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Open Access Publications from the University of California

Scholarly Works (34 results)

  • Article
  • Peer Reviewed
UC Santa Cruz Previously Published Works (2020)

Background

Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to current bioinformatic analyses and visualization tools, as short repeat sequences can map to multiple genomic loci resulting in their misclassification and misinterpretation. In fact, sequence data mapping to repeat elements are often discarded from analysis pipelines. Therefore, there is a continued need for standardized tools and techniques to interpret genomic data of repeats.

Results

We present the UCSC Repeat Browser, which consists of a complete set of human repeat reference sequences derived from annotations made by the commonly used program RepeatMasker. The UCSC Repeat Browser also provides an alignment from the human genome to these references, uses it to map the standard human genome annotation tracks, and presents all of them as a comprehensive interface to facilitate work with repetitive elements. It also provides processed tracks of multiple publicly available datasets of particular interest to the repeat community, including ChIP-seq datasets for KRAB Zinc Finger Proteins (KZNFs) - a family of proteins known to bind and repress certain classes of repeats. We used the UCSC Repeat Browser in combination with these datasets, as well as RepeatMasker annotations in several non-human primates, to trace the independent trajectories of species-specific evolutionary battles between LINE 1 retroelements and their repressors. Furthermore, we document at https://repeatbrowser.ucsc.edu how researchers can map their own human genome annotations to these reference repeat sequences.

Conclusions

The UCSC Repeat Browser allows easy and intuitive visualization of genomic data on consensus repeat elements, circumventing the problem of multi-mapping, in which sequencing reads of repeat elements map to multiple locations on the human genome. By developing a reference consensus, multiple datasets and annotation tracks can easily be overlaid to reveal complex evolutionary histories of repeats in a single interactive window. Specifically, we use this approach to retrace the history of several primate specific LINE-1 families across apes, and discover several species-specific routes of evolution that correlate with the emergence and binding of KZNFs.
    Cover page: The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
    • Article
    • Peer Reviewed
    LBL Publications (2005)

    Hundreds of highly conserved distal cis-regulatory elements have been characterized to date in vertebrate genomes1. Many thousands more are predicted based on comparative genomics2,3. Yet, in stark contrast to the genes they regulate, virtually none of these regions can be traced using sequence similarity in invertebrates, leaving their evolutionary origin obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a novel short interspersed repetitive element (SINE) retroposon family that was active in Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian at least 410 Mya4, and, remarkably, appears to be recently active in the "living fossil" Indonesian coelacanth, Latimeria menadoensis. We show that one copy is a distal enhancer, located 500kb from the neuro-developmental gene ISL1. Several others represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these is the >200bp ultraconserved region5, 100 percent identical in mammals, and 80 percent identical to the coelacanth SINE, that contains a 31aa alternatively spliced exon of the mRNA processing gene PCBP26. These add to a growing list of examples7 in which relics of transposable elements have acquired a function that serves their host, a process termed "exaptation"8, and provide an origin for at least some of the highly-conserved vertebrate-specific genomic sequences recently discovered using comparative genomics.

      Cover page: An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 are Derived from a Retroposon
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2015)
      A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees with the underlying genomes' ordering and orientation, creating a pan-genome reference ordering. We show this problem is NP-hard, but also demonstrate, empirically and within simulations, the performance of heuristic algorithms based upon a cactus graph decomposition to find locally maximal solutions. We describe an extension of our Cactus software to create a pan-genome reference for whole genome alignments, and demonstrate how it can be used to create novel genome browser visualizations using human variation data as a test. In addition, we test the use of a pan-genome for describing variations and as a reference for read mapping.
        Cover page: Building a Pan-Genome Reference for a Population
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2014)

        Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Availability and Implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/).

        genome@soe.ucsc.edu.

          Cover page: Navigating protected genomics data with UCSC Genome Browser in a Box.
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2016)

          Unlabelled

          Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.

          Availability and implementation

          The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license.

          Contact

          angie@soe.ucsc.edu

          Supplementary information

          Supplementary data are available at Bioinformatics online.
            Cover page: UCSC Data Integrator and Variant Annotation Integrator.
            • Article
            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2016)

            Unlabelled

            Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.

            Availability and implementation

            The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license.

            Contact

            angie@soe.ucsc.edu

            Supplementary information

            Supplementary data are available at Bioinformatics online.
              Cover page: UCSC Data Integrator and Variant Annotation Integrator
              • Article
              • Peer Reviewed
              UC Santa Cruz Previously Published Works (2021)

              Summary

              As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.

              Availability and implementation

              We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.

              Supplementary information

              Supplementary data are available at Bioinformatics online.
                Cover page: UCSC Cell Browser: visualize your single-cell data
                • Article
                • Peer Reviewed
                UC Santa Cruz Previously Published Works (2020)
                The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.
                  Cover page: UCSC Genome Browser enters 20th year
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2019)
                  The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.
                    Cover page: The UCSC Genome Browser database: 2019 update
                    • Article
                    • Peer Reviewed
                    UC Santa Cruz Previously Published Works (2016)
                    For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.
                      Cover page: The UCSC Genome Browser database: 2016 update.
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