title: Dissecting neural differentiation regulatory networks through epigenetic footprinting.
abstract: Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Ziller
authors.affiliation: Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 6997801, Israel.
authors.forename: Reuven
authors.initials: R
authors.lastname: Edri
authors.affiliation: Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 6997801, Israel.
authors.forename: Yakey
authors.initials: Y
authors.lastname: Yaffe
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Donaghey
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Ramona
authors.initials: R
authors.lastname: Pop
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: William
authors.initials: W
authors.lastname: Mallard
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Robbyn
authors.initials: R
authors.lastname: Issner
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Casey A
authors.initials: CA
authors.lastname: Gifford
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.|Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Alon
authors.initials: A
authors.lastname: Goren
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Xing
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Hongcang
authors.initials: H
authors.lastname: Gu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Davide
authors.initials: D
authors.lastname: Cachiarelli
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Tsankov
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Chuck
authors.initials: C
authors.lastname: Epstein
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Rinn
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Tarjei S
authors.initials: TS
authors.lastname: Mikkelsen
authors.affiliation: Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.|Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.affiliation: Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 6997801, Israel.
authors.forename: Yechiel
authors.initials: Y
authors.lastname: Elkabetz
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.|Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Meissner
mesh_terms: D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D006801:Humans; D058953:Neural Stem Cells / Q000166:cytology* / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering; D014157:Transcription Factors