Bisulfite sequencing(BS-seq)technology measures DNA methylation at single nucleotide resolution.A key task in BSseq data analysis is to identify differentially methylation(DM)under different conditions.Here we provide...Bisulfite sequencing(BS-seq)technology measures DNA methylation at single nucleotide resolution.A key task in BSseq data analysis is to identify differentially methylation(DM)under different conditions.Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS.DSS uses a beta-binomial model to characterize the sequence counts from BS-seq,and implements rigorous statistical method for hypothesis testing.It provides flexible functionalities for a variety of DM analyses.展开更多
The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and geno...The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing （RRGS）, which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion （up to 60%） of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD- seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.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
Background Wool fibers are valuable materials for textile industry.Typical wool fibers are divided into medullated and non-medullated types,with the former generated from primary wool follicles and the latter by eithe...Background Wool fibers are valuable materials for textile industry.Typical wool fibers are divided into medullated and non-medullated types,with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles.The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding.The fine wool sheep have a non-medullated coat.However,the critical period determining the type of wool follicles is the embryonic stage,which limits the phenotypic observation and variant contrast,making both selection and studies of wool type variation fairly difficult.Results During the breeding of a modern fine(MF)wool sheep population with multiple-ovulation and embryo transfer technique,we serendipitously discovered lambs with ancestral-like coarse(ALC)wool.Whole-genome rese-quencing confirmed ALC wool lambs as a variant type from the MF wool population.We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals,and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs.Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes.An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former.Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles.Conclusion In this study,we conducted genome-wide differential methylation site association analysis on differen-tial wool type trait,and located the only CpG locus that strongly associated with primary wool follicle development.Combined with transcriptome analysis,SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin.The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.展开更多
Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There a...Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There are significant differences in their phenotypic traits,including body image,growth performance,and meat quality.This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing(RRBS).It was observed that the pH at 45 min(pH_(45min),P=5.22e-13),lightness at 45 min(L^(*)_(45min),P=4.85e-5),and lightness at 24 h(L^(*)_(24h),P=3.57e-5)of CH pigs were higher than those of QY pigs.We detected 10699 differentially methylated cytosines(DMCs)and 2760 differentially methylated genes(DMGs)associated with these DMCs.Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway,Type II diabetes mellitus,Insulin signaling pathway,mTOR signaling pathway,and Insulin resistance.Furthermore,15 DMGs were associated with fat metabolism(ACACA,CAB39,CRADD,CRTC2,FASN,and GCK),muscle development(HK2,IKBKB,MTOR,PIK3CD,PPARGC1A,and RPTOR),or meat quality traits(PCK1,PRKAG2,and SLC2A4).The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.展开更多
Background:Tan sheep,an important local sheep breed in China,is famous for their fur quality.One-month-old Tan sheep have white,curly hair with beautiful flower spikes,commonly known as“nine bends”,which has high ec...Background:Tan sheep,an important local sheep breed in China,is famous for their fur quality.One-month-old Tan sheep have white,curly hair with beautiful flower spikes,commonly known as“nine bends”,which has high economic value.However,the“nine bends”characteristic gradually disappears with age;consequently,the economic value of the Tan sheep decreases.Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression.Until now,no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages.In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing,and compared the DNA methylation levels at three different growth stages:1,24,and 48 months old(mon1,mon24,and mon48,respectively).Results:In this study,11 skin samples from three growth stages(four for mon1,four for mon24,and three for mon48)were used for DNA methylation analysis and gene expression profiling.There were 52,288 and 236 differentially methylated genes(DMGs)identified between mon1 and mon24,mon1 and mon48,and mon24 and mon48,respectively.Of the differentially methylated regions,1.11%,7.61%,and 7.65% were in the promoter in mon1 vs.mon24,mon24 vs.mon48,and mon1 vs.mon48,respectively.DMGs were enriched in the MAPK and WNT signaling pathways,which are related to age growth and hair follicle morphogenesis processes.There were 51 DMGs associated with age growth and curly fleece formation.Four DMGs between mon1 and mon48(KRT71,CD44,ROR2 and ZDHHC13)were further validated by bisulfite sequencing.Conclusions:This study revealed dynamic changes in the genomic methylation profiles of mon1,mon24,and mon48 sheep,and the percentages of methylated cytosines were 3.38%,2.85% and 4.17%,respectively.Of the DMGs,KRT71 and CD44 were highly methylated in mon1,and ROR2 and ZDHHC13 were highly methylated in mon48.These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.展开更多
