3/ ACCESS-ATAC is simple to employ—we add a motif-agnostic Ddd enzyme (DddSs) to the standard Tn5 (ATAC) treatment of bulk or single-cell nuclei and use nextgen sequencing to read out chromatin accessibility. It adds no additional cost or effort to the conventional workflow. - ThreadSky

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lucapinello.bsky.social • 66 days ago

3/ ACCESS-ATAC is simple to employ—we add a motif-agnostic Ddd enzyme (DddSs) to the standard Tn5 (ATAC) treatment of bulk or single-cell nuclei and use nextgen sequencing to read out chromatin accessibility. It adds no additional cost or effort to the conventional workflow.

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lucapinello.bsky.social•66 days ago

4/ ACCESS-ATAC significantly improves TF binding site prediction, and in single-cell ACCESS-ATAC experiments, we resolve TF binding profiles at equal sensitivity to ATAC-seq with 2-3x fewer cells.

lucapinello.bsky.social•66 days ago

5/ The coolest feature of ACCESS-ATAC is the qualitatively new ability to analyze allelic TF occupancy and co-occupancy. We use a customized computational pipeline, OccuPIE, to generate a first-in-class allelic binding atlas of TFs across the genome.

lucapinello.bsky.social•66 days ago

6/ Through OccuPIE, we find that a large fraction of TFs show periodicity in their preference to co-occupy adjacent motifs. This periodicity approximates the turn of the DNA helix. This fascinating finding unlocks a key pattern that underlies genomic TF binding site selection.

lucapinello.bsky.social•66 days ago

7/ In sum, ACCESS-ATAC improves the resolution of ATAC-seq and opens up a new ability to analyze single-allele TF co-occupancy. Want to try it? Reach out-- we have built flexible experimental and computational workflows and would be happy to share reagents and expertise!

lucapinello.bsky.social•66 days ago

8/ We’d love your feedback and are excited to see ACCESS-ATAC adopted widely, inspiring new computational methods to harness the potential of this groundbreaking assay. Happy holidays! 🎄✨#ACCESSATAC #GeneRegulation

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