Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

Synorth is a web resource for exploring and categorizing the syntenic relationships in gene regulatory blocks across multiple genomes

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.publishedVersionPeer Reviewe

Placement of automated external defibrillators and logistics to facilitate early defibrillation in sudden cardiac arrest

Background and aim. Out-of-hospital cardiac arrest (OHCA) is a leading cause of death in many western countries. Much effort is put in to measures to improve survival. Early cardiopulmonary resuscitation (CPR) and the use of an automated external defibrillator (AED) significantly increase the chance of survival. In 2016, 5,312 cases of OHCA were reported to the Swedish Register for Cardiopulmonary Resuscitation (SRCR), but only 577 (11%) survived to 30-days. The bystander CPR rate in Sweden is high (73%), and AEDs are widely spread in all parts of the country; however, the use of public AEDs is low. If the use of AEDs could be increased, more patients could be saved. The aim of this thesis was to investigate, in four separate studies, how logistics and placement of AEDs can help facilitate early defibrillation. Methods and results: Study 1 A prospective study at five emergency dispatch centres in Sweden where dispatchers were given access to the Swedish AED registry and had instructions to refer callers to nearby AEDs in cases of suspected OHCA. Of 3,009 suspected OHCA calls over seven months, only 200 occurred within 100 metres of an AED, and in only two cases did dispatchers referred callers to a nearby AED. AED accessibility (opening hours of the venue) and the fact that the callers often were alone on the scene, were identified as barriers for referral. Study 2 A retrospective analysis of AED installation sites and locations of OHCA in public locations in Stockholm. We used renowned geographic information system (GIS) analyses and a freely available dataset of land use (Urban Atlas). Incidence of OHCA in public locations in “residential areas” was similar to “non-residential” but AED installation was significantly higher in “non-residential areas”. Study 3 An explorative study to investigate the feasibility of using unmanned aerial vehicles (UAV)/Drones to transport AEDs to decrease time to defibrillation. The study included live test flights of a UAV system as well as retrospective GIS analysis of suitable locations for installation of UAVs equipped with AEDs for maximum coverage of OHCA. Study 4 An overview of the Swedish AED registry (SAEDREG) shows a two-fold increase of registered AEDs since 2013 and that the majority (45%) of the n=15,849 AEDs are placed in offices/workplaces. In a select region of Sweden, a survey was directed to the owners of all n=218 AEDs that focused on AED functionality and reasons for not registering the AED in SAEDREG. An additional n=94 AEDs were found through customer registries from AED vendors. AED functionality was high in both groups. Owners of AEDs not registered in SAEDREG was often unaware of the national AED registry or stated difficulties with the registration process as the main cause for not registering AEDs in SAEDREG. Conclusions: Dispatch centres have the potential to refer callers to nearby AEDs at an early stage in OHCA but may need supporting training and software. There is a mismatch between where public OHCA occur and where AEDs are located. Most AEDs are found in offices and workplaces whereas most OHCA occur in residential areas. Drones have the potential to transport AEDs and compensate for prolonged ambulance response time, especially in rural areas. A high quality national AED register is important for increasing general awareness within the community, thus facilitating early defibrillation in OHCA; however, many AEDs are nonregistered or discarded in the validation process

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

Ancora is a web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements for multiple genomes

Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes

A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around developmental regulatory genes in which an insertion results in the same global expression pattern, irrespective of exact position. These areas coincide with vertebrate chromosomal segments containing identical gene order; a phenomenon known as conserved synteny and thought to be a vestige of evolution. Genomic comparative studies have found large numbers of highly conserved noncoding elements (HCNEs) spanning these and other loci. HCNEs are thought to act as transcriptional enhancers based on the finding that many of those that have been tested direct tissue specific expression in transient or transgenic assays. Although gene order in hox and other gene clusters has long been known to be conserved because of shared regulatory sequences or overlapping transcriptional units, the chromosomal areas found through insertional hotspots contain only one or a few developmental regulatory genes as well as phylogenetically unrelated genes. We have termed these regions genomic regulatory blocks (GRBs), and show that they underlie the phenomenon of conserved synteny through all sequenced vertebrate genomes. After teleost whole genome duplication, a subset of GRBs were retained in two copies, underwent degenerative changes compared with tetrapod loci that exist as single copy, and that therefore can be viewed as representing the ancestral form. We discuss these findings in light of evolution of vertebrate chromosomal architecture and the identification of human disease mutations

