Extrachromosomal circular DNA is common in yeast

Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs in the Saccharomyces cerevisiae genome using Circle-Seq, a highly sensitive eccDNA purification method. Yeast eccDNAs ranged from an arbitrary lower limit of 1 kb up to 38 kb and covered 23% of the genome, representing thousands of genes. EccDNA arose both from genomic regions with repetitive sequences ≥15 bases long and from regions with short or no repetitive sequences. Some eccDNAs were identified in several yeast populations. These eccDNAs contained ribosomal genes, transposon remnants, and tandemly repeated genes (HXT6/7, ENA1/2/5, and CUP1-1/-2) that were generally enriched on eccDNAs. EccDNAs seemed to be replicated and 80% contained consensus sequences for autonomous replication origins that could explain their maintenance. Our data suggest that eccDNAs are common in S. cerevisiae, where they might contribute substantially to genetic variation and evolution.Copy number variants (CNVs) are alterations in number of copies of particular genes or other extensive DNA sequences in a genome. Gene deletions and amplifications are important sources of genetic variation that have proven important in the evolution of multicellular organisms. The high prevalence of families of paralogous genes, such as globins, protein kinases, and serine proteases, strongly supports the idea that gene duplication and divergence underlie much of evolution (1). In human somatic cells, CNVs have been implicated in cancer (2) and aging (3), as well as developmental and neurological diseases (4, 5). The best-studied types of CNVs are chromosomal gene amplifications and deletions that can easily be characterized by genome sequencing or tiling arrays (6, 7) or as cytological visible homogeneously staining regions (8).Extrachromosomal circular DNAs (eccDNAs) represent a less studied form of CNVs although examples of eccDNAs have been detected in many organisms. In humans, eccDNAs are produced during Ig heavy-chain class switching (9). In higher plant genomes, repeat-derived eccDNAs are considered intermediates in the evolution of satellite repeats (10). In aging Saccharomyces cerevisiae cells, ribosomal rDNA circles accumulate (11). Also, in yeast, eccDNAs are generated from telomeric regions that contain many repeated sequences (12), and recombination between retrotransposon or their remnants in the form of solo long terminal repeats (LTRs) has been implicated in the formation of eccDNA (13, 14). Generally, eccDNAs are acentric and thus expected to missegregate during cell division, resulting in copy number variation (15). However, the abundance of eccDNAs and their role in evolution remains unknown.Simple recombinational models have been proposed that connect duplications, deletions, and eccDNA with one another. In the simplest model, a gene deletion can be produced by intrachromatid ectopic recombination between tandem repeats that flank the same gene, simultaneously producing a circular DNA element (Fig. 1A) (14). CNVs are also produced by other mechanisms that do not require a circular intermediate, such as replication slippage (16), interchromatid or interchromosome recombination between nonallelic homologs (17). However, DNA studies of several loci in human germ cells suggest that the frequency of intrachromatid ectopic recombination, which leads to eccDNA, could be just as high as other CNV events (18). Incorrect nonhomologous end joining of DNA ends can generate eccDNA (Fig. 1A) (2, 19),) in addition to other mechanisms (Fig. 1A). These mechanisms could include microhomology-mediated DNA repair processes at double-strand DNA breaks (20, 21), as well as processes independent of DNA breaks, such as replication errors near short inverted repeats (22) or small single-stranded DNA that prime formation of eccDNA (23).Open in a separate windowFig. 1.Genome-wide eccDNA measurement by Circle-Seq. (A) Models of extrachromosomal circular DNA (eccDNA) formation: intrachromatid ectopic homologous recombination (HR), nonhomologous end-joining (NHEJ), and other circularization mechanisms. (B) Circle-Seq procedure. From disrupted S. cerevisiae cells, eccDNA was purified by (1) column purification for circular DNA, (2) digestion of remaining linear DNA by plasmid-safe ATP-dependent DNase facilitated by NotI endonuclease, and (3) rolling-circle amplification by ϕ29 DNA polymerase and subsequent high-throughput DNA sequencing. (C) Sequenced 141-nucleotide reads were mapped to the S288C S. cerevisiae reference genome. Shown are data from reference sample R3 for part of chromosome IV. Green, paralogous genes; black, unique genes or ORFs; blue, read coverage mapped to the chromosome; gray boxes, individual reads with homology to the Watson (+) (light gray) and Crick (−) (dark gray) strands. (D) EccDNA was identified from regions covered by contiguous mapped reads >1 kb that were found to be significantly overrepresented by Monte Carlo simulation. Black bars, chromosomal regions recorded as eccDNAs; white bars, chromosomal regions excluded from the analysis (contiguous reads <1 kb).There is likely an intimate connection between deletions, duplications, and circular DNA forms: reintegration of a circular copy of a gene by homologous recombination results in a duplication, just as recombination between duplicates can generate circular DNA copies and deletions. Chromosomal CNVs have been generally detected well after their establishment. Thus, the mechanism for formation of copy number variable regions can be inferred only from their structure (24, 25). Detection of new, potentially transient chromosomal duplications is challenging because it involves detection of alterations in single DNA molecules within large cell populations. We reasoned that detection and recovery of eccDNAs might be more tractable than other CNVs because of the unique and well-studied biophysical and biochemical properties of circular DNA molecules.We developed a sensitive, genome-scale enrichment and detection method for eccDNA (Circle-Seq), based on well-established prokaryotic plasmid purification (26, 27) and deep sequencing technology. With Circle-Seq, we were able to purify, sequence, and map eccDNAs that, among them, cover nearly a quarter of the whole genome sequence of S. cerevisiae. We infer from the numerous eccDNA findings that circularization of genomic sequences is common enough to account for the generation of much of the variation in gene copy numbers observed in cancer and other human genetic diseases, as well as the process of evolution by duplication, deletion, and divergence.     

乙型肝炎病毒共价闭合环状DNA的扩增与清除动力学

HBV基因组是一种松弛环状的双链DNA(relaxed circular DNA,rcDNA)分子,其两条链均不闭合,在病毒的复制过程中,病毒DNA进入宿主细胞核,两条链的缺口被补齐,形成超螺旋的共价闭合环状DNA(covalently dosed circular DNA,cccDNA).cccDNA是HBV在肝内进行复制的原始模板,虽然其含量较少,但对病毒在宿主细胞内感染状态的建立以及维持病毒在细胞内的复制过程具有十分重要的意义.     

乙型肝炎患者血清中乙型肝炎病毒共价闭合环状DNA的检测

目的 检测不同肝脏病变程度的乙型肝炎患者外周血中的HBV共价闭合环状DNA(HBV cccDNA),评价其相关的影响因素和临床意义.方法 共观察57例乙型肝炎患者,其中轻度慢性乙型肝炎患者26例,重型乙型肝炎患者31例.患者入院后行PT、肝功能、肝炎病毒血清标志物等常规检测,并进行总HBV DNA和HBV cccDNA检测.Logistic逐步回归分析影响血清HBVcecDNA检出率的相关因素.结果重型乙型肝炎组13份血清标本HBV cccDNA为阳性,轻度慢性乙型肝炎组仅1份血清标本HBV cccDNA为阳性,血清HBV cccDNA的含量为1.25×103～4.88×104拷贝/mL,两组患者血清HBV cccDNA检出率差异有统计学意义(P=0.0014).血清HBV cccDNA检测诊断重型乙型肝炎患者的灵敏度和特异度分别为41.94%和96.15%.Logistic逐步回归分析显示,血清HBV ccvDNA的检出率与PT有关(X<'2>=7.2192,P=0.0072),而与患者的年龄、性别、血清总HBV DNA、TBil和ALT水平无相关性.结论 部分乙型肝炎患者特别是重型肝炎患者外周血中可以检测出HBV cccDNA,血清HBV cccDNA的检出可作为支持重型乙型肝炎诊断的指标之一.     

