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Exploring genome-wide organization of chromatin structure by ChIP-seq

Alon Goren

Associate Professor

Department of Medicine

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Goals & expected outcomes

Goals

  • Increase comfort in command line environment
  • Instill good practices, e.g.,
    • Do not trust anyone, including yourself
    • Document everything in a way that would make sense to you even in 10 years
    • Spot check everything, every time
    • Always label the axes including the units you use 

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Expected outcomes

  • Have a good understanding of the basics of chromatin biology, the main histone modifications and analysis of ChIP-seq datasets
  • Feel comfortable using bash and command line environment�

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Major HMs:��

  • H3K4me1 – Enhancers (active/poised)
  • H3K4me2 – Promoters & Enhancers (active/poised)
  • H3K4me3 – Promoters (active)
  • H3K9me3 – Heterochromatin
  • H3K27ac – Promoters & Enhancers (active/poised)
  • H3K27me3 – Promoters (active/poised)
  • H3K36me3 – transcribed genes

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Zhou, Goren & Bernstein Nature Reviews Genetics 2010

Histone modifications demarcate functional elements

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H3K36me3

Beginning

(Promoter)

End

Gene body

H3K4me3

A prototypical gene

The organization of histone modifications on genes

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Barth et al., Trends in Bio Sci. 2010

Beginning

(Promoter)

End

Gene body

The organization of histone modifications on genes

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Skene, Henikoff & Henikoff Nature Protocols 2018

CUT&RUN

(Cleavage under targets and release using nuclease) 

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Kaya-Okur et al. Nature Communications  2019

CUT&Tag

(Cleavage under targets and release using nuclease) 

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