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Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Created on 4th August 2016

Michael Guo; Satish K Nandakumar; Jacob C Ulirsch; Seyedeh Maryam Zekavat; Jason D Buenrostro; Pradeep Natarajan; Rany Salem; Roberto Chiarle; Mario Mitt; Mart Kals; Kalle Parn; Krista Fischer; Lili Milani; Reedik Magi; Priit Palta; Stacey B Gabriel; Andres Metspalu; Eric S Lander; Sekar Kathiresan; Joel N Hirschhorn; Tonu Esko; Vijay G Sankaran;

Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high coverage whole genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional ~17,000 samples. Our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic data sets provided evidence for causal mechanisms at several loci, including at a novel basophil count-associated locus near the master hematopoietic transcription factor CEBPA. The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance.

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