to the DNA's packaging proteins or the DNA molecules themselves without changing the underlying sequence. (Lord and Cruchaga 2014, Nature Neuroscience)
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the study of the mechanisms that allow cells to translate the nearly constant genome content of a multicellular organism into multiple functional and stable cellular conditions (Schwartzman and Tanay 2015)
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## What is epigenetics?

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The word literally means "on top of genetics," and it's the study of how individual genes can be activated or deactivated by life experiences. (<i>The Week</i>, 2013)
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<img src="/_modules/epigenome-quick-intro/week_epigenetics.png" width="500">
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## Bulk to single-cell: applications

- Rare populations
- Cell-to-cell heterogeneity (cancer, iPSCs, brain)
- Principles of gene regulation
- Surveillance

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## Single-cell challenges

- Sparsity
  - Minimal input DNA
  - Loss of already minimal material (e.g. BS, ChIP)
  - Data from a single cell is sparse
  - Number of cells assayable is low
- Noise (background or cross-contamination)
- Doublets or nulls
- Alleles
- To measure is to destroy

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## Overcoming challenges

Technology/equipment <br> Molecular techniques <br> Computation

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## Methods of focus

- Bisulfite-seq: DNA methylation
- ATAC-seq: Open chromatin
- ChIP-seq: Histone modification
- Hi-C: 3D DNA looping

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## Overcoming challenges

<span style="color:orange">Technology/equipment</span> <br> Molecular techniques <br> Computation

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## Mouth pipetting (Bisulfite-seq)

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## FACS (Bisulfite-seq)

<img src="/slides/single-cell-epigenomics/farlik2015_fig1.png" height="400"><br>
<a href="http://dx.doi.org/10.1101/gr.161679.113">Farlik et al. 2015</a>

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## Microfluidics (ATAC-seq)

<img src="/slides/single-cell-epigenomics/buenrostro2015_fig1.png" width="700"><br>
<a href="http://dx.doi.org/10.1038/nature14590">Buenrostro et al. 2015</a>

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## Droplets

<img src="/slides/single-cell-epigenomics/rotem2015_fig1.png"><br>
<a href="http://dx.doi.org/10.1038/nbt.3383">Rotem et al. 2015</a>

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## Overcoming challenges

Technology/equipment<br>
<span style="color:orange">Molecular techniques<br></span>
Computation

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## Post-bisulfite adapter tagging

<img src="/slides/single-cell-epigenomics/miura2012_fig1.png" height="400"><br>
<a href="http://dx.doi.org/10.1093/nar/gks454">Miura et al. 2012</a>

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## Single-strand protocols

<img src="/slides/single-cell-epigenomics/epignome_fig1.png" height="425"><br>
<a href="http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.f.369.html">Khanna et al. 2013</a>

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## Combinatorial indexing

<img src="/slides/single-cell-epigenomics/cusanovich2015_fig1.png" height="425"><br>
<a href="http://dx.doi.org/10.1126/science.aab1601">Cusanovich et al. 2015</a>

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<img src="/slides/single-cell-epigenomics/ramani2017_fig1.png" height="550"><br>
<a href="http://dx.doi.org/10.1038/nmeth.4155">Ramani et al. 2017</a>

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## Tn5 transposase fragmentation

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## Technology tradeoffs

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## Overcoming challenges

Technology/equipment<br>
Molecular techniques<br>
<span style="color:orange">Computation</span>

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## Contextualizing

<img src="/slides/single-cell-epigenomics/buenrostro2017_fig1.png" height="400"><br>
Buenrostro et al. 2017

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## Pooling or imputing

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## Trajectories

<img src="/slides/single-cell-epigenomics/farlik2015_fig2.png" height="500"><br>
<a href="http://dx.doi.org/10.1101/gr.161679.113">Farlik et al. 2015</a>

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## One read, many readouts

<img src="/slides/single-cell-epigenomics/landan2012_fig1.png"><br>
<a href="http://dx.doi.org/10.1126/science.aab1601">Landan et al. 2012</a>

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## Single-cell multi-omics

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## Strategies for single-cell multi-omics

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## G&T-seq

<img src="/slides/single-cell-epigenomics/macaulay2015_fig1.png" width="550"><br>
<a href="http://dx.doi.org/10.1038/nmeth.3370">Macaulay et al. 2015</a>

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## DR-seq

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## RNA + bisulfite-seq

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## Thanks for listening!

<span class="small footnote">
List of relevant literature: <a href="/single_cell_epigenomics.html">databio.org/single_cell_epigenomics.html</a>
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