title: High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
abstract: Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
authors: Laurent
authors: L
authors: Vanhille
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
authors: Aurélien
authors: A
authors: Griffon
authors: Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
authors: Muhammad Ahmad
authors: MA
authors: Maqbool
authors: Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
authors: Joaquin
authors: J
authors: Zacarias-Cabeza
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
authors: Lan T M
authors: LT
authors: Dao
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France [3] TGML, IBiSA platform, 13288 Marseille, France.
authors: Nicolas
authors: N
authors: Fernandez
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
authors: Benoit
authors: B
authors: Ballester
authors: Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
authors: Jean Christophe
authors: JC
authors: Andrau
authors: 1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
authors: Salvatore
authors: S
authors: Spicuglia
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D015870:Gene Expression / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008297:Male; D051379:Mice; D041681:NIH 3T3 Cells; D011401:Promoter Regions, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors