Epigenetic profiling of heterochromatic satellite DNA

Zakrzewski F, Weisshaar B, Fuchs J, Bannack E, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T (2011)
Chromosoma 120(4): 409-422.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Zakrzewski, Falk; Weisshaar, BerndUniBi ; Fuchs, Jorg; Bannack, Ekaterina; Minoche, Andre E; Dohm, Juliane C; Himmelbauer, Heinz; Schmidt, Thomas
Abstract / Bemerkung
Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.
Erscheinungsjahr
2011
Zeitschriftentitel
Chromosoma
Band
120
Ausgabe
4
Seite(n)
409-422
ISSN
0009-5915
eISSN
1432-0886
Page URI
https://pub.uni-bielefeld.de/record/2317352

Zitieren

Zakrzewski F, Weisshaar B, Fuchs J, et al. Epigenetic profiling of heterochromatic satellite DNA. Chromosoma. 2011;120(4):409-422.
Zakrzewski, F., Weisshaar, B., Fuchs, J., Bannack, E., Minoche, A. E., Dohm, J. C., Himmelbauer, H., et al. (2011). Epigenetic profiling of heterochromatic satellite DNA. Chromosoma, 120(4), 409-422. doi:10.1007/s00412-011-0325-x
Zakrzewski, F., Weisshaar, B., Fuchs, J., Bannack, E., Minoche, A. E., Dohm, J. C., Himmelbauer, H., and Schmidt, T. (2011). Epigenetic profiling of heterochromatic satellite DNA. Chromosoma 120, 409-422.
Zakrzewski, F., et al., 2011. Epigenetic profiling of heterochromatic satellite DNA. Chromosoma, 120(4), p 409-422.
F. Zakrzewski, et al., “Epigenetic profiling of heterochromatic satellite DNA”, Chromosoma, vol. 120, 2011, pp. 409-422.
Zakrzewski, F., Weisshaar, B., Fuchs, J., Bannack, E., Minoche, A.E., Dohm, J.C., Himmelbauer, H., Schmidt, T.: Epigenetic profiling of heterochromatic satellite DNA. Chromosoma. 120, 409-422 (2011).
Zakrzewski, Falk, Weisshaar, Bernd, Fuchs, Jorg, Bannack, Ekaterina, Minoche, Andre E, Dohm, Juliane C, Himmelbauer, Heinz, and Schmidt, Thomas. “Epigenetic profiling of heterochromatic satellite DNA”. Chromosoma 120.4 (2011): 409-422.

13 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.).
Zakrzewski F, Schmidt M, Van Lijsebettens M, Schmidt T., Plant J 90(6), 2017
PMID: 28257158
Satellite DNA: An Evolving Topic.
Garrido-Ramos MA., Genes (Basel) 8(9), 2017
PMID: 28926993
Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris).
Kowar T, Zakrzewski F, Macas J, Kobližková A, Viehoever P, Weisshaar B, Schmidt T., BMC Plant Biol 16(1), 2016
PMID: 27230558
Extending the sRNAome of apple by next-generation sequencing.
Visser M, van der Walt AP, Maree HJ, Rees DJ, Burger JT., PLoS One 9(4), 2014
PMID: 24752316
The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.
Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T., Plant J 78(6), 2014
PMID: 24661787
Euchromatic subdomains in rice centromeres are associated with genes and transcription.
Wu Y, Kikuchi S, Yan H, Zhang W, Rosenbaum H, Iniguez AL, Jiang J., Plant Cell 23(11), 2011
PMID: 22080597

77 References

Daten bereitgestellt von Europe PubMed Central.

Epigenetic regulation of centromeric chromatin: old dogs, new tricks?
Allshire RC, Karpen GH., Nat. Rev. Genet. 9(12), 2008
PMID: 19002142

