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Optimization of ‘Ultra-Low-Input’ (ULI)-Chromatin immunoprecipitation followed by Next Generation Sequencing (ChIP-seq) for rare in vivo samples

  • Project Leaders: Matthew Lorincz
  • Institutions: University of British Columbia (UBC)
  • Budget: $221847
  • Program/Competition: Strategic Opportunities Fund
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2015
  • Status: Closed

Each cell of an organism carries the same genetic sequence, yet the cells from complex organisms such as plants or humans exhibit different features and gene regulation patterns. The packaging of DNA into proteins called histones plays a critical role in the regulation of gene expression; the addition of covalent modifications to histones is one of the main factors dictating whether a gene will be expressed or silenced. The development of combined chromatin immunoprecipitation and next generation sequencing (ChIP-seq) technologies has enabled genome-wide epigenetic profiling of such marks in numerous cell lines and tissues. A major limitation of ChIP-seq, however, is the large number of cells (e.g. 106) required to generate high quality datasets, which makes the study of very rare cell populations extremely difficult. 

In this project, they adapted and expanded ULI-NChIP-seq, an ultra-low-input native ChIP and sequencing method they previously developed, to increase the number of histone and non-histone marks that can be studied, as well as decrease the required assay to allow the study of very rare cell populations.

By the end of the project, they have been able to: 1) Expand ULI-NChIP-seq to study all the histone marks studied in large epigenome consortiums, allowing to compare chromatin in rare cell populations to publically available chromatin maps; 2) Allow the study of non-histone proteins that bind chromatin, to allow further understanding gene regulation in rare tissues; 3) Reduce a further 10-fold the input size required to perform ULI-NChIP-seq, with an optimized oocyte and embryo preparation for ULI-ChIP-seq at 200 cells/selected histone mark, which gave an unprecedented view of chromatin in the oocyte and in the early embryo. The dataset generated in this project also led to a funded CIHR project grant ($726,750 over 5 years)