Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data

Background

Telomeres are the protective arrays of tandem TTAGGG sequence and associated proteins at the termini of chromosomes. Telomeres shorten at each cell division due to the end-replication problem and are maintained above a critical threshold in malignant cancer cells to prevent cellular senescence or apoptosis. With the recent advances in massive parallel sequencing, assessing telomere content in the context of other cancer genomic aberrations becomes an attractive possibility. We present the first comprehensive analysis of telomeric DNA content change in tumors using whole-genome sequencing data from 235 pediatric cancers.

Results

To measure telomeric DNA content, we counted telomeric reads containing TTAGGGx4 or CCCTAAx4 and normalized to the average genomic coverage. Changes in telomeric DNA content in tumor genomes were clustered using a Bayesian Information Criterion to determine loss, no change, or gain. Using this approach, we found that the pattern of telomeric DNA alteration varies dramatically across the landscape of pediatric malignancies: telomere gain was found in 32% of solid tumors, 4% of brain tumors and 0% of hematopoietic malignancies. The results were validated by three independent experimental approaches and reveal significant association of telomere gain with the frequency of somatic sequence mutations and structural variations.

Conclusions

Telomere DNA content measurement using whole-genome sequencing data is a reliable approach that can generate useful insights into the landscape of the cancer genome. Measuring the change in telomeric DNA during malignant progression is likely to be a useful metric when considering telomeres in the context of the whole genome.     

Indehiscent sporangia enable the accumulation of local fern diversity at the Qinghai-Tibetan Plateau

ABSTRACT: BACKGROUND: Indehiscent sporangia are reported for only a few of derived leptosporangiate ferns. Their evolution has been likely caused by conditions in which promotion of self-fertilization is an evolutionary advantageous strategy such as the colonization of isolated regions and responds to stressful habitat conditions. The Lepisorus clathratus complex provides the opportunity to test this hypothesis because these derived ferns include specimens with regular dehiscent and irregular indehiscent sporangia. The latter occurs preferably in well-defined regions in the Himalaya. Previous studies have shown evidence for multiple origins of indehiscent sporangia and the persistence of populations with indehiscent sporangia at extreme altitudinal ranges of the Qinghai-Tibetan Plateau (QTP). RESULTS: Independent phylogenetic relationships reconstructed using DNA sequences of the uniparentally inherited chloroplast genome and two low-copy nuclear genes confirmed the hypothesis of multiple origins of indehiscent sporangia and the restriction of particular haplotypes to indehiscent sporangia populations in the Lhasa and Nyingchi regions of the QTP. In contrast, the Hengduan Mountains were characterized by high haplotype diversity and the occurrence of accessions with and without indehiscent sporangia. Evidence was found for polyploidy and reticulate evolution in this complex. The putative case of chloroplast capture in the Nyingchi populations provided further evidence for the promotion of isolated but persistent populations by indehiscent sporangia. CONCLUSIONS: The presented results confirmed the hypothesis that indehiscent sporangia promote the establishment of persistent population in different regions of the QTP. These results are consistent with the expectations of reproductive reassurance by promotion of self-fertilization that played a critical role in the assembly of populations in isolated locations and/or extreme habitats.     

荧光偏振技术研究Bloom解旋酶催化核心与双链DNA的相互作用

Bloom 综合症(BLM)解旋酶是RecQ家族DNA解旋酶中的一个重要成员,参与了DNA复制、修复、转录、重组以及端粒的维持等细胞代谢过程,在维持染色体的稳定性中具有重要的作用．BLM解旋酶的突变可导致Bloom综合症,患者遗传不稳定易患多种类型癌症．本研究运用荧光偏振技术研究BLM解旋酶催化核心(BLM642-1290)与双链DNA(dsDNA)的相互作用,分析其相关特征参数,了解BLM642-1290解旋酶与dsDNA的结合和解链特性．结果表明,BLM642-1290解旋酶与dsDNA的结合和解链和dsDNA3’末端的单链DNA(ssDNA)长度有关;解旋酶优先结合于dsDNA底物的ssDNA末端,且每分子解旋酶可结合9.6 nt的ssDNA;dsDNA3’末端ssDNA的长度为9.6 nt时,解旋酶的解链效率达到最大且不再随其长度而变化．另外,BLM642-1290解旋酶也能够结合和解链钝末端dsDNA,但其结合亲和力和解链效率低于有3’末端ssDNA的dsDNA．推测BLM642-1290解旋酶在与dsDNA底物结合和解链时是单体形式,可能以尺蠖的形式解开dsDNA．这些结果可为进一步研究BLM解旋酶的功能特征提供理论基础．     

不同生态区云南黄连居群的染色体核型比较

采用根尖压片和卡宝品红染色法,对分布于高黎贡山的东、西坡不同生态带的8个云南黄连居群进行染色体核型比较分析。结果表明,8个居群染色体数目均为2n=2x=18,核型基本一致,除东坡一个居群为3A型外,其余均为2A型;总体上同一生态区域内各居群的核型表现出较大的相似性,但不同生态区域的居群间却存在较大的差异,主要为近端部和端部着丝点染色体的有无及数目在东西坡居群间存在较大变化;东坡居群的不对称程度均较西坡高。     

