Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation...Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation. Few methylation variants were known until recently, making it possible to begin to address major unanswered questions： the extent of natural methylation variation within plant genomes, its effects on phenotypic variation, its degree of depend- ence on genotype, and how it fits into an evolutionary context. Techniques like whole-genome bisulfite sequencing （WGBS） make it possible to determine cytosine methylation states at single-base resolution across entire genomes and populations. Application of this method to natural and novel experimental populations is revealing answers to these long-standing questions about the role of DNA methylation in plant genomes.展开更多
Bisulfite at low concentrations(L-NaHSO3) increases cyclic electron transport around photosystem I(PSI) and photosynthesis.However,little is known regarding the detailed contribution of cyclic electron transport to th...Bisulfite at low concentrations(L-NaHSO3) increases cyclic electron transport around photosystem I(PSI) and photosynthesis.However,little is known regarding the detailed contribution of cyclic electron transport to the promoted photosynthesis by L-NaHSO3.In the present work,we used tobacco mutant defective in ndhC-ndhK-ndhJ(ndhCKJ) to investigate the role of NAD(P)H dehydrogenase(NDH)-dependent cyclic electron transport around PSI in an increase in photosynthesis by L-NaHSO3.After the treatment of tobacco leaves with L-NaHSO3(10 μmol L-1),the NDH-dependent cyclic electron transport,monitored by a transient post-illumination increase in Chl fluorescence and the amount of NDH,was notably up-regulated in wild type(WT).The NDH-dependent cyclic electron transport was severely impaired in ndhCKJ and was not significantly affected by treatment with L-NaHSO3.Accordingly,the NDH-dependent transthylakoid membrane proton gradient(pH),as reflected by the slow phase of millisecond-delayed light emission(ms-DLE),was increased by L-NaHSO3 in WT,but not in ndhCKJ;the enhancement of cyclic photophosphorylation(PSP) activity by L-NaHSO3 was more obvious in WT than ndhCKJ.The accumulation of both superoxide and hydrogen peroxide was reduced in WT when subjected to L-NaHSO3 treatment,but not in ndhCKJ.Furthermore,the increase of photosynthetic O 2 evolution rate by L-NaHSO3 was more significant in WT than in ndhCKJ.We therefore conclude that L-NaHSO3 alleviates the photo-oxidative damage by the enhancement of NDH-dependent cyclic PSP,thereby improving photosynthesis.展开更多
Leaf senescence is driven by the expression of senescence-associated genes(SAGs).Development-specific genes often undergo DNA demethylation in their promoter and other regions,which regulates gene expression.Whether a...Leaf senescence is driven by the expression of senescence-associated genes(SAGs).Development-specific genes often undergo DNA demethylation in their promoter and other regions,which regulates gene expression.Whether and how DNA demethylation regulates the expression of SAGs and thus leaf senescence remain elusive.Whole-genome bisulfite sequencing(WGBS)analyses of wild-type(WT)and demeter-like 3(dml3)Arabidopsis leaves at three developmental stages revealed hypermethylation during leaf senescence in dml3 compared with WT,and 20556 differentially methylated regions(DMRs)were identified by comparing the methylomes of dml3 and WT in the CG,CHG,and CHH contexts.Furthermore,we identified that 335 DMR-associated genes(DMGs),such as NAC016 and SEN1,are upregulated during leaf senescence,and found an inverse correlation between the DNA methylation levels(especially in the promoter regions)and the transcript abundances of the related SAGs in WT.In contrast,in dml3 the promoters of SAGs were hypermethylated and their transcript levels were remarkably reduced,and leaf senescence was significantly delayed.Collectively,our study unraveled a novel epigenetic regulatory mechanism underlying leaf senescence in which DML3 is expressed at the onset of and during senescence to demethylate promoter,gene body or 3'UTR regions to activate a set of SAGs.展开更多
Sulfur dioxide（SO_2） is a harmful environmental pollutant. Inhaled SO_2 can be rapidly hydrated into its derivatives, bisulfite（HSO_3^-） and sulfite（SO_3^（2-））. SO_2 derivatives are well known as preservatives...Sulfur dioxide（SO_2） is a harmful environmental pollutant. Inhaled SO_2 can be rapidly hydrated into its derivatives, bisulfite（HSO_3^-） and sulfite（SO_3^（2-））. SO_2 derivatives are well known as preservatives and antioxidants, which are used in food and beverages to prevent oxidation and bacterial growth. Although SO_2 can be endogenously generated in mammals and exhibits unique bioactivities in regulating cardiovascular function, excessive SO_2 and its derivatives have toxic effects on humans and animals for triggering adverse reactions and