乙型肝炎病毒共价闭合环状DNA与松弛环状DNA对核苷(酸)类药物耐药变异的比较

目的 了解肝细胞内HBV共价闭合环状DNA( HBV cccDNA)核苷(酸)类药物耐药变异的情况,并比较其与松弛环状DNA(rcDNA)耐药变异的异同.方法 取40例慢性HBV感染肝移植患者的部分肝组织,采用十二烷基硫酸钠-蛋白质沉淀法结合DNA提取试剂盒分离提取肝内的HBV cccDNA和rcDNA.将抽提产物用不降解质粒的ATP依赖DNA酶酶切纯化后,用跨HBV基因组双链缺口并涵盖常见核苷类耐药位点(rt169～rt250)的引物行单轮PCR或套式PCR选择性扩增cccDNA.另用不跨双缺口的引物PCR扩增肝组织内的HBV rcDNA和患者肝移植术前的血清HBV rcDNA.用直接测序法对上述扩增产物进行基因测序并分析核苷(酸)类药物耐药位点的检出情况.结果 40例患者中,31例肝组织内检测到HBV cccDNA,35例肝组织检测到HBV rcDNA,21例肝移植术前血清中检测到HBV rcDNA.测序结果显示,2例肝组织内cccDNA、rcDNA和血清rcDNA均检测到rtM204Ⅰ变异;有2例患者肝内cccDNA、rcDNA分别存在rtM204Ⅰ、rtQ215H变异,而血清rcDNA未检测到相应变异;3例血清中分别存在rtM204V、rtM204V、rtV173L+ rtL180M+rtM204V变异,而肝内cccDNA和rcDNA未检测到相应变异.结论 慢性HBV感染者肝细胞内cccDNA可出现核苷(酸)类药物耐药变异,且肝组织内的cccDNA、rcDNA耐药变异株与血清中的rcDNA耐药变异株不完全一致.     

肝组织cccDNA水平与血清病毒学应答后治疗时间的关系

目的 探讨慢性乙型肝炎(CHB)患者肝组织cccDNA水平与外周血HBV DNA<1000 拷贝/ml后继续治疗时间的关系.方法 分别采用荧光定量PCR、酶联免疫吸附分析法检测58例CHB患者肝组织HBV cccDNA水平、肝组织和血清HBV DNA载量、HBV标志物,分析肝组织HBV cccDNA水平、肝组织总HBV DNA水平、HBeAg血清学转换与血清病毒学应答后继续治疗时间的关系.组间比较采用Nemenyi法,相关分析采用Spearman法.结果 肝组织HBVcccDNA水平在血清HBV DNA两阳性组间尢明显差异,而阴性组明显低于阳性组(χ2=9.6948,P<0.01;χ2=9.2824,P<0.01).35例达到血清病毒学应答后行肝活组织检查的患者,肝组织cccDNA水平随继续治疗时间的延长而降低(χ2≥6.4674,P<0.05),肝组织cccDNA水平在抗-Hbe(+)组明显低于HBeAg(+)组、HBeAg(-)/抗-Hbe(-)组(χ2=10.7482,P<0.01;χ2=11.7549,P<0.01).14例肝组织cccDNA水平低十检测限的患者,有12例已经发生HBeAg血清学转换,占抗-Hbe(+)组的2/3,其在血清病毒学应答后继续治疗时间平均为35个月,发生HBeAg血清学转换后继续治疗时间平均为30个月.结论 当患者发生血清病毒学应答后,肝组织cccDNA水平随继续治疗时间延长而降低;继续治疗35个月以上且血清抗-Hbe持续(+)30个月以上时,有2/3的患者肝组织cccDNA定量低于检测限水平.     

应用滚环扩增技术检测乙型肝炎病毒共价闭合环状DNA的研究

目的 应用滚环扩增(RCA)技术检测HBV共价闭合环状DNA(cccDNA),观察该方法的特异性和敏感性.方法 以HBV全基因质粒为模板,经酶切、连接、浓缩、胶回收纯化等步骤,构建和制备HBV cccDNA标准品.抽提7例慢性乙型肝炎患者肝组织总DNA,进行滚环扩增.用HBV cccDNA标准品、3.2 kb线性HBV DNA、健康肝组织总DNA及15例慢性乙型肝炎患者血清总DNA作为对照,验证此方法的特异性.将HBV cccDNA标准品进行系列稀释,了解该方法的敏感性.结果 成功构建了HBV cccDNA,并可用RCA方法进行扩增.RCA方法可从2 mg的慢性乙型肝炎患者肝组织中检测到HBV cccDNA,并可检测低至1×102拷贝/μL的HBV cccDNA.RCA方法不能检测3.2 kb线性HBV DNA,在健康肝组织及15例慢性乙型肝炎患者血清中亦检测不到HBV cccDNA.结论 RCA方法操作较方便,具有很高的特异性和敏感性.     

