Browsing Sars International Centre for Marine Molecular Biology by Issue Date
Now showing items 1-20 of 140
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Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
(Peer reviewed; Journal article, 2007-03-06)We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding ... -
Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis
(Journal article; Peer reviewed, 2007-10-31)Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis, is discussed. A Tc1/mariner superfamily transposon, Minos, has excision and transposition activities in Ciona. Minos enables ... -
Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes
(Journal article; Peer reviewed, 2007-10-31)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 ... -
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
(Journal article, 2007-11-07)Insect genomes contain larger blocks of conserved gene order (microsynteny) than would be expected under a random breakage model of chromosome evolution. We present evidence that microsynteny has been retained to keep large ... -
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
(Journal article; Peer reviewed, 2007-11-15)JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with ... -
In Silico Detection of Sequence Variations Modifying Transcriptional Regulation
(Journal article; Peer reviewed, 2008-01-18)Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked ... -
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
(Journal article; Peer reviewed, 2008-02-12)Metazoan genomes contain arrays of highly conserved noncoding elements (HCNEs) that span developmental regulatory genes and define regulatory domains. We describe Ancora http:// ancora.genereg.net, a web resource that ... -
cis–regulation and mis–regulation – Insights into genomic regulatory mechanisms underlying the control of fgf8a in zebrafish Danio rerio
(Doctoral thesis, 2008-06-19)Fibroblast growth factor 8 (Fgf8) is a potent vertebrate morphogen that plays decisive roles in multiple developmental processes, such as cellular proliferation, survival, differentiation, growth and migration. Fgf8 ... -
Profile analysis and prediction of tissue-specific CpG island methylation classes
(Journal article; Peer reviewed, 2009-04-21)Background: The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction ... -
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
(Journal article; Peer reviewed, 2009-08-21)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 ... -
Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura
(Journal article; Peer reviewed, 2009-10-01)Background: Hox genes are critical for patterning the bilaterian anterior-posterior axis. The evolution of their clustered genomic arrangement and ancestral function has been debated since their discovery. As acoels appear ... -
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons
(Journal article; Peer reviewed, 2009-12-06)Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) ... -
Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure and its association with oikosins in the urochordate Oikopleura
(Peer reviewed; Journal article, 2010)Oriented cellulose deposition is critical to plant patterning and models suggest microtubules constrain cellulose synthase movements through the plasma membrane. Though widespread in plants, urochordates are the only animals ... -
Translog, a web browser for studying the expression divergence of homologous genes
(Journal article; Peer reviewed, 2010-01-18)Background: Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous ... -
Prediction of CpG-island function: CpG clustering vs. sliding-window methods
(Peer reviewed; Journal article, 2010-05-26)Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ... -
Ciliary photoreceptors in the cerebral eyes of a protostome larva
(Peer reviewed; Journal article, 2011-03-01)Background: Eyes in bilaterian metazoans have been described as being composed of either ciliary or rhabdomeric photoreceptors. Phylogenetic distribution, as well as distinct morphologies and characteristic deployment of ... -
Genomic features and computational identification of human microRNAs under long-range developmental regulation
(Peer reviewed; Journal article, 2011-05-27)Background: Recent functional studies have demonstrated that many microRNAs (miRNAs) are expressed by RNA polymerase II in a specific spatiotemporal manner during the development of organisms and play a key role in ... -
Gene expression in bryozoan larvae suggest a fundamental importance of pre-patterned blastemic cells in the bryozoan life-cycle
(Peer reviewed; Journal article, 2011-06-06)Background: Bryozoa is a clade of aquatic protostomes. The bryozoan life cycle typically comprises a larval stage, which metamorphoses into a sessile adult that proliferates by asexual budding to form colonies. The homology ... -
Histone variant innovation in a rapidly evolving chordate lineage
(Peer reviewed; Journal article, 2011-07-15)Background: Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs ... -
Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification
(Journal article; Peer reviewed, 2012-01-13)Background: Nervous systems are thought to be important to the evolutionary success and diversification of metazoans, yet little is known about the origin of simple nervous systems at the base of the animal tree. Recent ...