5.9
CiteScore
5.9
Impact Factor
Volume 38 Issue 7
Jul.  2011
Turn off MathJax
Article Contents
Abstract
References
Article Navigation >  Journal of Genetics and Genomics  > 2011  >  38(7): 315-325

Use of methylation filtration and C0t fractionation for analysis of genome composition and comparative genomics in bread wheat

doi: 10.1016/j.jgg.2011.06.003
  • a 

    Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut 250004, India

  • b 

    Department of Biotechnology, Birla Institute of Technology, Mesra 835215, Ranchi, India

  • c 

    Department of Crop & Soil Sciences, Washington State University, Pullman 99163, USA

  • d 

    Department of Botany, University of Calcutta, Kolkata 700019, India

  • e 

    Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India

  • f 

    Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse-03, Gatersleben 06466, Germany

More Information
  • Corresponding author: E-mail address: pkgupta36@gmail.com (Pushpendra Kumar Gupta)
  • Received Date: 2010-11-16
  • Accepted Date: 2011-06-13
  • Rev Recd Date: 2011-06-08
    • Available Online: 2011-06-20
  • Publish Date: 2011-07-20
    Abstract
  • We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C0t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences (e.g., transposable elements and simple sequence repeats), protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/exclusion in methylation-filtered (MF) library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags (ESTs) available in the public domain. Only a limited overlap among MF, high C0t (HC), and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.
    • These authors contributed equally to this work.
    FullText(HTML)
    • References(59)
  • [1]
    Bedell, J.A., Budiman, M.A., Nunberg, A. et al. Sorghum genome sequencing by methylation filtration PLoS Biol., 3 (2005),p. e13
    [2]
    Birren, B., Green, D., Myers, M.R. et al.
    [3]
    Bryan, C.J., Collins, A.J., Stephenson, P. et al. Isolation and characterization of microsatellites from hexaploid bread wheat Theor. Appl. Genet., 94 (1997),pp. 557-563
    [4]
    Carels, N., Bernardi, G. Two classes of genes in plants Genetics, 154 (2000),pp. 1819-1825
    [5]
    Chan, A.P., Melake-Berhan, A., O’Brien, K. et al. BMC Genomics, 12 (2008),p. 282
    [6]
    Cuadrado, A., Schwarzacher, T. The chromosomal organization of simple sequence repeats in wheat and rye genomes Chromosoma, 107 (1998),pp. 587-594
    [7]
    Cuadrado, A., Cardoso, M., Jouve, N. Physical organization of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications Cytogenet. Genome Res., 120 (2008),pp. 210-219
    [8]
    Devos, K.M., Ma, J., Pontaroli, A.C. et al. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat Proc. Natl. Acad. Sci. USA, 102 (2005),pp. 19243-19248
    [9]
    Echenique, V., Stamova, B., Wolters, P. et al. Theor. Appl. Genet., 104 (2002),pp. 840-844
    [10]
    Erayman, M., Sandhu, D., Sidhu, D. et al. Demarcating gene-rich regions of the wheat genome Nucleic Acids Res., 32 (2004),pp. 3546-3565
    [11]
    Fellers, J.P. Genome filtering using methylation-sensitive restriction enzymes with six base pair recognition sites Plant Genome, 1 (2008),pp. 146-152
    [12]
    Fu, Y., Hsia, A.P., Guo, L. et al. Plant Physiol., 135 (2004),pp. 2040-2045
    [13]
    Gill, B.S., Friebe, B.
    [14]
    Gonzalez, I.L., Sylvester, J.E. Incognito rRNA and rDNA in databases and libraries Genome Res., 7 (1997),pp. 65-70
    [15]
    Gustafson, A.M., Allen, E., Givan, S. et al. Nucl. Acids Res., 33 (2005),pp. D637-D640
    [16]
    Houben, A., Field, B.L., Saunders, V. Microdissection and chromosome painting of plant B chromosomes Methods Cell Sci., 23 (2001),pp. 115-124
    [17]
    Jakše, J., Meyer, J.D., Suzuki, G. et al. Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration Mol. Genet. Genomics, 280 (2008),pp. 287-292
    [18]
    Kashkush, K., Feldman, M., Levy, A.A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat Nat. Genet., 33 (2003),pp. 102-106
    [19]
    Kumar, S., Singh, C.K., Bandopadhyay, R. Wheat genome sequence: challenges and success Curr. Sci., 100 (2011),pp. 455-457
    [20]
    La Rota, M., Kantety, R.V., Yu, J.K. et al. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley BMC Genomics, 6 (2005),p. 23
    [21]
    Lakey, N., Budiman, M.A., Nunberg, A., Citek, R., and Bedell, J.,2004. Methylation “filtering” to enrich for coding sequence regions. In: International Cotton Genome Initiative ICGI–2004 Workshop, October 10–13, Hyderabad, Andhra Pradesh, India, 166.
    [22]
    Lamoureux, D., Peterson, D.G., Li, W. et al. Genome, 48 (2005),pp. 1120-1126
    [23]
    Langdon, T., Thomas, A., Huang, L. et al. BMC Plant Biol., 9 (2009),p. 70
    [24]
    Li, W., Zhang, P., Fellers, J.P. et al. Sequence composition, organization, and evolution of the core Triticeae genome Plant J., 40 (2004),pp. 500-511
    [25]
    Messeguer, R., Ganal, M.W., Steffens, J.C. et al. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA Plant Mol. Biol., 16 (1991),pp. 753-770
    [26]
