Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.
Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.
Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jacob C
JC
Ulirsch
Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Satish K
SK
Nandakumar
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Li
L
Wang
Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
Felix C
FC
Giani
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Xiaolan
X
Zhang
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Peter
P
Rogov
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Alexandre
A
Melnikov
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Patrick
P
McDonel
Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ron
R
Do
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
Tarjei S
TS
Mikkelsen
Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: sankaran@broadinstitute.org.
Vijay G
VG
Sankaran
D017398:Alternative Splicing; D002460:Cell Line; D019070:Cell Lineage / Q000235:genetics; D004912:Erythrocytes; D004920:Erythropoiesis / Q000235:genetics; D015723:Gene Library; D017930:Genes, Reporter; D005821:Genetic Techniques; D014644:Genetic Variation; D006801:Humans; D012045:Regulatory Sequences, Nucleic Acid; D014158:Transcription, Genetic