diseases. A large number of fluorescent probes for SO_2 and its derivatives have been designed and reported due to their high sensitivity and selectivity, high temporal and spatial resolution, non-invasive and non-destructive detection as well as real-time visualization in situ. In this review, we have summarized the recent progress of Michael addition-based fluorescent probes for SO_2 and its derivatives. These probes are categorized and concluded according to the different α,β-unsaturated compounds（i.e., Michael acceptors）. The design strategies, sensing performances, detection mechanisms and applications of these probes are discussed in detailed. Finally, a general overview about the design of probes for SO_2 and its derivatives is provided, which will facilitate the development of ideal probes for SO_2 and its derivatives.展开更多
DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, t...DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//qianlab.genetics.ac.cn/HeteroMeth.展开更多
Recent understanding of the role of epigenetic regulation in health and disease has necessitated the development of newer and efficient methods to map the methylation pattern of target gene. In this article we report ...Recent understanding of the role of epigenetic regulation in health and disease has necessitated the development of newer and efficient methods to map the methylation pattern of target gene. In this article we report construction of a stage-scanning laser confocal microscope (SLCM) and associated protocol that determines the methylation status of target gene. We have adapted restricted Sanger’s sequencing where fluorescine labeled primers and dideoxy guanine fraction alone are used for target amplification and termination at cytosine positions. Amplified ssDNA bands are separated in 6% denaturing PAGE and scanned using SLCM to sequence the positions of methylated cytosines. We demonstrate that our me- thodology can detect < 100 femtomoles of DNA, and resolve the position of cytosine within ± 2 nucleotide. In a calibration run using a designer DNA of 99 bases, our methodology had resolved all the 11 cytosine positions of the DNA. We have further demonstrated the utility of apparatus by mapping methylation status in the Exon-1 region of a gene, E-Cadherin, in the plasma DNA sample of a healthy subject. We believe our approach constitute a low cost alternative to conventional DNA sequencers and can help develop methylation based DNA biomarkers for the diagnosis of disease and in therapeutics.展开更多
AIM: To understand CD133 promoter hypermethyl-ation and expression in 32 colorectal cancer cell lines. METHODS: Nucleic acid was isolated from 32 colorectal cancer cell lines and CD133 expression levels were measured ...AIM: To understand CD133 promoter hypermethyl-ation and expression in 32 colorectal cancer cell lines. METHODS: Nucleic acid was isolated from 32 colorectal cancer cell lines and CD133 expression levels were measured by reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR. Promoter methylation status of the CD133 gene was analyzed with a methylation-specific PCR after sodium-bisulfi te modification and by clonal sequencing analysis. The correlation between expression and promoter methylation of CD133 gene was confirmed with treatment of 5-aza-2’-deoxycytidine. RESULTS: We measured CD133 expression levels in 32 colorectal cancer cell lines. RT-PCR analysis showed undetectable or low levels of CD133 expression in 34.4%of cell lines. To verify the relation between CD133 expression and methylation status of the CD133 gene promoter in colorectal carcinogenesis, CD133 gene promoter hypermethylation was analyzed in 32 cancer cell lines. Promoter hypermethylation was detected in 13 (40.6%) of the cell lines using methylation specificPCR and confirmed by bisulfite sequencing analysis. Treatment of 11 of the cell lines with the demethylation agent 5-aza-2’-deoxycytidine recovered CD133 expression in most of them. CONCLUSION: Transcriptional repression of CD133 is caused by promoter hypermethylation of the CD133 CpG islands in some of colorectal cancer cell lines. The study may contribute to the understanding of the role of CD133 inactivation in the progression of colorectal cancers.展开更多