Sex reversal is a complex biological phenomenon that occurs in Cynoglossus semilaevis.Some genetic females may irreversibly convert to pseudomales,thus increasing aquaculture costs because males grow much more slowly ...Sex reversal is a complex biological phenomenon that occurs in Cynoglossus semilaevis.Some genetic females may irreversibly convert to pseudomales,thus increasing aquaculture costs because males grow much more slowly than females.In recent years,our studies have shown that genetic background is the primary factor contributing to sex reversal in tongue sole,and two linked loci on the Z chromosome were found to be associated with sex reversal.However,the role of epigenetics in sex reversal and temperature-independent sex determination has yet to be determined.In this study,we used reduced representation bisulfite sequencing(RRBS)to investigate the differences in methylation among female,male and pseudomale tongue sole and explored the possible pattern of DNA methylation associated with sex differentiation and sex reversal.A total of 32200,341115 and 2691 DMRs with average lengths of 163.45,170.15 and 128.77 bp,respectively,were identified between pseudomales and females,males and females,and pseudomales and males.Notably,the sex chromosome(Chr.Z)contained the greatest number of DMRs(303)between pseudomales and males.All the DMGs in each pairwise comparison were enriched in ubiquitin-mediated proteolysis,biosynthesis of secondary metabolites,thermogenesis and metabolic pathways,etc.In addition,differentially methylated genes possibly related to sex differentiation,such as dmrt1,nobox,foxl2,pdgfrb,rspo1,lhx9,emx2,arx,and piwil2,were screened.Methylation differential genes and metabolic pathways associated with sex differentiation have been identified,suggesting the vital role of methylation in gender reversal and sex determination.This study provides valuable insight into epigenetic mechanisms involved in sex differentiation and sex reversal in C.semilaevis.展开更多
Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine(5m C) oxidation deriv...Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine(5m C) oxidation derivatives including 5-hydroxymethylcytosine(5hm C), 5-formylcytsine(5f C) and 5-carboxycytosine(5ca C) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing(BS-seq), TAB-seq(TET-assisted bisulfite sequencing), ox BS-seq(oxidative bisulfite sequencing) and etc. These methods have been used to generate base-resolution maps of 5m C and its oxidation derivatives in genomic samples. The focus of this review will be to discuss the chemical methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.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
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
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
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(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factor...DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factors.However,the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities.Here,we performed double-strand bisulfite sequencing(DSBS)for 32 Chinese individuals representing four major ethnic groups including Han Chinese,Tibetan,Zhuang,and Mongolian.We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million Cp Gs in the population.We found global DNAm-based epigenetic structure is different from the genetic structure of the population,and ethnic difference only partially explains the variation of DNAm.Surprisingly,non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm.Differentially methylated regions(DMRs)among these ethnic groups were found around genes in diverse biological processes.Especially,these DMR-genes between Tibetan and nonTibetans were enriched around high-altitude genes including EPAS1 and EGLN1,suggesting DNAm alteration plays an important role in high-altitude adaptation.Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans'high-altitude adaptation.展开更多
Background:Essential tremor(ET)is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis.It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of...Background:Essential tremor(ET)is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis.It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET.DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET.Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET.Results:Using Nugen’s Ovation reduced representation bisulfite sequencing(RRBS),we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group.Identified genes were further analyzed with Ingenuity Pathway Analysis(IPA)by which we identified certain significant pathways,upstream regulators,diseases and functions,and networks associated with ET.Conclusions:Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples,suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis.The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease,particularly involving the cerebellum.展开更多
文摘Bisulfite sequencing(BS-seq)technology measures DNA methylation at single nucleotide resolution.A key task in BSseq data analysis is to identify differentially methylation(DM)under different conditions.Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS.DSS uses a beta-binomial model to characterize the sequence counts from BS-seq,and implements rigorous statistical method for hypothesis testing.It provides flexible functionalities for a variety of DM analyses.
