Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的...为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的呼和浩特市272个无关汉族男性个体样本进行扩增,统计38个Y-STR基因座的等位基因频率和法医遗传学参数;基于Y染色体短串联重复序列单倍型数据库(Y-chromosomal short tandem repeat haplotype reference database,YHRD)纳入的国内各群体单倍型数据计算群体间的遗传距离(pairwise genetic distance,Rst),并在此基础上进行多维尺度分析(multidimensional scaling,MDS)。38个Y-STR基因座共检出333个等位基因,基因多样性值(gene diversity,GD)为0.0434~0.9675。共检出269种单倍型,其中3种单倍型出现2次。单倍型多样性(haplotype diversity,HD)和单倍型识别率(discrimination power,DC)分别为0.9999和0.9890。群体比较结果显示,呼和浩特汉族与陕西汉族等同一种族或地理位置毗邻的群体的遗传距离较小,即遗传关系较近,反之则遗传关系较远。研究选取的包含38个YSTR基因座的复合检测体系具有较高的遗传多态性,适合呼和浩特汉族群体的法医学分析和群体遗传学研究。展开更多
流产组织胎儿STR(short tandem repeats)分型检测长久以来始终是法医DNA检验面临的一大难题,对于孕早期流产组织无法通过组织形态学检验获取绒毛组织时,母体与胎儿混合STR分型结果可以为强奸致孕案件嫌疑人认定提供关键依据。本研究应...流产组织胎儿STR(short tandem repeats)分型检测长久以来始终是法医DNA检验面临的一大难题,对于孕早期流产组织无法通过组织形态学检验获取绒毛组织时,母体与胎儿混合STR分型结果可以为强奸致孕案件嫌疑人认定提供关键依据。本研究应用新一代测序技术,在4份强奸致孕早期流产组织中成功检出母体与疑似胎儿混合STR分型或疑似胎儿单一STR分型,与Y-STR、侧翼序列信息联合应用,为嫌疑人认定提供了更为全面可靠的遗传学依据。展开更多
This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore t...This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore their potential as therapeutic targets,and discuss the implications for new treatment strategies.We offer valuable insights into relevant gene regulation and cellular mechanisms relevant for the targeted management of T2D.展开更多
目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模...目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。展开更多
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
文摘为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的呼和浩特市272个无关汉族男性个体样本进行扩增,统计38个Y-STR基因座的等位基因频率和法医遗传学参数;基于Y染色体短串联重复序列单倍型数据库(Y-chromosomal short tandem repeat haplotype reference database,YHRD)纳入的国内各群体单倍型数据计算群体间的遗传距离(pairwise genetic distance,Rst),并在此基础上进行多维尺度分析(multidimensional scaling,MDS)。38个Y-STR基因座共检出333个等位基因,基因多样性值(gene diversity,GD)为0.0434~0.9675。共检出269种单倍型,其中3种单倍型出现2次。单倍型多样性(haplotype diversity,HD)和单倍型识别率(discrimination power,DC)分别为0.9999和0.9890。群体比较结果显示,呼和浩特汉族与陕西汉族等同一种族或地理位置毗邻的群体的遗传距离较小,即遗传关系较近,反之则遗传关系较远。研究选取的包含38个YSTR基因座的复合检测体系具有较高的遗传多态性,适合呼和浩特汉族群体的法医学分析和群体遗传学研究。
文摘流产组织胎儿STR(short tandem repeats)分型检测长久以来始终是法医DNA检验面临的一大难题,对于孕早期流产组织无法通过组织形态学检验获取绒毛组织时,母体与胎儿混合STR分型结果可以为强奸致孕案件嫌疑人认定提供关键依据。本研究应用新一代测序技术,在4份强奸致孕早期流产组织中成功检出母体与疑似胎儿混合STR分型或疑似胎儿单一STR分型,与Y-STR、侧翼序列信息联合应用,为嫌疑人认定提供了更为全面可靠的遗传学依据。
文摘This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore their potential as therapeutic targets,and discuss the implications for new treatment strategies.We offer valuable insights into relevant gene regulation and cellular mechanisms relevant for the targeted management of T2D.
文摘目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。
