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We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

To study the function of RAP1, an essential gene involved in the regulation of transcriptional activation, silencing and the telomere function in Saccharomyces cerevisiae, we isolated a Candida glabrata gene that complements the growth defect of a S. cerevisiae rap1 conditional mutant. The DNA sequence of the cloned gene, which we designated CgRAP1, predicted a 2064 bp open reading frame encoding a 687 amino acid protein with an overall identity of 65% and a similarity of 78% to Rap1p from S. cerevisiae. Its DDBJ/EMBL/GenBank Accession No. is AB055655. Copyright © 2001 John Wiley & Sons, Ltd.

To study the function of RAP1, an essential gene involved in the regulation of transcriptional activation, silencing and the telomere function in Saccharomyces cerevisiae, we isolated a Candida glabratagene that complements the growth defect of a S. cerevisiae rap1conditional mutant. The DNA sequence of the cloned gene, which we designated CgRAP1, predicted a 2064 bp open reading frame encoding a 687 amino acid protein with an overall identity of 65% and a similarity of 78% to Rap1p from S. cerevisiae. Its DDBJ/EMBL/GenBank Accession No. is AB055655. Copyright © 2001 John Wiley & Sons, Ltd.

To study the function of GCR1, a gene involved in the expression of glycolytic genes in Saccharomyces cerevisiae, a Kluyveromyces lactis gene that complements the growth defect of a S. cerevisiae Δgcr1 mutant was isolated. Introduction of this gene into the Δgcr1 mutant also restored the activities of glycolytic enzymes. DNA sequencing of KlGCR1 predicted an open reading frame of a 767 amino acid protein with an overall identity of 33% and similarity of 48% to Gcr1p from S. cerevisiae. Its DDBJ/EMBL/GenBank Accession No. is AB046391. Copyright © 2001 John Wiley & Sons, Ltd.

To study the function of GCR1, a gene involved in the expression of glycolytic genes in Saccharomyces cerevisiae, a Kluyveromyces lactisgene that complements the growth defect of a S. cerevisiaeΔgcr1mutant was isolated. Introduction of this gene into the Δgcr1mutant also restored the activities of glycolytic enzymes. DNA sequencing of KlGCR1predicted an open reading frame of a 767 amino acid protein with an overall identity of 33% and similarity of 48% to Gcr1p from S. cerevisiae. Its DDBJ/EMBL/GenBank Accession No. is AB046391. Copyright © 2001 John Wiley & Sons, Ltd.

We have analyzed the in vivo importance of different regions of Rap1p, a yeast transcriptional regulator and telomere binding protein. A yeast strain (SCR101) containing a regulatable RAP1gene was used to test functional complementation by a range of Rap1p derivatives. These experiments demonstrated that the C terminus of the protein, containing the putative transcriptional activation domain and the regions involved in silencing and telomere function, is not absolutely essential for cell growth, a result confirmed by sporulation of a diploid strain containing a C terminal deletion derivative of RAP1. Northern analysis with cells that expressed Rap1p lacking the transcriptional activation domain revealed that this region is important for the expression of only a subset of Rap1p-activated genes. The one essential region within Rap1p is the DNA binding domain. We have investigated the possibility that this region has additional functions. It contains two Myb-like subdomains separated by a linker region. Individual point mutations in the linker region had no effect on Rap1p function, although deletion of the region abolished cell growth. The second Myb-like subdomain contains a large unstructured loop of unknown function. Domain swap experiments with combinations of elements from DNA binding domains of Rap1p homologues from different yeasts revealed that major changes can be made to the amino acid composition of this region without affecting Rap1p function.

ABSTRACTWe have analyzed the in vivo importance of different regions of Rap1p, a yeast transcriptional regulator and telomere binding protein. A yeast strain (SCR101) containing a regulatable RAP1gene was used to test functional complementation by a range of Rap1p derivatives. These experiments demonstrated that the C terminus of the protein, containing the putative transcriptional activation domain and the regions involved in silencing and telomere function, is not absolutely essential for cell growth, a result confirmed by sporulation of a diploid strain containing a C terminal deletion derivative ofRAP1. Northern analysis with cells that expressed Rap1p lacking the transcriptional activation domain revealed that this region is important for the expression of only a subset of Rap1p-activated genes. The one essential region within Rap1p is the DNA binding domain. We have investigated the possibility that this region has additional functions. It contains two Myb-like subdomains separated by a linker region. Individual point mutations in the linker region had no effect on Rap1p function, although deletion of the region abolished cell growth. The second Myb-like subdomain contains a large unstructured loop of unknown function. Domain swap experiments with combinations of elements from DNA binding domains of Rap1p homologues from different yeasts revealed that major changes can be made to the amino acid composition of this region without affecting Rap1p function.

No relevant conflicts of interest to declare.

Abstract 3496

There is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways and processes in the human. It is an expert‐authored and peer‐reviewed, curated collection of well‐documented molecular reactions that span the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm, and other model organisms. This unit describes how to use the Reactome database to learn the steps of a biological pathway; navigate and browse through the Reactome database; identify the pathways in which a molecule of interest is involved; use the Pathway and Expression analysis tools to search the database for and visualize possible connections within user‐supplied experimental data set and Reactome pathways; and the Species Comparison tool to compare human and model organism pathways. Curr. Protoc. Bioinform. 38:8.7.1‐8.7.23. © 2012 by John Wiley & Sons, Inc.