O6-methylguanine DNA methyltransferase(MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expre...O6-methylguanine DNA methyltransferase(MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expression and methylation levels in the early embryo and in different embryonic stages, as well as the relationship between MGMT and neural tube defects. Spina bifida aperta was induced in rats by a single intragastric administration of all-trans retinoic acid on embryonic day(E) 10, whereas normal control rats received the same amount of olive oil on the same embryonic day. DNA damage was assessed by detecting γ-H2 A.X in spina bifida aperta rats. Real time-polymerase chain reaction was used to examine mRNA expression of MGMT in normal control and spina bifida aperta rats. In normal controls, the MGMT mRNA expression decreased with increasing embryonic days, and was remarkably reduced from E11 to E14, reaching a minimum at E18. In the spina bifida aperta model, γ-H2 A.X protein expression was increased, and mRNA expression of MGMT was markedly decreased on E14, E16, and E18. Bisulfite sequencing polymerase chain reaction for MGMT promoter methylation demonstrated that almost all CpG sites in the MGMT promoter remained unmethylated in both spina bifida aperta rats and normal controls, and there was no significant difference in methylation level between the two groups on either E14 or E18. Our results show that DNA damage occurs in spina bifida aperta rats. The mRNA expression of MGMT is downregulated, and this downregulation is independent of promoter DNA methylation.展开更多
DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increa...DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.展开更多
DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed mo...DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed monkey(Rhinopithecus bieti)and the closely related golden snub-nosed monkey(R.roxellana).Our findings indicated a slight increase in overall DNA methylation levels in golden snub-nosed monkeys compared to Yunnan snub-nosed monkeys,suggesting a higher prevalence of hypermethylated genomic regions in the former.Comparative genomic methylation analysis demonstrated that genes associated with differentially methylated regions were involved in membrane fusion,vesicular formation and trafficking,hemoglobin function,cell cycle regulation,and neuronal differentiation.These results suggest that the high-altitude-related epigenetic modifications are extensive,involving a complete adaptation process from the inhibition of single Ca^(2+)channel proteins to multiple proteins collaboratively enhancing vesicular function or inhibiting cell differentiation and proliferation.Functional assays demonstrated that overexpression or down-regulation of candidate genes,such as SNX10,TIMELESS,and CACYBP,influenced cell viability under stress conditions.Overall,this research suggests that comparing DNA methylation across closely related species can identify novel candidate genomic regions and genes associated with local adaptations,thereby deepening our understanding of the mechanisms underlying environmental adaptations.展开更多
文摘Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation. Few methylation variants were known until recently, making it possible to begin to address major unanswered questions： the extent of natural methylation variation within plant genomes, its effects on phenotypic variation, its degree of depend- ence on genotype, and how it fits into an evolutionary context. Techniques like whole-genome bisulfite sequencing （WGBS） make it possible to determine cytosine methylation states at single-base resolution across entire genomes and populations. Application of this method to natural and novel experimental populations is revealing answers to these long-standing questions about the role of DNA methylation in plant genomes.
基金supported by the National Key Basic Research Program of China (2009CB118504)the National Natural Science Foundation of China (30870183,31070215)
文摘Bisulfite at low concentrations(L-NaHSO3) increases cyclic electron transport around photosystem I(PSI) and photosynthesis.However,little is known regarding the detailed contribution of cyclic electron transport to the promoted photosynthesis by L-NaHSO3.In the present work,we used tobacco mutant defective in ndhC-ndhK-ndhJ(ndhCKJ) to investigate the role of NAD(P)H dehydrogenase(NDH)-dependent cyclic electron transport around PSI in an increase in photosynthesis by L-NaHSO3.After the treatment of tobacco leaves with L-NaHSO3(10 μmol L-1),the NDH-dependent cyclic electron transport,monitored by a transient post-illumination increase in Chl fluorescence and the amount of NDH,was notably up-regulated in wild type(WT).The NDH-dependent cyclic electron transport was severely impaired in ndhCKJ and was not significantly affected by treatment with L-NaHSO3.Accordingly,the NDH-dependent transthylakoid membrane proton gradient(pH),as reflected by the slow phase of millisecond-delayed light emission(ms-DLE),was increased by L-NaHSO3 in WT,but not in ndhCKJ;the enhancement of cyclic photophosphorylation(PSP) activity by L-NaHSO3 was more obvious in WT than ndhCKJ.The accumulation of both superoxide and hydrogen peroxide was reduced in WT when subjected to L-NaHSO3 treatment,but not in ndhCKJ.Furthermore,the increase of photosynthetic O 2 evolution rate by L-NaHSO3 was more significant in WT than in ndhCKJ.We therefore conclude that L-NaHSO3 alleviates the photo-oxidative damage by the enhancement of NDH-dependent cyclic PSP,thereby improving photosynthesis.