    Messing, J., Bharti, A.K., Karlowski, W.M. et al. Sequence composition and genome organization of maize Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 14349-14354
    [27]
    Mette, M.F., Van Der Winden, J., Matzke, M. et al. Plant Physiol., 130 (2002),pp. 6-9
    [28]
    Meyers, B.C., Tingey, S.V., Morgante, M. Abundance, distribution and transcriptional activity of repetitive elements in the maize genome Genome Res., 11 (2001),pp. 1660-1676
    [29]
    Morgante, M., Hanafey, M., Powell, W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat. Genet., 30 (2002),pp. 194-200
    [30]
    Palmer, L.E., Rabinowicz, P.D., O’shaughnessy, A.L. et al. Maize genome sequencing by methylation filtration Science, 302 (2003),pp. 2115-2117
    [31]
    Paterson, A., Wicker, T., Rong, J., Estill, J., and Peterson, D.G, 2004. Efficient sequencing and assembly of the cotton genome, Incorporating Cot – based cloning and sequencing. In: International Cotton Genome Initiative ICGI–2004 Workshop, October 10–13, Hyderabad, Andhra Pradesh, India, 167.
    [32]
    Paux, E., Sourdille, P., Salse, J. et al. A physical map of the 1-gigabase bread wheat chromosome 3B Science, 322 (2008),pp. 101-104
    [33]
    Peterson, D.G., Schulze, S.R., Sciara, E.B. et al. Genome Res., 12 (2002),pp. 795-807
    [34]
    Qi, L.L., Echalier, B., Chao, S. et al. A chromosome bin map of 16,000 EST loci and distribution of genes among the three genomes of polyploid wheat Genetics, 168 (2004),pp. 701-712
    [35]
    Röder, M.S., Korzun, V., Gill, B.S. et al. The physical mapping of microsatellites markers in wheat Genome, 41 (1998),pp. 278-283
    [36]
    Rabinowicz, P.D., Citek, R., Budiman, M.A. et al. Differential methylation of genes and repeats in land plants Genome Res., 15 (2005),pp. 1431-1440
    [37]
    Rushton, P.J., Bokowiec, M.T., Han, S. et al. Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae Plant Physiol., 147 (2008),pp. 280-295
    [38]
    Sabot, F., Guyot, R., Wicker, T. et al. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations Mol. Genet. Genomics, 274 (2005),pp. 119-130
    [39]
    Safár, J., Bartos, J., Janda, J. et al. Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat Plant J., 39 (2004),pp. 960-968
    [40]
    Safár, J., Simková, H., Kubaláková, M. et al. Development of chromosome-specific BAC resources for genomics of bread wheat Cytogenet. Genome Res., 129 (2010),pp. 211-223
    [41]
    Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. et al. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics Proc. Natl. Acad. Sci. USA, 81 (1984),pp. 8014-8018
    [42]
    Salse, J., Bolot, S., Throude, M. et al. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution Plant Cell, 20 (2008),pp. 11-24
    [43]
    Sambrook, J., Russell, D.W.
    [44]
    Schmidt, T., Heslop-Harrison, J.S. The physical and genomic organization of microsatellites in sugar beet Proc. Natl. Acad. Sci. USA, 93 (1996),pp. 8761-8765
    [45]
    Singh, N.K., Dalal, V., Batra, K. et al. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes Funct. Integr. Genomics, 7 (2007),pp. 17-35
    [46]
    Springer, N.M., Xu, X., Barbazuk, W.B. Utility of different gene-enrichment approaches towards identifying and sequencing the maize gene space Plant Physiol., 136 (2004),pp. 3023-3033
    [47]
    Timko, M.P., Rushton, P.J., Laudeman, T.W. et al. Sequencing and analysis of the gene-rich space of cowpea BMC Genomics, 9 (2008),p. 103
    [48]
    Topp, C.N., Zhong, C.X., Dawe, R.K. Centromere-encoded RNAs are integral components of the maize kinetochore Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 15986-15991
    [49]
    Van der Hoeven, R., Ronning, C., Giovannoni, J. et al. Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing Plant Cell, 14 (2002),pp. 1441-1456
    [50]
    Vicient, C.M., Jaaskelainen, M., Kalendar, R. et al. Active retrotransposons are a common feature of grass genomes Plant Physiol., 125 (2001),pp. 1282-1292
    [51]
    Wang, Z., Gerstein, M., Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet., 10 (2009),pp. 57-63
    [52]
    Whitelaw, C.A., Barbazuk, W.B., Pertea, G. et al. Enrichment of gene-coding sequences in maize by genome filtration Science, 302 (2003),pp. 2118-2120
    [53]
    Wong, G.K.S., Wang, J., Tao, L. et al. Compositional gradients in Gramineae genes Genome Res., 12 (2002),pp. 851-856
    [54]
    Yu, J., Hu, S., Wang, J. et al. Science, 296 (2002),pp. 79-91
    [55]
    Yuan, Y., Sanmiguel, P.J., Bennetzen, J.L. Plant J., 34 (2003),pp. 249-255
    [56]
    Zhang, L.Y., Bernard, M., Leroy, P. et al. High transferability of bread wheat EST-derived SSRs to other cereals Theor. Appl. Genet., 111 (2005),pp. 677-687
    [57]
    Zhang, X., Yazaki, J., Sundaresan, A. et al. Cell, 126 (2006),pp. 1189-1201
    [58]
    Zilberman, D., Gehring, M., Tran, R.K. et al. Nat. Genet., 39 (2007),pp. 61-69
    [59]
    Šimková, H., Janda, J., Hřibová, E. et al. Cot-based cloning and sequencing of the short arm of wheat chromosome 1B Plant Soil Environ., 53 (2007),pp. 437-441
    • Relative Articles