GFP基因在新疆小拟南芥和拟南芥中的表达分析

以质粒pMCB30为模板,扩增GFP基因,连接到载体pCMBIA2300-35S-OCS上,构建过量表达载体p35S:GFP,将其转入农杆菌GV3101.通过农杆菌介导法将p35S:GFP载体分别转入新疆特色植物小拟南芥和拟南芥中.T0代经含有卡那霉素的1/2MS培养基筛选,获得了T1代转基因小拟南芥2株,T1代转基因拟南芥9株.通过激光共聚焦显微镜观察,在转基因小拟南芥和拟南芥的根尖细胞中均可检测到GFP绿色荧光蛋白;对转基因植株进行PCR扩增,均可检测到GFP基因,表明GFP基因已成功转入小拟南芥和拟南芥中.该研究建立了小拟南芥的遗传转化体系,为进一步利用GFP基因和进一步研究小拟南芥的功能基因奠定基础.     

濒危药用植物云南黄连传粉生态学研究

云南黄连为中药材黄连的原植物之一,为国家二级濒危保护植物。通过对云南黄连的开花物候、花部特征、繁育系统及传粉方式进行观察研究,以探讨云南黄连濒危机制,为其种质资源保护及人工抚育奠定基础。结果表明:(1)云南黄连的花期从12月份起至第二年的3月份,花期长达4个月,花序开花可持续45～60d,同一花序上不同花的开花时间相隔1～3d,单花花期可持续40～45d。(2)云南黄连为多歧聚伞花序,苞片包被花芽,花两性,雄蕊和心皮多数。(3)云南黄连的花粉-胚珠比(P/O)为9 000左右,杂交指数(OCI)值为4或5,为自交亲和但需要传粉者完成传粉的兼性异交型繁育系统,并存在无融合生殖现象。     

东乡野生稻耐冷渐渗系的细胞学观察及SSR分析

以前期鉴定筛选的2个东乡野生稻强耐冷渐渗系(IL5243和IL5335)为试材,研究其减数分裂时期的染色体行为特征及外源基因的渗入分子证据。结果表明:(1)IL5243和IL5335中正常减数分裂的花粉母细胞分别达89.93%和90.22%,最终形成正常的成熟花粉粒,花粉离体萌发率分别为(83.03±2.82)%和(81.96±1.73)%,与受体亲本无显著性差异。(2)在减数分裂I中,2个耐冷渐渗系均观察到低频率异常染色体行为,如单价体、"8"字型二价体、多价体,以及后期I有少数花粉母细胞(3.95%～5.15%)存在落后染色体等,表明其染色体组之间发生了交换和重组;在粗线期,2个强耐冷渐渗系均观察到较高频率(IL5243和IL5335分别为27.0%和38.9%)的双核仁,而其双亲都是单核仁。(3)SSR标记和Structure分析进一步证实了栽培稻和野生稻染色体组间发生了交换重组,东乡野生稻部分DNA片段已渗入到强耐冷渐渗系中,这为水稻耐冷基因的挖掘与利用奠定了重要基础。     

曼陀罗叶水浸液对大豆幼根生长及细胞分裂的影响

以曼陀罗叶干粉为供体,大豆种子为受体,用室内培养皿法研究了曼陀罗叶水浸液化感胁迫对大豆种子萌发、幼根生长、根毛发育和根尖细胞分裂的影响。结果表明:各试验浓度的曼陀罗叶干粉水浸提液均抑制了大豆种子的萌发以及幼根和侧根的生长,且幼根生长随胁迫浓度的增加呈现逐渐缩短变粗变褐的趋势;化感胁迫还使根尖分生区细胞的染色体畸变和微核高频率发生。根毛发生和根尖细胞的分裂对化感胁迫都表现出"低促高抑"的响应,即轻度胁迫能显著促进根毛的生长并提高根尖细胞的分裂指数,而高度胁迫对根毛的生长有极显著的抑制作用,且使根尖细胞的分裂指数显著下降。     

羽衣甘蓝小孢子胚胎发生观察及再生植株倍性鉴定

以5个不同基因型羽衣甘蓝品种为试材进行游离小孢子培养,研究小孢子发育时期与花蕾形态的关系、基因型对小孢子出胚率的影响、胚成苗及再生植株加倍和倍性鉴定。结果表明:(1)适宜于羽衣甘蓝游离小孢子培养的花蕾形态指标为:蕾长3.5～4.5mm、花瓣/花药为0.85～1.10。(2)在5个供试品种中,‘4105’出胚率最高,每蕾2.45个,其次是‘7341’,每蕾2.18个,‘7340’和‘7348’小孢子出胚情况较差,分别为每蕾1.36和0.51个,而‘7342’没有出胚。(3)采用150mg.L-1秋水仙碱浸泡幼苗根部24h,结合流式细胞仪快速检测植株倍性,发现二倍体总加倍率为78.4%,大大提高了小孢子再生植株的利用效率。