基金This work was supported by the National Key Research and Development Program of China(grant no.2019YFD1000300,to L.Chen)by Cornell University 1843351(to S.G.).
文摘Leaf senescence is driven by the expression of senescence-associated genes(SAGs).Development-specific genes often undergo DNA demethylation in their promoter and other regions,which regulates gene expression.Whether and how DNA demethylation regulates the expression of SAGs and thus leaf senescence remain elusive.Whole-genome bisulfite sequencing(WGBS)analyses of wild-type(WT)and demeter-like 3(dml3)Arabidopsis leaves at three developmental stages revealed hypermethylation during leaf senescence in dml3 compared with WT,and 20556 differentially methylated regions(DMRs)were identified by comparing the methylomes of dml3 and WT in the CG,CHG,and CHH contexts.Furthermore,we identified that 335 DMR-associated genes(DMGs),such as NAC016 and SEN1,are upregulated during leaf senescence,and found an inverse correlation between the DNA methylation levels(especially in the promoter regions)and the transcript abundances of the related SAGs in WT.In contrast,in dml3 the promoters of SAGs were hypermethylated and their transcript levels were remarkably reduced,and leaf senescence was significantly delayed.Collectively,our study unraveled a novel epigenetic regulatory mechanism underlying leaf senescence in which DML3 is expressed at the onset of and during senescence to demethylate promoter,gene body or 3'UTR regions to activate a set of SAGs.
基金financially supported by the National Key Research and Development Program of China (No. 2017YFD0501406)the National Natural Science Foundation of China (Nos. 31400301, 31560712)
文摘Sulfur dioxide（SO_2） is a harmful environmental pollutant. Inhaled SO_2 can be rapidly hydrated into its derivatives, bisulfite（HSO_3^-） and sulfite（SO_3^（2-））. SO_2 derivatives are well known as preservatives and antioxidants, which are used in food and beverages to prevent oxidation and bacterial growth. Although SO_2 can be endogenously generated in mammals and exhibits unique bioactivities in regulating cardiovascular function, excessive SO_2 and its derivatives have toxic effects on humans and animals for triggering adverse reactions and diseases. A large number of fluorescent probes for SO_2 and its derivatives have been designed and reported due to their high sensitivity and selectivity, high temporal and spatial resolution, non-invasive and non-destructive detection as well as real-time visualization in situ. In this review, we have summarized the recent progress of Michael addition-based fluorescent probes for SO_2 and its derivatives. These probes are categorized and concluded according to the different α,β-unsaturated compounds（i.e., Michael acceptors）. The design strategies, sensing performances, detection mechanisms and applications of these probes are discussed in detailed. Finally, a general overview about the design of probes for SO_2 and its derivatives is provided, which will facilitate the development of ideal probes for SO_2 and its derivatives.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences, China awarded to WQ (Grant No. XDA08020303)
文摘DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//qianlab.genetics.ac.cn/HeteroMeth.
文摘Recent understanding of the role of epigenetic regulation in health and disease has necessitated the development of newer and efficient methods to map the methylation pattern of target gene. In this article we report construction of a stage-scanning laser confocal microscope (SLCM) and associated protocol that determines the methylation status of target gene. We have adapted restricted Sanger’s sequencing where fluorescine labeled primers and dideoxy guanine fraction alone are used for target amplification and termination at cytosine positions. Amplified ssDNA bands are separated in 6% denaturing PAGE and scanned using SLCM to sequence the positions of methylated cytosines. We demonstrate that our me- thodology can detect < 100 femtomoles of DNA, and resolve the position of cytosine within ± 2 nucleotide. In a calibration run using a designer DNA of 99 bases, our methodology had resolved all the 11 cytosine positions of the DNA. We have further demonstrated the utility of apparatus by mapping methylation status in the Exon-1 region of a gene, E-Cadherin, in the plasma DNA sample of a healthy subject. We believe our approach constitute a low cost alternative to conventional DNA sequencers and can help develop methylation based DNA biomarkers for the diagnosis of disease and in therapeutics.
