title: Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders.
abstract: Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptionalcis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; The Broad Institute, Cambridge, MA 02142;
authors.forename: Aoi
authors.initials: A
authors.lastname: Wakabayashi
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; The Broad Institute, Cambridge, MA 02142;
authors.forename: Jacob C
authors.initials: JC
authors.lastname: Ulirsch
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; The Broad Institute, Cambridge, MA 02142; Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
authors.forename: Leif S
authors.initials: LS
authors.lastname: Ludwig
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; The Broad Institute, Cambridge, MA 02142;
authors.forename: Claudia
authors.initials: C
authors.lastname: Fiorini
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
authors.forename: Makiko
authors.initials: M
authors.lastname: Yasuda
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138;
authors.forename: Avik
authors.initials: A
authors.lastname: Choudhuri
authors.affiliation: The Broad Institute, Cambridge, MA 02142;
authors.forename: Patrick
authors.initials: P
authors.lastname: McDonel
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138; Howard Hughes Medical Institute, Chevy Chase, MD 20815.
authors.forename: Leonard I
authors.initials: LI
authors.lastname: Zon
authors.affiliation: Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; 02115; The Broad Institute, Cambridge, MA 02142; sankaran@broadinstitute.org.
authors.forename: Vijay G
authors.initials: VG
authors.lastname: Sankaran
mesh_terms: D029503:Anemia, Diamond-Blackfan / Q000235:genetics / Q000378:metabolism*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D064113:CRISPR-Cas Systems; D050982:GATA1 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D020014:K562 Cells; D009154:Mutation; D059372:Nucleotide Motifs; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D020218:Response Elements; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D014158:Transcription, Genetic
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D050982:GATA1 Transcription Factor; D011518:Proto-Oncogene Proteins; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; C494688:GATA1 protein, human; C067143:TAL1 protein, human
keywords: GATA1; Mendelian erythroid disorders; cis-regulatory elements; noncoding mutations