乙型肝炎病毒共价闭合环状DNA套式-实时荧光定量聚合酶链反应的建立

目的 建立检测HBV共价闭合环状DNA(cccDNA)的套式一实时荧光定量PCR法.方法 根据HBV cccDNA与松环DNA(rcDNA)结构上的差异,设计2对跨缺口的特异引物及1条位于负链缺口下游的特异TaqMan荧光探针.根据Plasmid-SafeTM ATP-Dependent Dnasc(PSAD)对rcDNA与cccDNA作用的不同,对模板DNA进行酶切纯化,降解reDNA,再进行套式PCR扩增,先用外引物和模板进行第一轮常规PCR,再用内引物、荧光探针和第一轮PCR产物进行实时荧光定量PCR,根据阳性参照标准品,得出待检标本定量值.结果 检测阳性参照标准品.得出该方法灵敏度可达2 lg拷贝/mL.用上述方法检测34份乙型肝炎患者血清HBV DNA阳性标本,25份血清HBVcccDNA阳性,28份外周血单个核细胞HBV cccDNA阳性.27份健康对照者血清HBV DNA阴性标本,6份HBV cccDNA阳性.对5份HBV cccDNA阳性标本扩增产物进行克隆测序,无碱基缺失、突变.与HBV不同基因型序列(A～G)比较,同源性为90.6%～99.1%,其中,与B、C基因型同源性为95.3%～99.1%,验证了方法的特异度.结论 套式-实时定量PCR法可检测乙型肝炎患者血清、PBMC中的HBV CCCDNA,且具有敏感、特异性.     

Effects of antiviral agents and HBV genotypes on intrahepatic covalently closed circular DNA in HBeAg-positive chronic hepatitis B patients

AIM： To evaluate the effects of antiviral agents and HBV genotypes on intrahepatic covalently closed circular DNA （ccc DNA） in HBeAg-positive chronic hepatitis B patients.
METHODS： Seventy-one patients received lamivudine （n = 35）, or sequential therapy with lamivudine- interferon alpha 2b （IFN-α 2b, n = 24） for 48 wk, or IFN-α 2b （n = 12） for 24 wk. All subjects were followed up for 24 wk. Intrahepatic ccc DNA was measured quantitatively by PCR. HBV genotypes were analyzed by PCR-RFLP.
RESULTS： Sequential lamivudine- INF-α therapy, lamivudine and INF-α monotherapy reduced ccc DNA of 1.7 log, 1.4 log and 0.8 log, respectively （P 〈 0.05）. Seventeen out of the 71 patieots developed HBeAg seroconversion, the reduction of ccc DNA in the HBeAg seroconversion patients was more significant than that in the HBeAg positive patients （3.0 log vs 1.6 log, P = 0.0407）. Twenty-four weeks after antiviral therapy withdrawal, 16 patients had a sustained virological response, the baseline intrahepatic ccc DNA in the patients with a sustained virological response was significantly lower than that in the patients with virological rebound （4.6 log vs 5.4 log, P = 0.0472）. HBV genotype C accounted for 85.9% （n = 61）, and genotype B for 14.1% （n = 10）, respectively, in the 71 patients. There was no significant difference in the change of ccc DNA level between HBV genotypes C and B （2.1 log vs 1.9 log）.
CONCLUSION： Forty-eight week sequential lamivudine- INF-α therapy and lamivudine monotherapy reduce ccc DNA more significantly than 24-wk INF-α monotherapy. Low baseline intrahepatic ccc DNA level may predict the long-term efficacy of antiviral treatment. HBV genotypes C and B have no obvious influence on ccc DNA load.     

Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo

Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. We have used quantitative genomic analysis to infer the key in vivo molecular parameters governing RecA loading by the helicase/nuclease RecBCD at recombination hot-spots, known as Chi. Our genomic analysis has also revealed that DSBR at the lacZ locus causes a second RecBCD-mediated DSBR event to occur in the terminus region of the chromosome, over 1 Mb away.DNA double-strand break repair (DSBR) is essential for cell survival and repair-deficient cells are highly sensitive to chromosome breakage. In Escherichia coli, a single unrepaired DNA DSB per replication cycle is lethal, illustrating the critical nature of the repair reaction (1). DSBR in E. coli is mediated by homologous recombination, which relies on the RecA protein to efficiently recognize DNA sequence identity between two molecules. RecA homologs are widely conserved from bacteriophages to mammals, where they are known as the Rad51 proteins (2). The RecA protein plays its central role by binding single-stranded DNA (ssDNA) to form a presynaptic filament that searches for a homologous double-stranded DNA (dsDNA) donor from which to repair. It then catalyzes a strand-exchange reaction to form a joint molecule (3), which is stabilized by the branch migration activities of the RecG and RuvAB proteins (4). The joint molecule is then resolved by cleavage at its four-way Holliday junction by the nuclease activity of RuvABC (5, 6).RecA binding at the site of a DSB is dependent on the activity of the RecBCD enzyme (Fig. 1A). RecBCD is a helicase-nuclease that binds to dsDNA ends, then separates and unwinds the two DNA strands using the helicase activities of the RecB and RecD subunits (see refs. 7 and 8 for recent reviews). RecD is the faster motor of the two and this consequently results in the formation of a ssDNA loop ahead of RecB (Loop 1 in Fig. 1A) (9). As the enzyme translocates along dsDNA, the 3′-terminated strand is continually passed through the Chi-scanning site thought to be located in the RecC protein (10). When a Chi sequence (the octamer 5′-GCTGGTGG-3′) enters this recognition domain, the RecD motor is disengaged and the 3′ strand continues to be unwound by RecB. Under in vitro conditions, where the concentration of magnesium exceeds that of ATP, the 3′ end (unwound by RecB) is rapidly digested before Chi recognition, whereas the 5′ end (unwound by RecD) is intermittently cleaved (11, 12). After Chi recognition the 3′ end is no longer cleaved but the nuclease domain of RecB continues to degrade the 5′ end as it exits the enzyme (11, 12). Under in vitro conditions where the concentration of ATP exceeds that of magnesium, unwinding takes place but the only site of cleavage detected is ∼5 nucleotides 3′ of the Chi sequence (13, 14). Because the RecB motor continues to operate while the RecD motor is disengaged, Loop 1 is converted to a second loop located between the RecB and RecC subunits or to a tail upon release of the Chi sequence from its recognition site. We therefore describe this single-stranded region as Loop/Tail 2 in Fig. 1A. After the whole of Loop 1 is converted to Loop/Tail 2, this second single-stranded region continues to grow as long as the RecB subunit unwinds the dsDNA. The RecBCD enzyme enables RecA protein to load on to Loop/Tail 2 to generate the presynaptic filament necessary to search for homology and initiate strand-exchange (15). Finally, the RecBCD enzyme stops translocation and disassembles as it dissociates from the DNA, releasing a DNA-free RecC subunit (16).Open in a separate windowFig. 1.DSBR in E. coli. (A and B) Schematic representation of DSB processing by the RecBCD complex. (A) Before Chi recognition, both the RecB and RecD motors progress along the DNA. RecD is the faster motor and as a result a loop of ssDNA (Loop 1) is formed ahead of the slower RecB motor. The 3′ ssDNA strand is scanned for the Chi sequence by the RecC protein. (B) After Chi recognition, RecBCD likely undergoes a conformational change so that only the RecB motor is engaged. The RecA protein is recruited by the RecB nuclease domain and loaded onto the ssDNA loop generated by RecB unwinding to promote RecA nucleoprotein filament formation. In this schematic representation, the Chi site is shown held in its recognition site. However, the Chi site will be released either by disassembly of the RecBCD complex or at some point before this and the second single-stranded region on the 3′ terminating strand will be converted from a loop to a tail. Therefore, this region is denoted Loop/Tail 2. The mathematical model described in SI Appendix does not depend on the ATP/magnesium dependent differential cleavage of DNA strands (7, 8), nor does it depend on the precise time that the 3′ end is released from the complex following Chi recognition. (C) The hairpin endonuclease SbcCD is used to cleave a 246-bp interrupted palindrome inserted in the lacZ gene of the E. coli chromosome. Cleavage of this DNA hairpin results in the generation of a site-specific DSB on only one of a pair of replicating sister chromosomes, thus leaving an intact sister chromosome to serve as a template for repair by homologous recombination.Our understanding of the action of RecBCD and RecA has been the result of more than 40 years of genetic analysis and biochemical investigation of these purified proteins in vitro. However, relatively little is known about their activities on the genomic scale. To investigate these reactions in vivo, we have used RecA chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) in an experimental system that allows us to introduce a single and fully repairable DSB into the chromosome of E. coli (1). Because DSBR by homologous recombination normally involves the repair of a broken chromosome by copying the information on an unbroken sister chromosome, our laboratory has previously developed a procedure for the cleavage of only one copy of two genetically identical sister chromosomes (1). We have made use of the observation that the hairpin nuclease SbcCD specifically cleaves only one of the two sister chromosomes following DNA replication through a 246-bp interrupted palindrome to generate a two-ended DSB (1). As shown in Fig. 1B, this break is fully repairable and we have shown that recombination-proficient cells suffer very little loss of fitness in repairing such breaks (17).Here we investigate in vivo and in a quantitative manner the first steps of DSBR: because the outcome of RecBCD action is understood to be the loading of RecA on DNA in a Chi-dependent manner, we use RecA-ChIP to reveal the consequences of RecBCD action on a genomic scale during DSBR. Analyses of most ChIP-Seq datasets focus on the identification of regions of significant enrichment of a given protein but do not take into account the underlying mechanisms giving rise to the binding (18). We reasoned that given the detailed mechanistic understanding of RecBCD in vitro, we could gain a deeper insight into its in vivo functions by developing a mathematical model of RecBCD action that would enable us to estimate the mechanistic parameters of the complex in live cells. Our ChIP data indicate that RecA is indeed loaded on to DNA in a Chi-dependent manner and we have used our mathematical model to infer the parameters of RecBCD action in vivo on a genomic scale. Furthermore, our analysis reveals that DSBR at lacZ induces DSBR in the terminus region of the chromosome, an unanticipated observation illuminated by the genomic scale of our data.     

