Gene expression: the technology

9 important questions on Gene expression: the technology

GRO-seq (Global Run-On Sequencing)

Mapping RNA in the making. Maps introns and exons. RNA-Seq maps only exons.

DNase I hypersensitive site mapping

Identifying sequences accessible in chromatin

Chip-Seq (Chromatin Immunoprecipitation)

Finding the Genomic Binding Site of a given (modified) protein
  1. Crosslink DNA + bound protein
  2. Fragment DNA
  3. Immunoprecipiate
  4. Release DNA (washing)
  5. Prepare library
  6. Sequence
  7. Map sequence tags to genome and identify peaks
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DCas9 fused to Biotin Ligase

Identify proteins associated with specific genomic site

Tools for measuring the transcriptome

  • RNA-Seq (Single cell)
  • GRO-Seq

Tools for finding the regulatory sites of the genome

  • DNase I mapping
  • ATAC-Seq (Single cell)

Tools for finding the Genomic Binding Site of a given (modified) protein


  • ChIP-seq
  • CUT&RUN (ChIC-Seq) (Single cell)

Mapping the 3D Genome

  • 3C, 4C
  • Hi-C (Single cell)

Identifying the proteins associated with a given genomic site

  • APEX

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