Molecular Cytogenetics | |
Immunofluorescent staining reveals hypermethylation of microchromosomes in the central bearded dragon, Pogona vitticeps | |
Janine E. Deakin3  Tariq Ezaz3  Sudha Rao1  Alexandra M. Livernois3  Renae Domaschenz2  | |
[1] Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra 2601, ACT, Australia;Present address: John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia;Institute for Applied Ecology, University of Canberra, Canberra 2601, ACT, Australia | |
关键词: Epigenetics; Histone modifications; Methylation; Reptiles; | |
Others : 1235197 DOI : 10.1186/s13039-015-0208-6 |
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received in 2015-10-26, accepted in 2015-12-18, 发布年份 2015 | |
【 摘 要 】
Background
Studies of model organisms have demonstrated that DNA cytosine methylation and histone modifications are key regulators of gene expression in biological processes. Comparatively little is known about the presence and distribution of epigenetic marks in non-model amniotes such as non-avian reptiles whose genomes are typically packaged into chromosomes of distinct size classes. Studies of chicken karyotypes have associated the gene-richness and high GC content of microchromosomes with a distinct epigenetic landscape. To determine whether this is likely to be a common feature of amniote microchromosomes, we have analysed the distribution of epigenetic marks using immunofluorescence on metaphase chromosomes of the central bearded dragon (Pogona vitticeps). This study is the first to study the distribution of epigenetic marks on non-avian reptile chromosomes.
Results
We observed an enrichment of DNA cytosine methylation, active modifications H3K4me2 and H3K4me3, as well as the repressive mark H3K27me3 in telomeric regions on macro and microchromosomes. Microchromosomes were hypermethylated compared to macrochromosomes, as they are in chicken. However, differences between macro- and microchromosomes for histone modifications associated with actively transcribed or repressed DNA were either less distinct or not detectable.
Conclusions
Hypermethylation of microchromosomes compared to macrochromosomes is a shared feature between P. vitticeps and avian species. The lack of the clear distinction between macro- and microchromosome staining patterns for active and repressive histone modifications makes it difficult to determine at this stage whether microchrosome hypermethylation is correlated with greater gene density as it is in aves, or associated with the greater GC content of P. vitticeps microchromosomes compared to macrochromosomes.
【 授权许可】
2015 Domaschenz et al.
【 预 览 】
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Fig. 1. | 81KB | Image | download |
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【 参考文献 】
- [1]Deakin JE, Domaschenz R, Siew Lim P, Ezaz T, Rao S. Comparative epigenomics: an emerging field with breakthrough potential to understand evolution of epigenetic regulation. AIMS Genet. 2014; 1:34-54.
- [2]Deakin JE, Ezaz T. Tracing the evolution of amniote chromosomes. Chromosoma. 2014; 123:201-216.
- [3]Uno Y, Nishida C, Tarui H, Ishishita S, Takagi C, Nishimura O et al.. Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLoS One. 2012; 7:e53027.
- [4]Grützner F, Zend-Ajusch E, Stout K, Munsche S, Niveleau A, Nanda I et al.. Chicken microchromosomes are hypermethylated and can be identified by specific painting probes. Cytogenet Cell Genet. 2001; 93:265-9.
- [5]Griffin DK, Haberman F, Masabanda J, O’Brien P, Bagga M, Sazanov A et al.. Micro- and macrochromosome paints generated by flow cytometry and microdissection: tools for mapping the chicken genome. Cytogenet Cell Genet. 1999; 87:278-281.
- [6]Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RPMA et al.. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics. 2008; 9:168. BioMed Central Full Text
- [7]Derjusheva S, Kurganova A, Habermann F, Gaginskaya E. High chromosome conservation detected by comparative chromosome painting in chicken, pigeon and passerine birds. Chromosom Res. 2004; 12:715-723.
- [8]McQueen HA, Siriaco G, Bird AP. Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Res. 1998; 8:621-630.
- [9]Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004; 432:695-716.
- [10]Smith J, Bruley CK, Paton IR, Dunn I, Jones CT, Windsor D et al.. Differences in gene density on chicken macrochromosomes and microchromosomes. Anim Genet. 2000; 31:96-103.
- [11]Auer H, Mayr B, Lambrou M, Schleger W. An extended chicken karyotype, including the NOR chromosome. Cytogenet Cell Genet. 1987; 45:218-221.
- [12]McQueen HA, Fantes J, Cross SH, Clark VH, Archibald AL, Bird AP. CpG islands of chicken are concentrated on microchromosomes. Nat Genet. 1996; 12:321-324.
- [13]Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 2005; 15:120-5.
- [14]Bisoni L, Batlle-morera L, Bird AP, Suzuki M, Mcqueen HA. Female-specific hyperacetylation of histone H4 in the chicken Z chromosome. Chromosom Res. 2005; 5:205-214.
- [15]Srikulnath K, Nishida C, Matsubara K, Uno Y, Thongpan A, Suputtitada S et al.. Karyotypic evolution in squamate reptiles: comparative gene mapping revealed highly conserved linkage homology between the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Lacertilia) and the Japanese four-striped rat snake (Elaphe quadrivirgata, Colubridae, Serpentes). Chromosome Res. 2009; 17:975-86.
- [16]Srikulnath K, Uno Y, Nishida C, Matsuda Y. Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the toxicofera clade. Chromosom Res. 2013; 21:805-819.
- [17]Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E et al.. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011; 477:587-91.
- [18]Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K et al.. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics. 2012; 13:604. BioMed Central Full Text
- [19]Matsubara K, Tarui H, Toriba M, Yamada K, Nishida-Umehara C, Agata K et al.. Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc Natl Acad Sci U S A. 2006; 103:18190-18195.
- [20]Ezaz T, Quinn AE, Miura I, Sarre SD, Georges A, Marshall Graves JA. The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes. Chromosom Res. 2005; 13:763-776.
- [21]Georges A, Li Q, Lian J, Meally DO, Deakin J, Wang Z et al.. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. Gigascience. 2015; 4:45. BioMed Central Full Text
- [22]O’Meally D, Miller H, Patel HR, Graves JAM, Ezaz T. The first cytogenetic map of the tuatara, Sphenodon punctatus. Cytogenet Genome Res. 2009; 127:213-23.
- [23]Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Matsuda Y. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosom Res. 2006; 14:187-202.
- [24]Young MJ, Meally DO, Sarre SD. Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps ( Squamata : Agamidae ). Chromosom Res. 2013; 21:361-374.
- [25]Witten G. Some Karyotypes of Australian Agamids (Reptilia : Lacertilia). Aust J Zool. 1983; 31:533-540.
- [26]Terrenoire E, McRonald F, Halsall JA, Page P, Illingworth RS, Taylor AMR et al.. Immunostaining of modified histones defines high-level features of the human metaphase epigenome. Genome Biol. 2010; 11:R110. BioMed Central Full Text
- [27]Zhang T, Cooper S, Brockdorff N, Ash L, Dot L. The interplay of histone modifications – writers that read. EMBO Rep. 2015; 16:1467-1481.
- [28]Barbin A, Montpellier C, Kokalj-Vokac N, Gibaud A, Niveleau A, Malfoy B et al.. New sites of methylcytosine-rich DNA detected on metaphase chromosomes. Hum Genet. 1994; 94:684-692.
- [29]Ingles ED, Deakin JE. Global DNA Methylation patterns on marsupial and devil facial tumour chromosomes. Mol Cytogenet. 2015; 8:74. BioMed Central Full Text
- [30]Rens W, Wallduck MS, Lovell FL, Ferguson-Smith MA, Ferguson-Smith AC. Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc Natl Acad Sci U S A. 2010; 107:17657-62.
- [31]Frediani M, Giraldi E, Ruffini Castiglione M. Distribution of 5-methylcytosine-rich regions in the metaphase chromosomes of Vicia faba. Chromosom Res. 1996; 4:141-146.
- [32]Brock GJR, Charlton J, Bird A. Densely methylated sequences that are preferentially localized at telomere-proximal regions of human chromosomes. Gene. 1999; 240:269-277.
- [33]Gonzalo S, Jaco I, Fraga MF, Chen T, Li E, Esteller M et al.. DNA methyltransferases control telomere length and telomere recombination in mammalian cells. Nat Cell Biol. 2006; 8:416-424.
- [34]Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 2007; 39:61-69.
- [35]Hellman A, Chess A. Gene body-specific methylation on the active X chromosome. Science. 2007; 315:1141-1143.
- [36]Loebel DA, Johnston PG. Analysis of DNase 1 sensitivity and methylation of active and inactive X chromosomes of kangaroos (Macropus robustus) by in situ nick translation. 1993;102:81–87.
- [37]Terrenoire E, Halsall JA, Turner BM. Immunolabelling of human metaphase chromosomes reveals the same banded distribution of histone H3 isoforms methylated at lysine 4 in primary lymphocytes and cultured cell lines. BMC Genet. 2015; 16:1-7. BioMed Central Full Text
- [38]Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics. 2009; 10:143. BioMed Central Full Text
- [39]Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science. 2007; 318:798-801.
- [40]Schoeftner S, Blasco MA. Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol. 2008; 10:228-236.
- [41]Koina E, Chaumeil J, Greaves IK, Tremethick DJ, Graves JAM. Specific patterns of histone marks accompany X chromosome inactivation in a marsupial. Chromosome Res. 2009; 17:115-26.
- [42]Ezaz T, O’Meally D, Quinn AE, Sarre SD, Georges A, Marshall Graves JA. A simple non-invasive protocol to establish primary cell lines from tail and toe explants for cytogenetic studies in Australian dragon lizards (Squamata: Agamidae). Cytotechnology. 2008; 58:135-139.
- [43]Alsop AE, Miethke P, Rofe R, Koina E, Sankovic N, Deakin JE et al.. Characterizing the chromosomes of the Australian model marsupial Macropus eugenii (tammar wallaby). Chromosom Res. 2005; 13:627-636.
- [44]Deakin JE, Bender HS, Pearse AM, Rens W, O’Brien PCM, Ferguson-Smith MA et al.. Genomic restructuring in the tasmanian devil facial tumour: Chromosome painting and gene mapping provide clues to evolution of a transmissible tumour. PLoS Genet. 2012; 8:e1002483.