BAL31-NGS approach for identification of telomeres de novo in large genomes

被引:19
作者
Peska, Vratislav [1 ,2 ]
Sitova, Zdenka [1 ,3 ]
Fajkus, Petr [1 ,2 ,3 ]
Fajkus, Jiri [1 ,2 ,3 ]
机构
[1] Masaryk Univ, Mendel Ctr Plant Genom & Prote, Cent European Inst Technol, Kamenice 5, CZ-62500 Brno, Czech Republic
[2] Czech Acad Sci, Inst Biophys, Kralovopolska 135, CZ-61265 Brno, Czech Republic
[3] Masaryk Univ, Natl Ctr Biomol Res, Lab Funct Genom & Prote, Fac Sci, Kamenice 5, CZ-62500 Brno, Czech Republic
关键词
Telomere; NGS; BAL31; RepeatExplorer; Tandem Repeats Finder; Tandem Repeats Merger; MACRONUCLEAR DNA; REPEAT SEQUENCE; 1ST EVIDENCE; BOMBYX-MORI; EVOLUTION; RNA; CHROMOSOMES; VERTEBRATE; GENERATION; CESTRUM;
D O I
10.1016/j.ymeth.2016.08.017
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n =14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples. (C) 2016 Elsevier Inc. All rights reserved.
引用
收藏
页码:16 / 27
页数:12
相关论文
共 110 条
[1]   TELOMERIC LOCATION OF GIARDIA RDNA GENES [J].
ADAM, RD ;
NASH, TE ;
WELLEMS, TE .
MOLECULAR AND CELLULAR BIOLOGY, 1991, 11 (06) :3326-3330
[2]   Aloe L. -: a second plant family without (TTTAGGG)n telomeres [J].
Adams, SP ;
Leitch, IJ ;
Bennett, MD ;
Leitch, AR .
CHROMOSOMA, 2000, 109 (03) :201-205
[3]   TELOMERIC SITE POSITION HETEROGENEITY IN MACRONUCLEAR DNA OF PARAMECIUM-PRIMAURELIA [J].
BAROIN, A ;
PRAT, A ;
CARON, F .
NUCLEIC ACIDS RESEARCH, 1987, 15 (04) :1717-1728
[4]   Tandem repeats finder: a program to analyze DNA sequences [J].
Benson, G .
NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580
[5]   Aspergillus nidulans maintains short telomeres throughout development [J].
Bhattacharyya, A ;
Blackburn, EH .
NUCLEIC ACIDS RESEARCH, 1997, 25 (07) :1426-1431
[6]   TANDEMLY REPEATED SEQUENCE AT TERMINI OF EXTRACHROMOSOMAL RIBOSOMAL-RNA GENES IN TETRAHYMENA [J].
BLACKBURN, EH ;
GALL, JG .
JOURNAL OF MOLECULAR BIOLOGY, 1978, 120 (01) :33-53
[7]   IDENTIFICATION OF A TELOMERIC DNA-SEQUENCE IN TRYPANOSOMA-BRUCEI [J].
BLACKBURN, EH ;
CHALLONER, PB .
CELL, 1984, 36 (02) :447-457
[8]  
Blankenberg Daniel, 2010, Curr Protoc Mol Biol, VChapter 19, DOI 10.1002/0471142727.mb1910s89
[9]   FUNCTIONAL-CHARACTERIZATION AND DEVELOPMENTAL REGULATION OF MOUSE TELOMERASE RNA [J].
BLASCO, MA ;
FUNK, W ;
VILLEPONTEAU, B ;
GREIDER, CW .
SCIENCE, 1995, 269 (5228) :1267-1270
[10]   Evidence for an alternative mechanism for maintaining telomere length in human tumors and tumor-derived cell lines [J].
Bryan, TM ;
Englezou, A ;
DallaPozza, L ;
Dunham, MA ;
Reddel, RR .
NATURE MEDICINE, 1997, 3 (11) :1271-1274