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.DNA methylation plays an important role in the regulation of the expression of genes and the maintenance of transposable element (TE) silencing. In contrast to animals, in which methylation is often restricted to the CG context, plants exhibit robust methylation in every possible context CG, CHG (H is A, T, or C), and CHH. Previous research has identified different pathways responsible for the maintenance and establishment of DNA methylation patterns. In Arabidopsis thaliana, METHYLTRANSFERASE1 (MET1), a homolog of mammalian Dnmt1, mainly maintains methylation at the CG context, whereas CHROMOMETHYLASE3 (CMT3) mainly maintains CHG methylation. DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) and CHROMOMETHYLASE2 (CMT2) maintain CHH methylation in the chromosome arms and pericentromeric regions, respectively (1–3). On the other hand, establishment of DNA methylation is performed by DRM2 through a complex pathway termed RNA-directed DNA methylation (RdDM) (4).To date, the majority of our knowledge about DNA methylation is derived from the model plant Arabidopsis. These studies have allowed the identification of different components involved in different methylation pathways, the genome-wide identification of methylation patterns, and the study of effects of DNA methylation on gene expression. The knowledge acquired from Arabidopsis can now be used as the basis for investigations of methylation in agronomically important plants. However, thus far very few crop species have been subjected to detailed DNA methylation studies (5). Cassava (Manihot esculenta) is cultivated for its starch-rich tuberous roots and is one of the world’s most important staple crops, especially in tropical America, Africa, and Asia (6). Cassava is a source of carbohydrates for nearly a billion people, but it is especially important for a large portion of Africa, where it serves as a subsistence crop because of its ability to tolerate drought and grow on poor soils, conditions unsuitable for rice and maize (6, 7). The genome sequence of cassava has been described recently with an estimated genome size of roughly 760 million base pairs (7). We have used bisulfite sequencing (BS-seq) to examine DNA methylation in cassava at single-base pair resolution. Broadly, the pattern of DNA methylation of both protein-coding genes and TEs is similar to other plants, although DNA methylation levels in cassava are higher than those in Arabidopsis. LTR retrotransposons, such as GYPSY and COPIA, tend to be more heavily methylated than other TEs. Interestingly, differentially expressed gene pairs derived from the last genome duplication tend to show differential gene body methylation, with the highly expressed paralogs displaying significantly higher gene body methylation. We also find that the most differentially gene body-methylated paralogs have distinct biological functions compared with genes that have maintained similar gene body methylation patterns.     

慢性乙型肝炎患者树突状细胞功能与单个核细胞乙型肝炎病毒共价闭合环状DNA的关系

目的 探讨慢性乙型肝炎(CHB)患者外周血单个核细胞(PBMC)及树突状细胞(DC)内HBV共价闭合环状DNA(HBV cccDNA)的存在状况,DC成熟度及功能状态与DC或PBMC中HBV cccDNA载量的关系.方法 分离29例CHB患者和10例健康对照者的PBMC,用重组人粒细胞-巨噬细胞集落刺激因子(GM-CS...     

