Genome-wide interrogation of Mammalian stem cell fate determinants by nested chromosome deletions

• Published in: PLoS genetics Vol. 6; no. 12; p. e1001241
• Main Authors: Fortier, Simon, Bilodeau, Mélanie, Macrae, Tara, Laverdure, Jean-Philippe, Azcoitia, Valeria, Girard, Simon, Chagraoui, Jalila, Ringuette, Nancy, Hébert, Josée, Krosl, Jana, Mayotte, Nadine, Sauvageau, Guy
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-12-2010; Public Library of Science (PLoS)
• Subjects: Animals; Cell Biology; Cell cycle; Cell Differentiation; Cell Line; Chromosome Deletion; Chromosome Mapping; Chromosomes; Developmental Biology/Cell Differentiation; Embryonic stem cells; Embryonic Stem Cells - cytology; Female; Gene mutations; Genetic aspects; Genetics; Genetics and Genomics/Functional Genomics; Genome; Humans; Male; Mammals - genetics; Medical research; Mice; Physiological aspects; Proteins; Stem cells; Canada
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1001241

Understanding the function of important DNA elements in mammalian stem cell genomes would be enhanced by the availability of deletion collections in which segmental haploidies are precisely characterized. Using a modified Cre-loxP-based system, we now report the creation and characterization of a collection of ∼1,300 independent embryonic stem cell (ESC) clones enriched for nested chromosomal deletions. Mapping experiments indicate that this collection spans over 25% of the mouse genome with good representative coverage of protein-coding genes, regulatory RNAs, and other non-coding sequences. This collection of clones was screened for in vitro defects in differentiation of ESC into embryoid bodies (EB). Several putative novel haploinsufficient regions, critical for EB development, were identified. Functional characterization of one of these regions, through BAC complementation, identified the ribosomal gene Rps14 as a novel haploinsufficient determinant of embryoid body formation. This new library of chromosomal deletions in ESC (DelES: http://bioinfo.iric.ca/deles) will serve as a unique resource for elucidation of novel protein-coding and non-coding regulators of ESC activity.