Repbase Update (www.girinst.org) is a relational database of repetitive elements representing over 8500 families and subfamilies of transposable elements (TEs) from eukaryotes. Each family is identifiable by a unique name, and its annotation includes species of origin, systematic classification, keywords, reference to the scientific literature, names of contributors, brief commentaries, etc. Most of the 5198 repetitive families added to Repbase Update (RU) during the last cycle are either unreported anywhere else, or have been thoroughly revised. Our approach is based on computer-assisted reconstruction and analysis of public DMA sequence data. Original contributions are first reported in an electronic journal named Repbase Reports. RU is used throughout the world by academic and research institutions for basic research and genome annotations. This database became a unique resource for individual research projects of biological and medical importance and for creation of secondary databases. During the next five years RU needs to grow at the rate of ~1000 entries per year to meet the demand created by the genome-sequencing projects. This information will be extracted, reconstructed, analyzed, annotated, classified, indexed and made available to researchers over the internet. In addition we will discover and study diverse superfamilies and conserved repeats, which are of primary interest for cutting-edge research. We propose the following specific aims to meet the challenge: (1) continue detection, reconstruction, annotation and electronic distribution of reference sequences for repetitive families from all sequenced eukaryotic species (2) continue studies of TEs in newly sequenced eukaryotic genomes in collaboration with sequencing consortia (3) continue systematic identification and analysis of new superfamilies and classes of transposable elements (TEs) (4) excavate and characterize remnants of TEs overrepresented in conserved non-coding regions and cis-regulatory modules in eukaryotic genomes (5) organize two conferences devoted to stimulation of Repbase-related research, data submission, data dissemination, training and standardization of repeat nomenclature.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Biotechnology Resource Grants (P41)
Project #
5P41LM006252-15
Application #
8300202
Study Section
Special Emphasis Panel (ZLM1-AP-M (J2))
Program Officer
Ye, Jane
Project Start
1996-09-30
Project End
2014-04-30
Budget Start
2012-05-01
Budget End
2013-04-30
Support Year
15
Fiscal Year
2012
Total Cost
$551,544
Indirect Cost
$206,058
Name
Genetic Information Research Institute
Department
Type
DUNS #
946494259
City
Mountain View
State
CA
Country
United States
Zip Code
94043
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Wheeler, Travis J; Clements, Jody; Eddy, Sean R et al. (2013) Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res 41:D70-82
Lehnert, Stefan; Kapitonov, Vladimir; Thilakarathne, Pushpike J et al. (2011) Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. BMC Genomics 12:257
Kojima, Kenji K; Kapitonov, Vladimir V; Jurka, Jerzy (2011) Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol 28:17-20
Jurka, Jerzy; Bao, Weidong; Kojima, Kenji K (2011) Families of transposable elements, population structure and the origin of species. Biol Direct 6:44
Prochnik, Simon E; Umen, James; Nedelcu, Aurora M et al. (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329:223-6
Bao, Weidong; Jurka, Jerzy (2010) Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1). Gene 465:9-16
Bao, Weidong; Jurka, Matthew G; Kapitonov, Vladimir V et al. (2009) New superfamilies of eukaryotic DNA transposons and their internal divisions. Mol Biol Evol 26:983-93
Jurka, Jerzy (2009) "Genomic Impact of Eukaryotic Transposable Elements", Pacific Grove, California, February 6-10, 2009. Gene 448:103
Kapitonov, Vladimir V; Tempel, Sebastien; Jurka, Jerzy (2009) Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene 448:207-13

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