文摘The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing （RRGS）, which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion （up to 60%） of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD- seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.
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.
基金the programs of National Key R&D Program of China(2021YFF1000700)National Natural Science Foundation of China(32002145)+1 种基金the Major Project for Cultivation Technology of New Varieties of Genetically Modified Organisms of the Ministry of Agriculture(grant Nos.2016ZX08008-001 and 2013ZX08008-001)Ningxia Agricultural Breeding Project(NXNYYZ2015010).
文摘Background Wool fibers are valuable materials for textile industry.Typical wool fibers are divided into medullated and non-medullated types,with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles.The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding.The fine wool sheep have a non-medullated coat.However,the critical period determining the type of wool follicles is the embryonic stage,which limits the phenotypic observation and variant contrast,making both selection and studies of wool type variation fairly difficult.Results During the breeding of a modern fine(MF)wool sheep population with multiple-ovulation and embryo transfer technique,we serendipitously discovered lambs with ancestral-like coarse(ALC)wool.Whole-genome rese-quencing confirmed ALC wool lambs as a variant type from the MF wool population.We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals,and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs.Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes.An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former.Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles.Conclusion In this study,we conducted genome-wide differential methylation site association analysis on differen-tial wool type trait,and located the only CpG locus that strongly associated with primary wool follicle development.Combined with transcriptome analysis,SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin.The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.
基金supported by the grants from the Sichuan Science and Technology Program, China (2020YFN0024)the China Agriculture Research System of MOF and MARA (CARS-35-01A)+3 种基金the National Key R&D Program of China (2018YFD0501204)the National Natural Science Foundation of China (C170102)the Sichuan Innovation Team of Pig, China (sccxtd-2021-08)supported by the High-performance Computing Platform of Sichuan Agricultural University, China
文摘Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There are significant differences in their phenotypic traits,including body image,growth performance,and meat quality.This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing(RRBS).It was observed that the pH at 45 min(pH_(45min),P=5.22e-13),lightness at 45 min(L^(*)_(45min),P=4.85e-5),and lightness at 24 h(L^(*)_(24h),P=3.57e-5)of CH pigs were higher than those of QY pigs.We detected 10699 differentially methylated cytosines(DMCs)and 2760 differentially methylated genes(DMGs)associated with these DMCs.Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway,Type II diabetes mellitus,Insulin signaling pathway,mTOR signaling pathway,and Insulin resistance.Furthermore,15 DMGs were associated with fat metabolism(ACACA,CAB39,CRADD,CRTC2,FASN,and GCK),muscle development(HK2,IKBKB,MTOR,PIK3CD,PPARGC1A,and RPTOR),or meat quality traits(PCK1,PRKAG2,and SLC2A4).The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.
基金supported by the talent cultivation and developmental support program of China Agricultural University,an award to study the cultivation of high-quality mutton sheep varieties(or lines)from Ningxia province(NXNYYZ20150101)the Natural Science Foundation of Hebei Province of China for Youths(C2019402261).
文摘Background:Tan sheep,an important local sheep breed in China,is famous for their fur quality.One-month-old Tan sheep have white,curly hair with beautiful flower spikes,commonly known as“nine bends”,which has high economic value.However,the“nine bends”characteristic gradually disappears with age;consequently,the economic value of the Tan sheep decreases.Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression.Until now,no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages.In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing,and compared the DNA methylation levels at three different growth stages:1,24,and 48 months old(mon1,mon24,and mon48,respectively).Results:In this study,11 skin samples from three growth stages(four for mon1,four for mon24,and three for mon48)were used for DNA methylation analysis and gene expression profiling.There were 52,288 and 236 differentially methylated genes(DMGs)identified between mon1 and mon24,mon1 and mon48,and mon24 and mon48,respectively.Of the differentially methylated regions,1.11%,7.61%,and 7.65% were in the promoter in mon1 vs.mon24,mon24 vs.mon48,and mon1 vs.mon48,respectively.DMGs were enriched in the MAPK and WNT signaling pathways,which are related to age growth and hair follicle morphogenesis processes.There were 51 DMGs associated with age growth and curly fleece formation.Four DMGs between mon1 and mon48(KRT71,CD44,ROR2 and ZDHHC13)were further validated by bisulfite sequencing.Conclusions:This study revealed dynamic changes in the genomic methylation profiles of mon1,mon24,and mon48 sheep,and the percentages of methylated cytosines were 3.38%,2.85% and 4.17%,respectively.Of the DMGs,KRT71 and CD44 were highly methylated in mon1,and ROR2 and ZDHHC13 were highly methylated in mon48.These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.
