title: Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells.
abstract: A 30-node signed and directed network responsible for self-renewal and pluripotency of mouse embryonic stem cells (mESCs) was extracted from several ChIP-Seq and knockdown followed by expression prior studies. The underlying regulatory logic among network components was then learned using the initial network topology and single cell gene expression measurements from mESCs cultured in serum/LIF or serum-free 2i/LIF conditions. Comparing the learned network regulatory logic derived from cells cultured in serum/LIF vs. 2i/LIF revealed differential roles for Nanog, Oct4/Pou5f1, Sox2, Esrrb and Tcf3. Overall, gene expression in the serum/LIF condition was more variable than in the 2i/LIF but mostly consistent across the two conditions. Expression levels for most genes in single cells were bimodal across the entire population and this motivated a Boolean modeling approach. In silico predictions derived from removal of nodes from the Boolean dynamical model were validated with experimental single and combinatorial RNA interference (RNAi) knockdowns of selected network components. Quantitative post-RNAi expression level measurements of remaining network components showed good agreement with the in silico predictions. Computational removal of nodes from the Boolean network model was also used to predict lineage specification outcomes. In summary, data integration, modeling, and targeted experiments were used to improve our understanding of the regulatory topology that controls mESC fate decisions as well as to develop robust directed lineage specification protocols.
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Huilei
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Yen-Sin
authors.initials: YS
authors.lastname: Ang
authors.affiliation: Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Ana
authors.initials: A
authors.lastname: Sevilla
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Ihor R
authors.initials: IR
authors.lastname: Lemischka
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Avi
authors.initials: A
authors.lastname: Ma'ayan
mesh_terms: D000818:Animals; D002460:Cell Line; D003198:Computer Simulation; D053595:Embryonic Stem Cells / Q000502:physiology*; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D053263:Gene Regulatory Networks / Q000235:genetics* / Q000502:physiology*; D051379:Mice; D039904:Pluripotent Stem Cells / Q000502:physiology*; D015203:Reproducibility of Results; D049490:Systems Biology