title: Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.
abstract: Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here we describe 'enhancer-FACS-seq' (eFS) for highly parallel identification of active, tissue-specific enhancers in Drosophila melanogaster embryos. Analysis of enhancers identified by eFS as being active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, previously uncharacterized mesodermal transcription factors. Naive Bayes classifiers using transcription factor binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded in them.
authors.affiliation: Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Gisselbrecht
authors.forename: Luis A
authors.initials: LA
authors.lastname: Barrera
authors.forename: Martin
authors.initials: M
authors.lastname: Porsch
authors.forename: Anton
authors.initials: A
authors.lastname: Aboukhalil
authors.forename: Preston W
authors.initials: PW
authors.lastname: Estep
authors.forename: Anastasia
authors.initials: A
authors.lastname: Vedenko
authors.forename: Alexandre
authors.initials: A
authors.lastname: Palagi
authors.forename: Yongsok
authors.initials: Y
authors.lastname: Kim
authors.forename: Xianmin
authors.initials: X
authors.lastname: Zhu
authors.forename: Brian W
authors.initials: BW
authors.lastname: Busser
authors.forename: Caitlin E
authors.initials: CE
authors.lastname: Gamble
authors.forename: Antonina
authors.initials: A
authors.lastname: Iagovitina
authors.forename: Aditi
authors.initials: A
authors.lastname: Singhania
authors.forename: Alan M
authors.initials: AM
authors.lastname: Michelson
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D005434:Flow Cytometry / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D049452:Green Fluorescent Proteins / Q000096:biosynthesis / Q000235:genetics; D008648:Mesoderm; D017422:Sequence Analysis, DNA
chemical_list: D049452:Green Fluorescent Proteins