Single-cell CRISPR technology deciphers role of chromatin accessibility in cancer

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Sumary of Single-cell CRISPR technology deciphers role of chromatin accessibility in cancer:

  • In a new resource for the scientific community, published today in Nature Biotechnology, researchers in the lab of Neville Sanjana, PhD, at the New York Genome Center (NYGC) and New York University (NYU) developed CRISPR-sciATAC, a novel integrative genetic screening platform that jointly captures CRISPR gene perturbations and single-cell chromatin accessibility genome-wide..
  • With this technology, they profile changes in genome organization and create a large-scale atlas of how loss of individual chromatin-altering enzymes impacts the human genome..
  • The new method harnesses the programmability of the gene editing system CRISPR to knock-out nearly all chromatin-related genes in parallel, offering researchers deeper insights into the role of DNA accessibility in cancer and in rare diseases involving chromatin..
  • Recent advances in single-cell technologies have given scientists the ability to profile chromatin, the complex of DNA and proteins that resides within the nucleus of individual cells..
  • In an initial demonstration of CRISPR-sciATAC, the Sanjana Lab team designed a CRISPR library to target 20 chromatin-modifying genes that are commonly mutated in different cancers, including breast, colon, lung and brain cancers..
  • Many of these enzymes act as tumor suppressors and their loss results in global changes in chromatin accessibility..
  • Here, in a uniform genetic background, we have accessibility data capturing the impact of every chromatin-related gene..
  • This provides a detailed map between each gene and how its loss impacts genome organization with single-cell resolution,”.
  • The atlas shows that different subunits within each of the 17 chromatin remodeling complexes targeted can have different effects on genome accessibility..
  • Surprisingly, nearly all of these complexes have subunits where loss triggers increased accessibility and other subunits with the opposite effect..
  • Overall, the greatest disruption in transcription factor binding sites, which are important functional elements in the genome, was observed after loss of AT-rich interactive domain-containing protein 1A (ARID1A), a member of the BAF complex..
  • In addition to the CRISPR-sciATAC method, the team also developed a suite of computational methods to map the dynamic movements of the nucleosomes, which are the protein clusters that DNA is wrapped around..
  • This is exactly what the team found at specifical transcription factor binding sites involved in cell proliferation after CRISPR knock-out of ARID1A..
  • When targeting a different chromatin-modifying enzyme, these same sites underwent an expansion in nucleosome spacing, demonstrating the dynamics of nucleosome positioning at specific sites in the genome..
  • The CRISPR-sciATAC method allowed the team to systematically explore this genome plasticity for multiple chromatin-modifying enzymes and transcription factor binding sites..
  • “We really focused on making CRISPR-sciATAC an accessible technique — we wanted it to be something that any lab could do…

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