title: Systematic mapping of functional enhancer-promoter connections with CRISPR interference.
abstract: Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.|Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Charles P
authors.initials: CP
authors.lastname: Fulco
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Mathias
authors.initials: M
authors.lastname: Munschauer
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Rockwell
authors.initials: R
authors.lastname: Anyoha
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Glen
authors.initials: G
authors.lastname: Munson
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.|Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.|Department of Biology, MIT, Cambridge, MA 02139, USA.
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Grossman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Perez
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Kane
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.|Computational and Systems Biology Program, MIT, Cambridge, MA 02139, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Cleary
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. engreitz@broadinstitute.org lander@broadinstitute.org.|Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.|Department of Biology, MIT, Cambridge, MA 02139, USA.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. engreitz@broadinstitute.org lander@broadinstitute.org.
authors.forename: Jesse M
authors.initials: JM
authors.lastname: Engreitz
mesh_terms: D064113:CRISPR-Cas Systems; D049109:Cell Proliferation / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004194:Disease / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics / Q000502:physiology*; D050982:GATA1 Transcription Factor / Q000235:genetics; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020014:K562 Cells; D011401:Promoter Regions, Genetic / Q000235:genetics / Q000502:physiology*; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D050982:GATA1 Transcription Factor; C494688:GATA1 protein, human; C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc