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151.
Background
Mammalian CpG islands (CGIs) normally escape DNA methylation in all adult tissues and developmental stages. However, in our previous study we unexpectedly identified many methylated CGIs in human peripheral blood leukocytes. Methylated CpG dinucleotides convert to TpG dinucleotides through deaminization of their cytosine bases more frequently than hypomethylated CpG dinucleotides. Therefore, we wondered how methylated CGIs in germline or non-germline cells maintain their CpG-rich sequences. It is known that events such as germline hypomethylation, CpG selection, biased gene conversion (BGC), and frequent CpG fixation can contribute to the maintenance of CpG-rich sequences in methylated CGIs in germline or non-germline cells. However, it has not been investigated which of the processes maintain CpG-rich sequences of methylated CGIs in each genomic position.Results
In this study, we comprehensively examined the contribution of the processes described above to the maintenance of CpG-rich sequences in methylated CGIs in germline and non-germline cells which were classified by genomic positions. Approximately 60–80% of CGIs with high methylation in H1 cell line (H1-HM) in all the genomic positions showed a low average CpG → TpG/CpA substitution rate. In contrast, fewer than half the numbers of CGIs with H1-HM in all the genomic positions showed a low average CpG → TpG/CpA substitution rate and low levels of methylation in sperm cells (SPM-LM). Furthermore, a small fraction of CGIs with a low average CpG → TpG/CpA substitution rate and high levels of methylation in sperm cells (SPM-HM) showed CpG selection.On the other hand, independent of the positions in genes, most CGIs with SPM-HM showed a slightly higher average TpG/CpA → CpG substitution rate compared with those with SPM-LM.Conclusions
Relatively high numbers (approximately 60–80%) of CGIs with H1-HM in all the genomic positions preserve their CpG-rich sequences by a low CpG → TpG/CpA substitution rate caused mainly by their SPM-LM, and for those with SPM-HM partly by CpG selection and TpG/CpA → CpG fixation. BGC has little contribution to the maintenance of CpG-rich sequences of CGIs with SPM-HM which were classified by genomic positions.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1286-x) contains supplementary material, which is available to authorized users. 相似文献152.
Abscisic acid (ABA) is not a plant-specific compound but one found in organisms across kingdoms from bacteria to animals,
suggesting that it is a ubiquitous and versatile substance that can modulate physiological functions of various organisms.
Recent studies have shown that plants developed an elegant system for ABA sensing and early signal transduction mechanisms
to modulate responses to environmental stresses for survival in terrestrial conditions. ABA-induced increase in stress tolerance
has been reported not only in vascular plants but also in non-vascular bryophytes. Since bryophytes are the key group of organisms
in the context of plant evolution, clarification of their ABA-dependent processes is important for understanding evolutionary
adaptation of land plants. Molecular approaches using Physcomitrella patens have revealed that ABA plays a role in dehydration stress tolerance in mosses, which comprise a major group of bryophytes.
Furthermore, we recently reported that signaling machinery for ABA responses is also conserved in liverworts, representing
the most basal members of extant land plant lineage. Conservation of the mechanism for ABA sensing and responses in angiosperms
and basal land plants suggests that acquisition of this mechanism for stress tolerance in vegetative tissues was one of the
critical evolutionary events for adaptation to the land. This review describes the role of ABA in basal land plants as well
as non-land plant organisms and further elaborates on recent progress in molecular studies of model bryophytes by comparative
and functional genomic approaches. 相似文献
153.
Genetic networks and soft computing 总被引:1,自引:0,他引:1
Mitra S Das R Hayashi Y 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2011,8(1):94-107
The analysis of gene regulatory networks provides enormous information on various fundamental cellular processes involving growth, development, hormone secretion, and cellular communication. Their extraction from available gene expression profiles is a challenging problem. Such reverse engineering of genetic networks offers insight into cellular activity toward prediction of adverse effects of new drugs or possible identification of new drug targets. Tasks such as classification, clustering, and feature selection enable efficient mining of knowledge about gene interactions in the form of networks. It is known that biological data is prone to different kinds of noise and ambiguity. Soft computing tools, such as fuzzy sets, evolutionary strategies, and neurocomputing, have been found to be helpful in providing low-cost, acceptable solutions in the presence of various types of uncertainties. In this paper, we survey the role of these soft methodologies and their hybridizations, for the purpose of generating genetic networks. 相似文献
154.