Serum HBcrAg is better than HBV RNA and HBsAg in reflecting intrahepatic covalently closed circular DNA

The correlation between serum HBcrAg and HBV RNA is unclear, and correlations of intrahepatic cccDNA with HBcrAg, HBV RNA and HBsAg are rarely reported in the same cohort. This study aimed to assess the correlation of HBcrAg with HBV RNA and HBsAg, and investigate whether serum HBcrAg is superior to serum HBV RNA and HBsAg in reflecting intrahepatic HBV cccDNA in HBeAg‐positive and HBeAg‐negative CHB patients. In this study, 85 HBeAg‐positive and 25 HBeAg‐negative patients who have never received antiviral therapy were included. Among HBeAg‐positive patients, HBcrAg was correlated positively with HBsAg (r = 0.564, P < 0.001) and HBV RNA (r = 0.445, P < 0.001), and HBV RNA was also correlated positively with HBsAg (r = 0.323, P = 0.003). Among HBeAg‐negative patients, no significant correlation was observed between HBcrAg, HBsAg and HBV RNA. By multivariable linear regression, HBcrAg (β = ?0.563, P < 0.001), HBsAg (β = ?0.328, P < 0.001) and HBV RNA (β = 0.180, P = 0.003) were all associated with cccDNA levels among HBeAg‐positive patients, but only serum HBcrAg was associated with cccDNA level (β = 0.774, P = 0.000) among HBeAg‐negative patients. HBcrAg was better correlated with cccDNA as compared to HBsAg and HBV RNA, irrespective of HBeAg status. Among HBeAg‐positive patients, though HBcrAg level was influenced by hepatic inflammatory activity and HBV DNA levels, the good correlations of HBcrAg with cccDNA persisted after stratification by inflammatory activity and HBV DNA levels. In conclusion, correlations of serum HBcrAg, HBV RNA and HBsAg levels differ significantly between HBeAg‐positive and HBeAg‐negative patients, but serum HbcrAg correlates with cccDNA levels better than HBV RNA and HBsAg, irrespective of HBeAg status.     

Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins

Exonuclease 1 (Exo1) is a 5′→3′ exonuclease and 5′-flap endonuclease that plays a critical role in multiple eukaryotic DNA repair pathways. Exo1 processing at DNA nicks and double-strand breaks creates long stretches of single-stranded DNA, which are rapidly bound by replication protein A (RPA) and other single-stranded DNA binding proteins (SSBs). Here, we use single-molecule fluorescence imaging and quantitative cell biology approaches to reveal the interplay between Exo1 and SSBs. Both human and yeast Exo1 are processive nucleases on their own. RPA rapidly strips Exo1 from DNA, and this activity is dependent on at least three RPA-encoded single-stranded DNA binding domains. Furthermore, we show that ablation of RPA in human cells increases Exo1 recruitment to damage sites. In contrast, the sensor of single-stranded DNA complex 1—a recently identified human SSB that promotes DNA resection during homologous recombination—supports processive resection by Exo1. Although RPA rapidly turns over Exo1, multiple cycles of nuclease rebinding at the same DNA site can still support limited DNA processing. These results reveal the role of single-stranded DNA binding proteins in controlling Exo1-catalyzed resection with implications for how Exo1 is regulated during DNA repair in eukaryotic cells.All DNA maintenance processes require nucleases, which enzymatically cleave the phosphodiester bonds in nucleic acids. Exo1, a member of the Rad2 family of nucleases, participates in DNA mismatch repair (MMR), double-strand break (DSB) repair, nucleotide excision repair (NER), and telomere maintenance (1–3). Exo1 is the only nuclease implicated in MMR, where its 5ʹ to 3ʹ exonuclease activity is used to remove long tracts of mismatch-containing single-stranded DNA (ssDNA) (2, 4–7). In addition, functionally deficient Exo1 variants have been identified in familial colorectal cancers, and Exo1-null mice exhibit a significant increase in tumor development, decreased lifespan, and sterility (8, 9). Exo1 also promotes DSB repair via homologous recombination (HR) by processing the free DNA ends to generate kilobase-length ssDNA resection products (1, 10–12). The resulting ssDNA is paired with a homologous DNA sequence located on a sister chromatid, and the missing genetic information is then restored via DNA synthesis. The central role of Exo1 in DNA repair is highlighted by the large set of genetic interactions between Exo1 and nearly all other DNA maintenance and metabolism pathways (13).Exo1 generates long tracts of ssDNA in both MMR and DSB repair (3). This ssDNA is rapidly bound by replication protein A (RPA), a ubiquitous heterotrimeric protein that participates in all DNA transactions that generate ssDNA intermediates (14). RPA protects the ssDNA from degradation, participates in DNA damage response signaling, and acts as a loading platform for downstream DSB repair proteins (15–17). RPA also coordinates DNA resection by removing secondary ssDNA structures and by modulating the Bloom syndrome, RecQ helicase-like (BLM)/DNA2- and Exo1-dependent DNA resection pathways (18–21). Reconstitution of both the yeast and human BLM (Sgs1 in yeast)/DNA2-dependent resection reactions established that RPA stimulates DNA unwinding by BLM/Sgs1 and enforces a 5′-endonuclease polarity on DNA2 (20, 22). However, the effect of RPA on Exo1 remains unresolved. Independent studies using reconstituted yeast proteins reported that RPA could both inhibit (23) and stimulate yeast Exo1 (yExo1) (18). Similarly, human RPA has variously been reported to stimulate (19) or inhibit human Exo1 (hExo1) (4, 5, 21).In addition to RPA, human cells also encode SOSS1, a heterotrimeric ssDNA-binding complex that is essential for HR (24). SOSS1 consists of INTS3 (SOSSA), hSSB1 (SOSSB1), and C9orf80 (SOSSC) (24–26). SOSSB1 encodes a single ssDNA-binding domain that bears structural homology to Escherichia coli ssDNA-binding protein (SSB) (24). SOSS1 foci form rapidly after induction of DNA breaks, and ablation of SOSS1 severely reduces DNA resection, γH2AX foci formation, and HR at both ionizing radiation- and restriction endonuclease-induced DSBs (12, 24, 25, 27). In vitro, SOSS1 stimulates hExo1-mediated DNA resection and may help to load hExo1 at ss/dsDNA junctions (21). However, the functional relationship between SOSS1 and RPA during hExo1 resection remains unresolved.Here, we use high-throughput single-molecule DNA curtains and quantitative cell biology to reveal the interplay between human and yeast Exo1 and SSBs during DNA resection. We show that both human and yeast Exo1s are processive nucleases, but are rapidly stripped from DNA by RPA. RPA inhibition is dependent on its multiple DNA binding domains. Remarkably, SOSS1 and other SSBs with fewer than three DNA binding domains support long-range resection by hExo1. In human cells, depletion of RPA increases the rate of hExo1 recruitment to laser-induced DNA damage but reduces the extent of resection. In the presence of RPA, both human and yeast Exo1 can resect DNA using a distributive, multiple-turnover mechanism, potentially reconciling prior conflicting in vitro observations. Together, our work reveals the mechanistic basis for how RPA and SOSS1 differentially modulate hExo1 activity and highlights an additional, unexpected role for these SSBs in DNA resection. We anticipate that these findings will shed light on how Exo1 is regulated in multiple genome maintenance pathways.     

Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK

FtsK is a hexameric DNA translocase that participates in the final stages of bacterial chromosome segregation. Here we investigate the DNA-binding and translocation activities of FtsK in real time by imaging fluorescently tagged proteins on nanofabricated curtains of DNA. We show that FtsK preferentially loads at 8-bp KOPS (FtsK Orienting Polar Sequences) sites and that loading is enhanced in the presence of ADP. We also demonstrate that FtsK locates KOPS through a mechanism that does not involve extensive 1D diffusion at the scale of our resolution. Upon addition of ATP, KOPS-bound FtsK translocates in the direction dictated by KOPS polarity, and once FtsK has begun translocating it does not rerecognize KOPS from either direction. However, FtsK can abruptly change directions while translocating along DNA independent of KOPS, suggesting that the ability to reorient on DNA does not arise from DNA sequence-specific effects. Taken together, our data support a model in which FtsK locates KOPS through random collisions, preferentially engages KOPS in the ADP-bound state, translocates in the direction dictated by the polar orientation of KOPS, and is incapable of recognizing KOPS while translocating along DNA.     

From the Cover: Structure of PolC reveals unique DNA binding and fidelity determinants

PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-Å resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique β-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity.     

HBV感染者血清中HBVcccDNA、HBeAg及HBV DNA的关系

探讨HBV感染者血清HBVcccDNA与血清HBV DNA及HBeAg的关系。分别以PER分子信标技术和ELISA方法对非HBV相关肝炎、HBV健康携带者、急性乙型肝炎（AHB）、慢性乙型肝炎（CHB）、乙肝肝硬化、乙肝患者血清中HBVcccDNA HBV DNA含量及HBeAg进行了检测。HBVcccDNA仅见于HBV DNA阳性血清中；HBeAg阳性组的HBVcccDNA阳性率显著高于HBeAg阴性组（P〈0．05）；145例HBV DNA阳性患者中，HBVcccDNA阳性组HBVD—NA水平显著高于HBVcccDNA阴性组（P〈0．01）。血清HBVcccDNA可能是乙肝病毒在患者体内大量复制的血清标志。