TeCK Database: A comprehensive collection of telomeric and centromeric sequences with their associated proteins

Gowthaman, Ragul; Krishnamoorthy, Saranya; Nandakumar, Renuka Devi; Ayyarappan, Vishalini

doi:10.6026/97320630002073

Cited by 4 publications

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“…The TeloPIN (Telomeric Proteins Interaction Network) database was a collection of interaction data in human and mouse cells from available literature and GEO (gene expression omnibus) data [ 36 ] but it is no longer active. The same is true for the TeCK database that has been previously published as a collection of telomeric and centromeric sequences as well as telomerase, centromere and kinetochore binding proteins [ 37 ].…”

Section: Introductionmentioning

confidence: 83%

TelNet - a database for human and yeast genes involved in telomere maintenance

et al. 2018

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BackgroundThe ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood. Currently, a database that integrates information on TM relevant genes is missing.DescriptionTo provide a resource for studies that dissect TM features, we here introduce the TelNet database at http://www.cancertelsys.org/telnet/. It offers a comprehensive compilation of more than 2000 human and 1100 yeast genes linked to telomere maintenance. These genes were annotated in terms of TM mechanism, associated specific functions and orthologous genes, a TM significance score and information from peer-reviewed literature. This TM information can be retrieved via different search and view modes and evaluated for a set of genes as demonstrated for an exemplary application.ConclusionTelNet supports the annotation of genes identified from bioinformatics analysis pipelines to reveal possible connections with TM networks. We anticipate that TelNet will be a helpful resource for researchers that study telomeres.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0617-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 83%

TelNet - a database for human and yeast genes involved in telomere maintenance

et al. 2018

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“…The collection of information includes sequences, alignments, secondary and tertiary structures, mutations known to cause human telomerase-deficiency diseases, and current telomerase researchers. The previously published TeCK database (http://www.bioinfosastra.com/services/teck/index.html) is a collection of telomeric and centromeric sequences as well as telomerase, centromere and kinetochore binding proteins This database appears to be no longer available (33). The MiCroKiTS (Midbody, Centrosome, Kinetochore, Telomere and Spindle) database focuses on information about proteins relevant for the molecular mechanisms during cell division and also includes telomere proteins (34).…”

Section: Introductionmentioning

confidence: 99%

TelNet- a database for human and yeast genes involved in telomere maintenance

Braun

Chung

Kepper

et al. 2017

Preprint

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Structure—function relationships in telomerase genes

Sýkorová

Fajkus

2009

Biology of the Cell

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The TERT (telomerase reverse transcriptase) subunit of telomerase is an intensively studied macromolecule due to its key importance in maintaining genome integrity and role in cellular aging and cancer. In an effort to provide an up-to-date overview of the topic, we discuss the structure of TERT genes, their alternative splicing products and their functions. Nucleotide databases contain more than 90 full-length cDNA sequences of telomerase protein subunits. Numerous in silico, in vitro and in vivo experimental techniques have revealed a great deal of structural and functional data describing particular features of the telomerase subunit in various model organisms. We explore whether particular findings are generally applicable to telomerases or species-specific. We also discuss in an evolutionary context the role of identified functional TERT subdomains. IntroductionTelomeres are nucleoprotein structures at the ends of eukaryotic chromosomes which protect linear chromosomes against damage and recognition by endogenous nucleases. The vital role of these structures has been demonstrated in observations of a breakage-fusion-bridge cycle by Barbara McClintock (1938) in plants and response to X-ray mediated damage by Hermann Muller (1938) in Drosophila. With understanding of the mechanism of DNA replication, the "end-replication problem" of linear chromosomes became apparent (Olovnikov, 1971; Watson, 1972;Olovnikov, 1973). However, fundamental features of telomere structure and protective function were not solved until later when the ends of Tetrahymena macronuclear minichromosomes were sequenced (Klobutcher et al., 1981) and the activity of telomerase, the enzyme responsible for their synthesis described (Greider and Blackburn, 1985; 1 To whom correspondence should be addressed (email fajkus@sci.muni.cz). Key words: alternative splicing, gene structure, telomerase. Abbreviations used: CTE, C-terminal extension; EST, expressed sequence tag; DAT, dissociate activities of telomerase; Est, ever-shorter telomere; FHC cell, fetal human colon cell; POT1, protection of telomeres protein 1; RT, reverse transcriptase; SWI/SNF, switch/sucrose non-fermentable; TERT, telomerase reverse transcriptase; AtTERT, Arabidopsis thaliana TERT; hTERT, human TERT; OsTERT, rice (Oryza sativa) TERT; TR, telomerase RNA; TRF2, telomere repeat factor 2. Greider and Blackburn, 1987). It is known now that telomere structure is formed by telomeric DNA, histone octamers and specific proteins that bind telomeric DNA either directly or indirectly by proteinprotein interactions (Fajkus and Trifonov, 2001; de Lange, 2005; Bianchi and Shore, 2008;Palm and de Lange, 2008) (Figure 1). The number of components of the telomere supramolecular structure, and knowledge of their roles in protecting and maintaining telomeres, have increased enormously within the last 15 years. Clearly telomerase is among the most important molecules in the field of telomere biology and is the subject of this review. General telomerase biologyTelomerase adds telomeric DNA re...

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TeCK Database: A comprehensive collection of telomeric and centromeric sequences with their associated proteins

Cited by 4 publications

References 5 publications

TelNet - a database for human and yeast genes involved in telomere maintenance

TelNet - a database for human and yeast genes involved in telomere maintenance

TelNet- a database for human and yeast genes involved in telomere maintenance

Structure—function relationships in telomerase genes

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