Benjamin Doughty

All Publications

• Genome-wide enhancer maps link risk variants to disease genes. Nature Nasser, J., Bergman, D. T., Fulco, C. P., Guckelberger, P., Doughty, B. R., Patwardhan, T. A., Jones, T. R., Nguyen, T. H., Ulirsch, J. C., Lekschas, F., Mualim, K., Natri, H. M., Weeks, E. M., Munson, G., Kane, M., Kang, H. Y., Cui, A., Ray, J. P., Eisenhaure, T. M., Collins, R. L., Dey, K., Pfister, H., Price, A. L., Epstein, C. B., Kundaje, A., Xavier, R. J., Daly, M. J., Huang, H., Finucane, H. K., Hacohen, N., Lander, E. S., Engreitz, J. M. 2021

  Abstract

  Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. We recently developed the activity-by-contact (ABC) model to predict which enhancers regulate which genes and validated the model using CRISPR perturbations in several cell types4. Here we apply this ABC model to create enhancer-genemaps in 131 human cell types and tissues, and use these maps to interpret the functions of GWAS variants. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577 genes that appear to influence multiple phenotypes through variants in enhancers that act in different cell types. In inflammatory bowel disease (IBD), causal variants are enriched in predicted enhancers by more than 20-fold in particular cell types such as dendritic cells, and ABC achieves higher precision than other regulatory methods at connecting noncoding variants to target genes. These variant-to-function maps reveal an enhancer that contains an IBD risk variant and that regulates the expression of PPIF to alter the membrane potential of mitochondria in macrophages. Our study reveals principles of genome regulation, identifies genes that affect IBD and provides a resource and generalizable strategy to connect risk variants of common diseases to their molecular and cellular functions.

  View details for DOI 10.1038/s41586-021-03446-x

  View details for PubMedID 33828297

• HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes. Proceedings of the National Academy of Sciences of the United States of America Marshall, J. L., Doughty, B. R., Subramanian, V., Guckelberger, P., Wang, Q., Chen, L. M., Rodriques, S. G., Zhang, K., Fulco, C. P., Nasser, J., Grinkevich, E. J., Noel, T., Mangiameli, S., Bergman, D. T., Greka, A., Lander, E. S., Chen, F., Engreitz, J. M. 2020; 117 (52): 33404–13

  Abstract

  Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.

  View details for DOI 10.1073/pnas.2010738117

  View details for PubMedID 33376219