title: Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms.
abstract: 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 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered 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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.|Department of Genetics, Harvard Medical School, Boston, MA 02115.|Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Guo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.
authors.forename: Satish K
authors.initials: SK
authors.lastname: Nandakumar
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.
authors.forename: Jacob C
authors.initials: JC
authors.lastname: Ulirsch
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02214.|Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02214.|Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02214.
authors.forename: Seyedeh M
authors.initials: SM
authors.lastname: Zekavat
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Buenrostro
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02214.|Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02214.|Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02214.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Natarajan
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.|Department of Genetics, Harvard Medical School, Boston, MA 02115.|Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115.
authors.forename: Rany M
authors.initials: RM
authors.lastname: Salem
authors.affiliation: Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA 02115.|Department of Molecular Biotechnology and Health Science, University of Torino, 10126 Torino, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Chiarle
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Mario
authors.initials: M
authors.lastname: Mitt
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Mart
authors.initials: M
authors.lastname: Kals
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Kalle
authors.initials: K
authors.lastname: Pärn
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Krista
authors.initials: K
authors.lastname: Fischer
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Lili
authors.initials: L
authors.lastname: Milani
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.|Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland.
authors.forename: Priit
authors.initials: P
authors.lastname: Palta
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.
authors.forename: Stacey B
authors.initials: SB
authors.lastname: Gabriel
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142; sankaran@broadinstitute.org lander@broadinstitute.org tesko@broadinstitute.org.|Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Systems Biology, Harvard Medical School, Boston, MA 02115.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02214.|Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02214.|Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02214.
authors.forename: Sekar
authors.initials: S
authors.lastname: Kathiresan
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142.|Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.|Department of Genetics, Harvard Medical School, Boston, MA 02115.|Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115.
authors.forename: Joel N
authors.initials: JN
authors.lastname: Hirschhorn
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142; sankaran@broadinstitute.org lander@broadinstitute.org tesko@broadinstitute.org.|Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.|Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115.|Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Tõnu
authors.initials: T
authors.lastname: Esko
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142; sankaran@broadinstitute.org lander@broadinstitute.org tesko@broadinstitute.org.|Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.
authors.forename: Vijay G
authors.initials: VG
authors.lastname: Sankaran
mesh_terms: D001483:Base Sequence; D001491:Basophils / Q000166:cytology; D022762:CCAAT-Enhancer-Binding Proteins / Q000235:genetics*; D002454:Cell Differentiation / Q000235:genetics; D019070:Cell Lineage / Q000235:genetics; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic; D004957:Estonia; D005260:Female; D050989:GATA2 Transcription Factor / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study; D006410:Hematopoiesis / Q000235:genetics*; D006801:Humans; D007958:Leukocyte Count; D008297:Male; D020641:Polymorphism, Single Nucleotide; D000073336:Whole Genome Sequencing
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; C515848:CEBPA protein, human; D050989:GATA2 Transcription Factor; C494711:GATA2 protein, human
keywords: CEBPA; GWAS; basophils; genome sequencing; hematopoiesis