Core A - Establishing the regulatory mechanisms defining cellular function

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Project Summary The coordinated regulation of chromatin structure, transcription factor binding and RNA expression is fundamental to cellular differentiation. Methods for measuring different layers of gene regulation within single cells can be used to determine essential regulators of cell differentiation and function as sensitive markers of cellular identity and lineage potential. To this end, we (Buenrostro) have recently developed SHARE-seq (Simultaneous High-throughput ATAC and RNA Expression with sequencing), for joint measurement of chromatin accessibility and gene expression within the same single-cell, at low-cost and massive throughput. Using SHARE-seq, we have shown that co-analysis of ATAC- and RNA-seq data from the same cell can be used to associate transcription factors to their target regulatory regions and distal regulatory elements to their target genes, enabling the definition of causal gene regulatory networks. Furthermore, we have shown that changes in chromatin accessibility precedes changes in gene expression, foreshadowing lineage commitment, and identifying a role for chromatin accessibility in priming chromatin for gene activation. Here, we propose the establishment of the Gene Regulation Core (GRC), which will be led by Dr. Jason Buenrostro at Harvard University's Department of Stem Cell and Regenerative Biology. As part of this P01 proposal, the GRC will enable the P01 members with SHARE-seq and other genomic technologies established in the Buenrostro lab, which can be used to functionally annotate regulatory regions, identify key transcription factors and chromatin regulators, define gene regulatory networks and parse cellular states. The GRC will work closely with the P01 labs to design experiments, and organize and collect hematopoietic samples (Aim 1). The GRC will use SHARE-seq to jointly profile chromatin accessibility and RNA expression at the single cell level. This will include extending SHARE-seq to capabilities uniquely enabled by SHARE-seq, such as the readout of transcribed lineage barcodes and Clonal Hematopoiesis-associated mutations (Aim 2). Finally, the GRC will be responsible for the primary processing of the data, data management, developing web interface tools and organizing data discussions and workshops between the P01 labs (Aim 3). Overall, the GRC will offer a complete solution for the single-cell genomics needs of the P01 community through a unique and innovative suite of genomic technologies.