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes

AbstractPan-vertebrate developmental cis-regulatory elements are discernible as highly conserved noncoding elements (HCNEs) and are often dispersed over large areas around the pleiotropic genes whose expression they control. On the loci of two developmental transcription factor genes, SOX3 and PAX6, we demonstrate that HCNEs conserved between human and zebrafish can be systematically and reliably tested for their regulatory function in multiple stable transgenes in zebrafish, and their genomic reach estimated with confidence using synteny conservation and HCNE density along these loci. HCNEs of both human and zebrafish function as specific developmental enhancers in zebrafish. We show that human HCNEs result in expression patterns in zebrafish equivalent to those in mouse, establishing zebrafish as a suitable model for large-scale testing of human developmental enhancers. Orthologous human and zebrafish enhancers underwent functional evolution within their sequence and often directed related but non-identical expression patterns. Despite an evolutionary distance of 450 million years, one pax6 HCNE drove expression in identical areas when comparing zebrafish vs. human HCNEs. HCNEs from the same area often drive overlapping patterns, suggesting that multiple regulatory inputs are required to achieve robust and precise complex expression patterns exhibited by developmental genes

Employing BAC-reporter constructs in the sea anemone Nematostella vectensis

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 53 (2013): 832-846, doi:10.1093/icb/ict091.Changes in the expression and function of genes drive evolutionary change. Comparing how genes are regulated in different species is therefore becoming an important part of evo-devo studies. A key tool for investigating the regulation of genes is represented by Bacterial Artificial Chromosomes-reporter constructs (BAC). BACs are large insert libraries, often >>100 kb, which thus capture the genomic sequences surrounding a gene of interest, including all, or nearly all, of the elements underpinning regulation. Recombinant BACs, containing a reporter gene in place of the endogenous coding sequence of genes, can be utilized to drive the expression of reporter genes under the regulatory control of the gene of interest while still embedded within its genomic context. Systematic deletions within the BAC reporter construct can be used to identify the minimal reporter in an unbiased way, avoiding the risk of overlooking regulatory elements that may be many kilobases away from the transcription start-site. Nematostella vectensis (Edwardsiidae, Anthozoa, Cnidaria) has become an important model in regenerative biology, ecology, and especially in studies of evo-devo and gene-regulatory networks due to its interesting phylogenetic position and amenability to molecular techniques. The increasing interest in this rising model system also led to a demand for methods that can be used to study the regulation of genes in Nematostella. Here we present our progress in employing BAC reporter constructs to visualize gene-expression in Nematostella. Using a new Nematostella-specific recombination cassette, we made nine different BAC reporter constructs. Although five BAC recombinants gave variable effects, three constructs, namely Nv-bra:eGFP::L10 BAC, Nv-dpp:eGFP::L10 BAC, and Nv-grm:eGFP::L10 BAC, delivered promising results. We show that these three constructs express the reporter gene eGFP in 10.4% – 17.2% of all analyzed larvae, out of which 26.2 – 41.9% express GFP in a mosaic fashion within the expected domain. In addition to the expression within the known domains, we also observed cases of misexpression of eGFP and examples that could represent actual expression outside the described domain. Furthermore, we deep-sequenced and assembled five different BACs containing Nv-chordin, Nv-foxa, Nv-dpp, Nv-wnta, and Nvwnt1, to improve assembly around these genes. The use of BAC reporter constructs will foster cis-regulatory analyses in Nematostella and thus help to improve our understanding of the regulatory network in this cnidarian system. Ultimately, this will advance the comparison of gene-regulation across species and lead to a much better understanding of evolutionary changes and novelties.2014-08-1

Transcriptional features of genomic regulatory blocks

CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances