When needles look like hay: How to find tissue-specific enhancers in model organism genomes

• Published in: Developmental biology Vol. 350; no. 2; pp. 239 - 254
• Main Authors: Haeussler, Maximilian, Joly, Jean-Stéphane
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.02.2011; Elsevier
• Subjects: Algorithms; Animals; Animals, Genetically Modified; Base Sequence; binding sites; Cis-regulation; Cis-regulatory element; Computer applications; Data processing; Enhancer Elements, Genetic; Enhancers; Fish; genes; Genes, Regulator; Genome; Genome analysis; Genomes; genomics; guidelines; Hay; High-Throughput Screening Assays; Humans; Life Sciences; Medaka; Neurons and Cognition; Non-coding elements; Nucleotides; Organ Specificity; Promoters; researchers; Reviews; Transcriptional regulation; Transgenesis; Transgenic animals; Zebrafish; Non-coding elements; Enhancers; Cis-regulation; Genome analysis; Medaka; Fish; Zebrafish; Transcriptional regulation; Transgenesis; Cis-regulatory element
• ISSN: 0012-1606; 1095-564X; 1095-564X
• DOI: 10.1016/j.ydbio.2010.11.026

A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project. ► For in vivo tests of cis-regulatory region, various experimental shortcuts have been found. ► Cross-species conservation reduces the search space. ► Long-range effects and promoter interactions can complicate the identification. ► Cell culture essays might be of limited use for developmental enhancers. ► Sequence predictions enrich but are not generic enough for most developing tissues.