基金Supported by (in part) The Korea Science and Engineering Foundation (KOSEF) funded by the Korean government (MEST R01-2008-000-20108-0)
文摘AIM: To understand CD133 promoter hypermethyl-ation and expression in 32 colorectal cancer cell lines. METHODS: Nucleic acid was isolated from 32 colorectal cancer cell lines and CD133 expression levels were measured by reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR. Promoter methylation status of the CD133 gene was analyzed with a methylation-specific PCR after sodium-bisulfi te modification and by clonal sequencing analysis. The correlation between expression and promoter methylation of CD133 gene was confirmed with treatment of 5-aza-2’-deoxycytidine. RESULTS: We measured CD133 expression levels in 32 colorectal cancer cell lines. RT-PCR analysis showed undetectable or low levels of CD133 expression in 34.4%of cell lines. To verify the relation between CD133 expression and methylation status of the CD133 gene promoter in colorectal carcinogenesis, CD133 gene promoter hypermethylation was analyzed in 32 cancer cell lines. Promoter hypermethylation was detected in 13 (40.6%) of the cell lines using methylation specificPCR and confirmed by bisulfite sequencing analysis. Treatment of 11 of the cell lines with the demethylation agent 5-aza-2’-deoxycytidine recovered CD133 expression in most of them. CONCLUSION: Transcriptional repression of CD133 is caused by promoter hypermethylation of the CD133 CpG islands in some of colorectal cancer cell lines. The study may contribute to the understanding of the role of CD133 inactivation in the progression of colorectal cancers.
基金supported by the National Natural Science Foundation of China,No.81671469,81171072(to ZWY)the National Basic Research Program of China(973 Program),No.2013CB945402(to ZWY)the Program for Liaoning Innovative Research Team in University of China,No.LT2013016(to ZWY)
文摘O6-methylguanine DNA methyltransferase(MGMT), a DNA repair enzyme, has been reported in some congenital malformations, but it is less frequently reported in neural tube defects. This study investigated MGMT mRNA expression and methylation levels in the early embryo and in different embryonic stages, as well as the relationship between MGMT and neural tube defects. Spina bifida aperta was induced in rats by a single intragastric administration of all-trans retinoic acid on embryonic day(E) 10, whereas normal control rats received the same amount of olive oil on the same embryonic day. DNA damage was assessed by detecting γ-H2 A.X in spina bifida aperta rats. Real time-polymerase chain reaction was used to examine mRNA expression of MGMT in normal control and spina bifida aperta rats. In normal controls, the MGMT mRNA expression decreased with increasing embryonic days, and was remarkably reduced from E11 to E14, reaching a minimum at E18. In the spina bifida aperta model, γ-H2 A.X protein expression was increased, and mRNA expression of MGMT was markedly decreased on E14, E16, and E18. Bisulfite sequencing polymerase chain reaction for MGMT promoter methylation demonstrated that almost all CpG sites in the MGMT promoter remained unmethylated in both spina bifida aperta rats and normal controls, and there was no significant difference in methylation level between the two groups on either E14 or E18. Our results show that DNA damage occurs in spina bifida aperta rats. The mRNA expression of MGMT is downregulated, and this downregulation is independent of promoter DNA methylation.
文摘DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.
基金supported by the National Natural Science Foundation of China(32330015,31821001)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)。
文摘DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed monkey(Rhinopithecus bieti)and the closely related golden snub-nosed monkey(R.roxellana).Our findings indicated a slight increase in overall DNA methylation levels in golden snub-nosed monkeys compared to Yunnan snub-nosed monkeys,suggesting a higher prevalence of hypermethylated genomic regions in the former.Comparative genomic methylation analysis demonstrated that genes associated with differentially methylated regions were involved in membrane fusion,vesicular formation and trafficking,hemoglobin function,cell cycle regulation,and neuronal differentiation.These results suggest that the high-altitude-related epigenetic modifications are extensive,involving a complete adaptation process from the inhibition of single Ca^(2+)channel proteins to multiple proteins collaboratively enhancing vesicular function or inhibiting cell differentiation and proliferation.Functional assays demonstrated that overexpression or down-regulation of candidate genes,such as SNX10,TIMELESS,and CACYBP,influenced cell viability under stress conditions.Overall,this research suggests that comparing DNA methylation across closely related species can identify novel candidate genomic regions and genes associated with local adaptations,thereby deepening our understanding of the mechanisms underlying environmental adaptations.