K, Plant Mol Bio Reporter 9(3), 1991

FM, 1987
Do Plants Have a One-Way Ticket to Genomic Obesity?
Bennetzen JL, Kellogg EA., Plant Cell 9(9), 1997
PMID: 12237393
The mammalian epigenome.
Bernstein BE, Meissner A, Lander ES., Cell 128(4), 2007
PMID: 17320505
DNA methylation patterns and epigenetic memory.
Bird A., Genes Dev. 16(1), 2002
PMID: 11782440
Perceptions of epigenetics.
Bird A., Nature 447(7143), 2007
PMID: 17522671
The diversity of RNA silencing pathways in plants.
Brodersen P, Voinnet O., Trends Genet. 22(5), 2006
PMID: 16567016
Transcription and RNAi in heterochromatic gene silencing.
Buhler M, Moazed D., Nat. Struct. Mol. Biol. 14(11), 2007
PMID: 17984966
Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes.
Cao X, Jacobsen SE., Proc. Natl. Acad. Sci. U.S.A. 99 Suppl 4(), 2002
PMID: 12151602
Gardening the genome: DNA methylation in Arabidopsis thaliana.
Chan SW, Henderson IR, Jacobsen SE., Nat. Rev. Genet. 6(5), 2005
PMID: 15861207
Specialization and evolution of endogenous small RNA pathways.
Chapman EJ, Carrington JC., Nat. Rev. Genet. 8(11), 2007
PMID: 17943195
The evolutionary dynamics of repetitive DNA in eukaryotes.
Charlesworth B, Sniegowski P, Stephan W., Nature 371(6494), 1994
PMID: 8078581
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE., Nature 452(7184), 2008
PMID: 18278030
Molecular organization of terminal repetitive DNA in Beta species.
Dechyeva D, Schmidt T., Chromosome Res. 14(8), 2006
PMID: 17195925
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H., Nucleic Acids Res. 36(16), 2008
PMID: 18660515
Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
Dohm JC, Lange C, Reinhardt R, Himmelbauer H., Plant J. 57(1), 2008
PMID: 18764921
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC., Nature 391(6669), 1998
PMID: 9486653
Genome size and the proportion of repeated nucleotide sequence DNA in plants.
Flavell RB, Bennett MD, Smith JB, Smith DB., Biochem. Genet. 12(4), 1974
PMID: 4441361
Chromosomal histone modification patterns--from conservation to diversity.
Fuchs J, Demidov D, Houben A, Schubert I., Trends Plant Sci. 11(4), 2006
PMID: 16546438

J, 2010
Small silencing RNAs: an expanding universe.
Ghildiyal M, Zamore PD., Nat. Rev. Genet. 10(2), 2009
PMID: 19148191
Heterochromatin revisited.
Grewal SI, Jia S., Nat. Rev. Genet. 8(1), 2007
PMID: 17173056
Epigenetic inheritance in plants.
Henderson IR, Jacobsen SE., Nature 447(7143), 2007
PMID: 17522675
Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.
Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE., Nat. Genet. 38(6), 2006
PMID: 16699516
A bacterial artificial chromosome (BAC) library of sugar beet and a physical map of the region encompassing the bolting gene B.
Hohmann U, Jacobs G, Telgmann A, Gaafar RM, Alam S, Jung C., Mol. Genet. Genomics 269(1), 2003
PMID: 12715161
Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content.
Houben A, Demidov D, Gernand D, Meister A, Leach CR, Schubert I., Plant J. 33(6), 2003
PMID: 12631322
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.
Jackson JP, Lindroth AM, Cao X, Jacobsen SE., Nature 416(6880), 2002
PMID: 11898023
Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana.
Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE., Chromosoma 112(6), 2004
PMID: 15014946
Translating the histone code.
Jenuwein T, Allis CD., Science 293(5532), 2001
PMID: 11498575
The SRA methyl-cytosine-binding domain links DNA and histone methylation.
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE., Curr. Biol. 17(4), 2007
PMID: 17239600
Construction and characterization of a sugar beet (Beta vulgaris) fosmid library.
Lange C, Holtgrawe D, Schulz B, Weisshaar B, Himmelbauer H., Genome 51(11), 2008
PMID: 18956027
Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice.
Lee HR, Neumann P, Macas J, Jiang J., Mol. Biol. Evol. 23(12), 2006
PMID: 16987952
GTP/GDP exchange by Sec12p enables COPII vesicle bud formation on synthetic liposomes.
Futai E, Hamamoto S, Orci L, Schekman R., EMBO J. 23(21), 2004
PMID: 15457212
The role of RNA interference in heterochromatic silencing.
Lippman Z, Martienssen R., Nature 431(7006), 2004
PMID: 15372044
Epigenetic regulation of transposable elements in plants.
Lisch D., Annu Rev Plant Biol 60(), 2009
PMID: 19007329
Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR., Cell 133(3), 2008
PMID: 18423832
Evolution and function of B chromosome 45S rDNA sequences in Brachycome dichromosomatica.
Marschner S, Meister A, Blattner FR, Houben A., Genome 50(7), 2007
PMID: 17893741
RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe.
Martienssen RA, Zaratiegui M, Goto DB., Trends Genet. 21(8), 2005
PMID: 15979194
RNA-mediated chromatin-based silencing in plants.
Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ., Curr. Opin. Cell Biol. 21(3), 2009
PMID: 19243928
Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats.
May BP, Lippman ZB, Fang Y, Spector DL, Martienssen RA., PLoS Genet. 1(6), 2005
PMID: 16389298