  • Relative Articles

    [1]Huijing Ma, Mengxia Wang, Yong E. Zhang, Shengjun Tan. The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization[J]. Journal of Genetics and Genomics, 2023, 50(7): 462-472. doi: 10.1016/j.jgg.2023.04.003
    [2]Zhiyao Lv, Rui Dai, Haoran Xu, Yongxin Liu, Bo Bai, Ying Meng, Haiyan Li, Xiaofeng Cao, Yang Bai, Xianwei Song, Jingying Zhang. The rice histone methylation regulates hub species of the root microbiota[J]. Journal of Genetics and Genomics, 2021, 48(9): 836-843. doi: 10.1016/j.jgg.2021.06.005
    [3]Xue Bai, Feifei Li, Zhihua Zhang. A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements[J]. Journal of Genetics and Genomics, 2021, 48(11): 1007-1019. doi: 10.1016/j.jgg.2021.07.005
    [4]Anne-Marie Madore, Lucile Pain, Anne-Marie Boucher-Lafleur, Andréanne Morin, Jolyane Meloche, Marie-Michelle Simon, Bing Ge, Tony Kwan, Warren A. Cheung, Tomi Pastinen, Catherine Laprise. Asthma-associated polymorphisms in 17q12-21 locus modulate methylation and gene expression of GSDMA in naïve CD4+ T cells[J]. Journal of Genetics and Genomics, 2020, 47(3): 171-174. doi: 10.1016/j.jgg.2020.03.002
    [5]Hyerim Kim, Xudong Wang, Peng Jin. Developing DNA methylation-based diagnostic biomarkers[J]. Journal of Genetics and Genomics, 2018, 45(2): 87-97. doi: 10.1016/j.jgg.2018.02.003
    [6]Pan Chen, Xiangbin Ruan, Yongqiang Chen, Shilong Chu, Kunlun Mo, Chao Wu, Wei Liu, Bin Yin, Junjie Zhou, Liang Li, Lin Hou, Jiangang Yuan, Boqin Qiang, Jiekai Chen, Pengcheng Shu, Xiaozhong Peng. Generating a reporter mouse line marking medium spiny neurons in the developing striatum driven by Arpp21 cis-regulatory elements[J]. Journal of Genetics and Genomics, 2018, 45(12): 673-676. doi: 10.1016/j.jgg.2018.09.007
    [7]Wanjing Shang, Fei Wang, Gaofeng Fan, Haopeng Wang. Key elements for designing and performing a CRISPR/Cas9-based genetic screen[J]. Journal of Genetics and Genomics, 2017, 44(9): 439-449. doi: 10.1016/j.jgg.2017.09.005
    [8]Xiaojing Yan, Xiaomei Dong, Lei Liu, Yongqing Yang, Jinsheng Lai, Yan Guo. DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through[J]. Journal of Genetics and Genomics, 2016, 43(8): 513-523. doi: 10.1016/j.jgg.2016.03.010
    [9]Jun Liu, Guifang Jia. Methylation Modifications in Eukaryotic Messenger RNA[J]. Journal of Genetics and Genomics, 2014, 41(1): 21-33. doi: 10.1016/j.jgg.2013.10.002
    [10]Moshe Szyf. DNA Methylation, Behavior and Early Life Adversity[J]. Journal of Genetics and Genomics, 2013, 40(7): 331-338. doi: 10.1016/j.jgg.2013.06.004
    [11]Pingchuan Li, Feray Demirci, Gayathri Mahalingam, Caghan Demirci, Mayumi Nakano, Blake C. Meyers. An Integrated Workflow for DNA Methylation Analysis[J]. Journal of Genetics and Genomics, 2013, 40(5): 249-260. doi: 10.1016/j.jgg.2013.03.010