Feng Li Yoichi Hasegawa Masako Saito Sachiko Shirasawa Aki Fukushima Toyoaki Ito Hiroshi Fujii Sachie Kishitani Hiroyasu Kitashiba Takeshi Nishio 《DNA research》2011,18(5):401-411
A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. 相似文献
155.
Ahmed Wael A. Mori Terumi Nishimura Yoichi Nakata Seiichi Kato Takema Abdelhamid Wam Kurahashi Hiroki Suzuki Kenji 《Sleep and biological rhythms》2011,9(2):73-77
Sleep and Biological Rhythms - The pathogenesis of obstructive sleep apnea (OSA) is not fully understood, particularly at the genetic level. The orexins have pleiotropic effects on several aspects... 相似文献
156.
Auerbach AD Burn J Cassiman JJ Claustres M Cotton RG Cutting G den Dunnen JT El-Ruby M Vargas AF Greenblatt MS Macrae F Matsubara Y Rimoin DL Vihinen M Van Broeckhoven C 《Nature reviews. Genetics》2011,12(12):881; discussion 881
157.
To understand the physiological basis of methanogenic archaea living on interspecies H(2) transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain ΔH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H(2) supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F(420)-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that α subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic methanogens to syntrophic growth is more complicated than that of hitherto proposed. 相似文献
158.
Chow S Jeffs A Miyake Y Konishi K Okazaki M Suzuki N Abdullah MF Imai H Wakabayasi T Sakai M 《PloS one》2011,6(12):e29280
The pronghorn spiny lobster, Panulirus penicillatus, is a circumtropical species which has the widest global distribution among all the species of spiny lobster, ranging throughout the entire Indo-Pacific region. Partial nucleotide sequences of mitochondrial DNA COI (1,142-1,207 bp) and 16S rDNA (535-546 bp) regions were determined for adult and phyllosoma larval samples collected from the Eastern Pacific (EP)(Galápagos Islands and its adjacent water), Central Pacific (CP)(Hawaii and Tuamotu) and the Western Pacific (WP)(Japan, Indonesia, Fiji, New Caledonia and Australia). Phylogenetic analyses revealed two distinct large clades corresponding to the geographic origin of samples (EP and CP+WP). No haplotype was shared between the two regional samples, and average nucleotide sequence divergence (Kimura's two parameter distance) between EP and CP+WP samples was 3.8±0.5% for COI and 1.0±0.4% for 16S rDNA, both of which were much larger than those within samples. The present results indicate that the Pacific population of the pronghorn spiny lobster is subdivided into two distinct populations (Eastern Pacific and Central to Western Pacific), with no gene flow between them. Although the pronghorn spiny lobster have long-lived teleplanic larvae, the vast expanse of Pacific Ocean with no islands and no shallow substrate which is known as the East Pacific Barrier appears to have isolated these two populations for a long time (c.a. 1MY). 相似文献
159.
Kawarada H Yoshikawa Y Yasui H Kuwahara S Habata Y Saito R 《Metallomics : integrated biometal science》2011,3(7):675-679
Several Zn(II) complexes (2a-e) of 1-arylmethyl-2,5-dihydro-4-hydroxy-5-oxo-1H-pyrrole-3-carboxylates (1a-e), known drug candidates for diabetic complications, were synthesized and proved to have in vitro insulin-mimetic activities, suggesting that these complexes are potential chemotherapeutics that are effective against both diabetes and diabetic complications. 相似文献
160.
Furuya Y Chan J Wan EC Koskinen A Diener KR Hayball JD Regner M Müllbacher A Alsharifi M 《PloS one》2011,6(10):e25765