基金supported financially by the National Key Research and Development Program,China(2022YFD2400405)Special Scientific Research Funds for Central Nonprofit Institutes,Chinese Academy of Fishery Sciences,China(2023TD25).
文摘Sex reversal is a complex biological phenomenon that occurs in Cynoglossus semilaevis.Some genetic females may irreversibly convert to pseudomales,thus increasing aquaculture costs because males grow much more slowly than females.In recent years,our studies have shown that genetic background is the primary factor contributing to sex reversal in tongue sole,and two linked loci on the Z chromosome were found to be associated with sex reversal.However,the role of epigenetics in sex reversal and temperature-independent sex determination has yet to be determined.In this study,we used reduced representation bisulfite sequencing(RRBS)to investigate the differences in methylation among female,male and pseudomale tongue sole and explored the possible pattern of DNA methylation associated with sex differentiation and sex reversal.A total of 32200,341115 and 2691 DMRs with average lengths of 163.45,170.15 and 128.77 bp,respectively,were identified between pseudomales and females,males and females,and pseudomales and males.Notably,the sex chromosome(Chr.Z)contained the greatest number of DMRs(303)between pseudomales and males.All the DMGs in each pairwise comparison were enriched in ubiquitin-mediated proteolysis,biosynthesis of secondary metabolites,thermogenesis and metabolic pathways,etc.In addition,differentially methylated genes possibly related to sex differentiation,such as dmrt1,nobox,foxl2,pdgfrb,rspo1,lhx9,emx2,arx,and piwil2,were screened.Methylation differential genes and metabolic pathways associated with sex differentiation have been identified,suggesting the vital role of methylation in gender reversal and sex determination.This study provides valuable insight into epigenetic mechanisms involved in sex differentiation and sex reversal in C.semilaevis.
基金supported by the National Basic Research Foundation of China(2014CB964900 to Yi Chengqi)the National Natural Science Foundation of China(3127083821472009 to Yi Chengqi)
文摘Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine(5m C) oxidation derivatives including 5-hydroxymethylcytosine(5hm C), 5-formylcytsine(5f C) and 5-carboxycytosine(5ca C) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing(BS-seq), TAB-seq(TET-assisted bisulfite sequencing), ox BS-seq(oxidative bisulfite sequencing) and etc. These methods have been used to generate base-resolution maps of 5m C and its oxidation derivatives in genomic samples. The focus of this review will be to discuss the chemical methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.
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.
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 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the National Key Research and Development Program of China(2016YFC0900402)the Basic Science Center Program(32288101)+1 种基金the National Natural Science Foundation of China(32030020 and 31961130380)the Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)。
文摘DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factors.However,the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities.Here,we performed double-strand bisulfite sequencing(DSBS)for 32 Chinese individuals representing four major ethnic groups including Han Chinese,Tibetan,Zhuang,and Mongolian.We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million Cp Gs in the population.We found global DNAm-based epigenetic structure is different from the genetic structure of the population,and ethnic difference only partially explains the variation of DNAm.Surprisingly,non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm.Differentially methylated regions(DMRs)among these ethnic groups were found around genes in diverse biological processes.Especially,these DMR-genes between Tibetan and nonTibetans were enriched around high-altitude genes including EPAS1 and EGLN1,suggesting DNAm alteration plays an important role in high-altitude adaptation.Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans'high-altitude adaptation.
基金Our RRBS fastq files were submitted to GEO(Access number:GSE134426).
文摘Background:Essential tremor(ET)is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis.It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET.DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET.Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET.Results:Using Nugen’s Ovation reduced representation bisulfite sequencing(RRBS),we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group.Identified genes were further analyzed with Ingenuity Pathway Analysis(IPA)by which we identified certain significant pathways,upstream regulators,diseases and functions,and networks associated with ET.Conclusions:Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples,suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis.The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease,particularly involving the cerebellum.
