FlyBase at 25: looking to the future

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Abstract

Since 1992, FlyBase ( flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.

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Most cited references 24

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Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Sushmita Roy, Jason Ernst, Peter V. Kharchenko … (2011)

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

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Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

Koen Venken, Joseph Carlson, Karen L. Schulze … (2009)

We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95% of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using ΦC31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

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Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Dayu Zhang, Frank Booth, Joseph Carlson … (2011)

Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysis indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.

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Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (hwp): nar

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date (Print): 04 January 2017

Publication date (Electronic): 30 October 2016

Publication date PMC-release: 30 October 2016

Volume: 45

Issue: Database issue , Database issue

Pages: D663-D671

Affiliations

[1 ]The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA

[2 ]Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK

[3 ]Department of Biology, Indiana University, Bloomington, IN 47405, USA

[4 ]Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

Author notes

[* ]To whom correspondence should be addressed. Tel: +1 617 495 9925; Fax: +1 617 495 1354; Email: sian@ 123456morgan.harvard.edu

[† ]The members of the FlyBase Consortium are listed in the Acknowledgments.

Author information

L. Sian Gramates http://orcid.org/0000-0002-6700-3797

Article

DOI: 10.1093/nar/gkw1016

PMC ID: 5210523

PubMed ID: 27799470

SO-VID: 23705520-1a70-4b88-9142-6c3192820ea7

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

History

Date accepted : 18 October 2016

Date revision received : 14 October 2016

Date received : 30 September 2016

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Pages: 9

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cover-date 04 January 2017

ScienceOpen disciplines: Genetics

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ScienceOpen disciplines: Genetics

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FlyBase at 25: looking to the future

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Genomic Prediction

Most cited references 24

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

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