Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features

<p>Abstract</p> <p>Background</p> <p>There is accumulating evidence that the milieu of repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, can play an important role in regulating chromosomal processes such as transcription, replication and recombination. The availability of whole-genome sequences has allowed us to annotate the genome environment of any locus in detail. The development of genome wide experimental analyses of gene expression, chromatin modification and chromatin proteins means that it is now possible to identify potential links between chromosomal processes and the underlying genome environment. There is a need for novel bioinformatic tools that facilitate these studies.</p> <p>Results</p> <p>We developed the Genome Environment Browser (GEB) in order to visualise the integration of experimental data from large scale high throughput analyses with repeat sequence features that define the local genome environment. The browser has incorporated dynamic scales adjustable in real-time, which enables scanning of large regions of the genome as well as detailed investigation of local regions on the same page without the need to load new pages. The interface also accommodates a 2-dimensional display of repetitive features which vary substantially in size, such as LINE-1 repeats. Specific queries for preliminary quantitative analysis of genome features can also be formulated, results of which can be exported for further analysis.</p> <p>Conclusion</p> <p>The Genome Environment Browser is a versatile program which can be easily adapted for displaying all types of genome data with known genomic coordinates. It is currently available at <url>http://web.bioinformatics.ic.ac.uk/geb/</url>.</p

Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation

BACKGROUND: X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist. The mechanism of Xist RNA spreading and Xist-dependent silencing is poorly understood. A large body of evidence indicates that silencing is more efficient on the X chromosome than on autosomes, leading to the idea that the X chromosome has acquired sequences that facilitate propagation of silencing. LINE-1 (L1) repeats are relatively enriched on the X chromosome and have been proposed as candidates for these sequences. To determine the requirements for efficient silencing we have analysed the relationship of chromosome features, including L1 repeats, and the extent of silencing in cell lines carrying inducible Xist transgenes located on one of three different autosomes. RESULTS: Our results show that the organisation of the chromosome into large gene-rich and L1-rich domains is a key determinant of silencing efficiency. Specifically genes located in large gene-rich domains with low L1 density are relatively resistant to Xist-mediated silencing whereas genes located in gene-poor domains with high L1 density are silenced more efficiently. These effects are observed shortly after induction of Xist RNA expression, suggesting that chromosomal domain organisation influences establishment rather than long-term maintenance of silencing. The X chromosome and some autosomes have only small gene-rich L1-depleted domains and we suggest that this could confer the capacity for relatively efficient chromosome-wide silencing. CONCLUSIONS: This study provides insight into the requirements for efficient Xist mediated silencing and specifically identifies organisation of the chromosome into gene-rich L1-depleted and gene-poor L1-dense domains as a major influence on the ability of Xist-mediated silencing to be propagated in a continuous manner in cis

GenomeView : a next-generation genome browser

Due to ongoing advances in sequencing technologies, billions of nucleotide sequences are now produced on a daily basis. A major challenge is to visualize these data for further downstream analysis. To this end, we present GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data, with dynamic navigation and semantic zooming, from the whole genome level to the single nucleotide. At the same time, the tool enables visualization of whole genome alignments of dozens of genomes relative to a reference sequence. GenomeView is unique in its capability to interactively handle huge data sets consisting of tens of aligned genomes, thousands of annotation features and millions of mapped short reads both as viewer and editor. GenomeView is freely available as an open source software package

Requirements of Modern Genome Browsers

Genome browsers are widely used tools for the visualization of a genome and related data. The demands placed on genome browsers due to the size, variety, and complexity of the data produced by modern biotechnology is increasing. These demands are poorly understood, and are not documented. Our study is establishing and documenting a clear set of requirements for genome browsers. Our study reviewed all widely used genome browsers, as well as notable research prototypes of genome browsers. This involved a review of the literature, executing typical uses of the genome browsers, program comprehension, reverse engineering, and code analysis. The key outcome of the study is a clear set of requirements in the form of a requirement document which conforms to the IEEE Std 830-1998 Standard of a Software Requirement Specification. This contains a domain model of concepts, the functional requirements as use cases, a definition of visualizations as metaphors, glyphs, or icons, formal specification of the system in Z notation and a specification of all widely used file formats. Genome browsers share a set of basic features like display, scroll, zoom, and search. However, they differ in their performance, maturity level and the implementation technologies. Our requirements also document the major non-functional requirements. The outcome of our study can be used in several ways: it can be used as a guide for future developers of Genome Browsers; it can form the basis of future enhancements of features in existing genome browsers; and it can motivate the invention of new algorithms, data structures, or file formats for implementations

Phylogenomics of vertebrate serpins

Kumar A. Phylogenomics of vertebrate serpins. Bielefeld (Germany): Bielefeld University; 2010.The serpins constitute a superfamily of proteins that fold into a conserved tertiary structure and employ a sophisticated, irreversible suicide-mechanism of inhibition. More than 6000 serpins have been identified, occurring in all three forms of the life - the eukaryotes, the prokaryotes and the archea. Vertebrate serpins can be conveniently classified into six groups (V1 - V6), based on three independent biological features - gene organization, diagnostic amino acid sites and rare indels. In the present work, the phylogenetic relationships of serpins from Nematostella vectensis, Strongylocentrotus purpuratus, Ciona intestinalis, four fish species, frog, chicken and mammals were investigated, using gene architecture analyses and stringent criteria for identification of orthologs. With some deviations, all vertebrate serpin genes fit into one of the six exon/intron gene classes previously identified, dating the existence and maintenance of these gene organizations before or close to the divergence of fishes. Group V1 and V2 gene families underwent rapid adaptive radiation along the lineages leading to mammals as indicated by an up to nine-fold increased number of family members, accompanied by a rapid functional diversification. In contrast, gene groups V3 to V6 display a rather conservative evolution with little changes since the divergence of fishes and the other vertebrates. The orthology assessment indicates that all vertebrates are equipped with a subset of strongly conserved serpins with functions that can be clearly correlated with basic vertebrate-specific physiology. None of serpin genes from C. intestinalis shares a common exon-intron architecture organisation with any of the vertebrate serpin gene classes, nor was it possible to identify orthologs of vertebrates. The lack of gene architecture similarity and the complete absence of orthology between urochordate and vertebrate serpins indicate that major changes with bursts of character acquisition must have occurred during evolution of serpins in the time interval separating urochordates from chordates, indicating massive intron gains or losses and events providing C and N-terminal sequence extensions characteristic for today's vertebrate serpins. Lancelets and sea urchin genomes, in contrast, share one orthologous serpin with vertebrates. Rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group V3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait. Phylogenomic comparisons show that, after establishment of canonical exon-intron patterns in the serpin superfamily at the dawn of vertebrate evolution, multiple intron acquisition events have occurred during diversification of a lineage of actinopterygian fishes. The novel introns were acquired within a limited time interval (on an evolutionary timescale), and no such events were observed in other groups of vertebrates. Examination of the sequences flanking the intron insertion points revealed that the genetic requirements for acquisition of novel introns might be less stringent than previously suggested. Finally, we argue that genome compaction, a phenomenon associated with the fish lineage depicting preferential intron gain, might promote intron acquisition

ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)

The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe

LIPIcs, Volume 277, GIScience 2023, Complete Volume

LIPIcs, Volume 277, GIScience 2023, Complete Volum

12th International Conference on Geographic Information Science: GIScience 2023, September 12–15, 2023, Leeds, UK

No abstract available