JM, Plant Mol Bio Reporter 22(1), 2004
Mobilization and evolutionary history of miniature inverted-repeat transposable elements (MITEs) in Beta vulgaris L.
Menzel G, Dechyeva D, Keller H, Lange C, Himmelbauer H, Schmidt T., Chromosome Res. 14(8), 2006
PMID: 17171577
Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris).
Menzel G, Dechyeva D, Wenke T, Holtgrawe D, Weisshaar B, Schmidt T., Ann. Bot. 102(4), 2008
PMID: 18682437
Histone modifications and dynamic regulation of genome accessibility in plants.
Pfluger J, Wagner D., Curr. Opin. Plant Biol. 10(6), 2007
PMID: 17884714

J, 1989
Cloning and characterization of a Beta vulgaris satellite DNA family.
Schmidt T, Metzlaff M., Gene 101(2), 1991
PMID: 2055488
Distribution and evolution of two satellite DNAs in the genus Beta.
Schmidt T, Jung C, Metzlaff M., Theor. Appl. Genet. 82(6), 1991
PMID: IND92005175
Histone H3 Lys 4 methylation: caught in a bind?
Sims RJ 3rd, Reinberg D., Genes Dev. 20(20), 2006
PMID: 17043307
Transposable elements and the epigenetic regulation of the genome.
Slotkin RK, Martienssen R., Nat. Rev. Genet. 8(4), 2007
PMID: 17363976
DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis.
Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF., EMBO J. 21(23), 2002
PMID: 12456661
The language of covalent histone modifications.
Strahl BD, Allis CD., Nature 403(6765), 2000
PMID: 10638745
Repeat elements and the Arabidopsis DNA methylation landscape.
Teixeira FK, Colot V., Heredity (Edinb) 105(1), 2010
PMID: 20461104
A role for RNAi in the selective correction of DNA methylation defects.
Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, Voinnet O, Wincker P, Esteller M, Colot V., Science 323(5921), 2009
PMID: 19179494
Bursts of retrotransposition reproduced in Arabidopsis.
Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T., Nature 461(7262), 2009
PMID: 19734880
Functional elements residing within satellite DNAs.
Ugarkovic D., EMBO Rep. 6(11), 2005
PMID: 16264428
Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi.
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA., Science 297(5588), 2002
PMID: 12193640
Epigenetic interactions between transposons and genes: lessons from plants.
Weil C, Martienssen R., Curr. Opin. Genet. Dev. 18(2), 2008
PMID: 18339541
An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.
Wenke T, Holtgrawe D, Horn AV, Weisshaar B, Schmidt T., Plant Mol. Biol. 71(6), 2009
PMID: 19697140
Genetic and functional diversification of small RNA pathways in plants.
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC., PLoS Biol. 2(5), 2004
PMID: 15024409

AUTHOR UNKNOWN, 0
Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris.
Zakrzewski F, Wenke T, Holtgrawe D, Weisshaar B, Schmidt T., BMC Plant Biol. 10(), 2010
PMID: 20064260
The epigenetic landscape of plants.
Zhang X., Science 320(5875), 2008
PMID: 18436779
The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata.
Zhang W, Yi C, Bao W, Liu B, Cui J, Yu H, Cao X, Gu M, Liu M, Cheng Z., Plant Physiol. 139(1), 2005
PMID: 16113220
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR., Cell 126(6), 2006
PMID: 16949657
Genome-wide analysis of DNA methylation patterns.
Zilberman D, Henikoff S., Development 134(22), 2007
PMID: 17928417
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S., Nat. Genet. 39(1), 2006
PMID: 17128275

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21594600
PubMed | Europe PMC

Suchen in

Google Scholar