    [12]Wen Li, Wei Yang, Xiu-Jie Wang. Pseudogenes: Pseudo or Real Functional Elements?[J]. Journal of Genetics and Genomics, 2013, 40(4): 171-177. doi: 10.1016/j.jgg.2013.03.003
    [13]Ayaz Ahmad, Xiaofeng Cao. Plant PRMTs Broaden the Scope of Arginine Methylation[J]. Journal of Genetics and Genomics, 2012, 39(5): 195-208. doi: 10.1016/j.jgg.2012.04.001
    [14]Wensheng Wang, Xiuqin Zhao, Yajiao Pan, Linghua Zhu, Binying Fu, Zhikang Li. DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress[J]. Journal of Genetics and Genomics, 2011, 38(9): 419-424. doi: 10.1016/j.jgg.2011.07.006
    [15]Yue-Sheng Long, Jia-Ming Qin, Tao Su, Qi-Hua Zhao, Yong-Hong Yi, Wei-Ping Liao. Human transcription factor genes involved in neuronal development tend to have high GC content and CpG elements in the proximal promoter region[J]. Journal of Genetics and Genomics, 2011, 38(4): 157-163. doi: 10.1016/j.jgg.2011.03.003
    [16]Meishan Zhang, Josphert N. Kimatu, Kezhang Xu, Bao Liu. DNA cytosine methylation in plant development[J]. Journal of Genetics and Genomics, 2010, 37(1): 1-12. doi: 10.1016/S1673-8527(09)60020-5
    [17]Jie Lan, Song Hua, Hailin Zhang, Yongli Song, Jun Liu, Yong Zhang. Methylation patterns in 5′ terminal regions of pluripotency-related genes in bovine in vitro fertilized and cloned embryos[J]. Journal of Genetics and Genomics, 2010, 37(5): 297-304. doi: 10.1016/S1673-8527(09)60047-3
    [18]Yanli Lu, Tingzhao Rong, Moju Cao. Analysis of DNA methylation in different maize tissues[J]. Journal of Genetics and Genomics, 2008, 35(1): 41-48. doi: 10.1016/S1673-8527(08)60006-5
    [19]Jiang Tan, Hui Huang, Wei Huang, Lin Li, Jianhua Guo, Baiqu Huang, Jun Lu. The genomic landscapes of histone H3-Lys9 modifications of gene promoter regions and expression profiles in human bone marrow mesenchymal stem cells[J]. Journal of Genetics and Genomics, 2008, 35(10): 585-593. doi: 10.1016/S1673-8527(08)60079-X
    [20]Jinghe Liu, Xingwei Liang, Jiaqiao Zhu, Liang Wei, Yi Hou, Da-Yuan Chen, Qing-Yuan Sun. Aberrant DNA methylation in 5′ regions of DNA methyltransferase genes in aborted bovine clones[J]. Journal of Genetics and Genomics, 2008, 35(9): 559-568. doi: 10.1016/S1673-8527(08)60076-4
    • Supplements(0)
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索
    Get Citation
    PDF

    Article Metrics

    Article views (72) PDF downloads (0) Cited by ()
    Proportional views
    Related

    Editorial Office

    Journal of Genetics and Genomics

    京ICP备09063187号-7

    No.1, West Beichen Road, Chaoyang District, Beijing 100101, P.R.China

    +86-10-64806528+86-10-64807786jgg@genetics.ac.cn

    Supported by: Beijing Renhe Information Technology Co. Ltd  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return