Open chromatin and ATAC-seq

Nathan Sheffield, PhD
www.databio.org/slides

What does the genome encode?


Regulatory DNA is important

Challenges to studying regulatory DNA

  • Variation: age, cell-type, environment, disease
  • Amount: 2% protein coding vs 25%? regulatory
  • Target: what gene does it affect?
  • Function: is it a promoter, silencer, insulator, enhancer?
  • Rigidity: genetic code vs TF motifs

We can computationally identify genes and even predict function. Regulatory DNA is more difficult.

How can we identify regulatory DNA?


https://en.wikipedia.org/wiki/Chromatin

Alberts 2002

How can we identify regulatory DNA?

  • DNase: classic 'gold standard' to identify open chromatin
  • FAIRE: Formaldehyde-assisted isolation of regulatory elements
  • ChIP: Chromatin immunoprecipitation
  • ATAC: Assay for transposase-accessible chromatin

DNase-seq: Biology

ChIP-seq

ATAC-seq: Experiment (Buenrostro et al. 2013)

Chromatin and transcription factors (Thurman et al. 2012)

Chromatin accessibility across cell types
Footprinting

Vernon et al. 2012

DNase

  • Open chromatin coincides with active regulatory DNA
  • ... but exact annotation or binding is not provided
  • ChIP seq advantage and disadvantage is in its target. it also requires antibodies and provides more diffuse signal

How can we identify what regulatory DNA is doing?

Image credit: "The genetic code" by OpenStax College, Biology.