Single cell epigenomics

by Nathan Sheffield

What is epigenomics?

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

Rosa et al. 2013

The epigenome


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

Bulk to single-cell: applications

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

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

Overcoming challenges

Technology/equipment
Molecular techniques
Computation

Methods of focus

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

Overcoming challenges

Technology/equipment
Molecular techniques
Computation

Mouth pipetting (Bisulfite-seq)


Guo et al. 2013

FACS (Bisulfite-seq)


Farlik et al. 2015

Microfluidics (ATAC-seq)


Buenrostro et al. 2015

Droplets


Rotem et al. 2015

Overcoming challenges

Technology/equipment
Molecular techniques
Computation

Post-bisulfite adapter tagging


Miura et al. 2012

Single-strand protocols


Khanna et al. 2013

Combinatorial indexing


Cusanovich et al. 2015

Ramani et al. 2017

Tn5 transposase fragmentation


Adey et al. 2010

Technology tradeoffs


Overcoming challenges

Technology/equipment
Molecular techniques
Computation

Contextualizing


Buenrostro et al. 2017

Pooling or imputing

Trajectories


Farlik et al. 2015

One read, many readouts


Landan et al. 2012

Single-cell multi-omics

Stategies for single-cell multi-omics


Bock et al. 2016

G&T-seq


Macaulay et al. 2015

DR-seq


Dey et al. 2015

RNA + bisulfite-seq


Hu et al. 2016
Thanks for listening!

Slides at http://databio.org/slides/single_cell_epigenomics.html

List of relevant literature: databio.org/single_cell_epigenomics.html