title: A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.
abstract: BACKGROUND
  Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences.
  
  
  RESULTS
  We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly.
  
  
  CONCLUSIONS
  This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.
authors.forename: Robin P
authors.initials: RP
authors.lastname: Smith
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Riesenfeld
authors.forename: Alisha K
authors.initials: AK
authors.lastname: Holloway
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.forename: Karl K
authors.initials: KK
authors.lastname: Murphy
authors.forename: Natalie M
authors.initials: NM
authors.lastname: Feliciano
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Orecchia
authors.forename: Nir
authors.initials: N
authors.lastname: Oksenberg
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Pollard
authors.forename: Nadav
authors.initials: N
authors.lastname: Ahituv
mesh_terms: D000818:Animals; D001483:Base Sequence; D004210:Dissection; D004625:Embryo, Nonmammalian / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D009841:Oligonucleotides / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D058615:Synthetic Biology / Q000379:methods*; D015027:Zebrafish / Q000196:embryology / Q000235:genetics*
chemical_list: D009841:Oligonucleotides