Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation.     

The effect of two cryopreservation methods on human sperm DNA damage

Several methods are currently available for selection when conducting sperm cryopreservation, however, these methods might cause different degrees of damage on sperm DNA. The aim of the this study is to compare the effects of storage at −80 °C (in ultra-low temperature refrigerator) and at −196 °C (in liquid nitrogen) on sperm DNA damage, thus to provide a reference for choosing the right method according to different aims. We randomly collected 28 semen samples from college students of Chongqing city. The samples stored at −80 °C were neat semen samples and the samples stored at −196 °C were mixed with additional cryoprotectants. Each sample was subjected to two freezing-thawing cycles, and the sperm DNA damage levels of fresh and thawed samples were measured by single cell gel electrophoresis (SCGE) and sperm chromatin structure assay (SCSA). Both SCGE and SCSA assays showed cryopreservation induced significant damage to sperm DNA. However, storage at −196 °C lead to more severe damage to sperm DNA than storage at −80 °C measured by SCSA. Sperm DNA damage increased simultaneously with the higher frequency of freezing-thawing cycles. We concluded that storage of neat semen samples at −80 °C had milder damage to sperm DNA than storage at −196 °C mixed with cryoprotectants. To avoid additional sperm DNA damage, repeated freezing and thawing should be prevented.     

Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers

The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg²⁺‐dependent self‐association of linear 12‐mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call “oligomers”, are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10‐nm fibers, rather than folded 30‐nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl₂, but became disrupted in the absence of MgCl₂, conditions that also dissociated the oligomers in vitro. These results indicate that a 10‐nm array of nucleosomes has the intrinsic ability to self‐assemble into large chromatin globules stabilized by nucleosome–nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.     

祛痰通阳汤对慢性心衰大鼠心肌损伤的保护作用及机制

目的:观察不同剂量祛痰通阳汤对慢性心衰大鼠心肌损伤的保护作用及可能机制。方法:将90只Wistar大鼠随机均分正常组、模型组、卡托普利组、祛痰通阳汤低、中、高剂量六组。为建立慢性心力衰竭模型,除正常组外的五组大鼠均以2ml/kg给予阿霉素腹腔,一周1次,共6周。注射造模成功后次日进行灌胃给予对应的不同药物,连续给药治疗四周后,应用ELISA法测定各组大鼠血浆脑尿钠肽(Brain natriuretic peptide,BNP)水平,称重计算心脏质量指数并采用投射电镜观察心肌细胞结构,通过实时荧光定量PCR法测定检测Kelch样环氧氯丙烷相关蛋白-1 (epoxy chloropro-pane Kelch sample related protein-1,Keap1)和核因子E2相关因子2(nuclearfactor erythroid-2 related factor 2,Nrf2)mRNA的表达。结果:1.电镜结果显示:正常组肌丝排列规则,肌节结构清晰,心肌细胞线粒体清晰且形态正常;细胞核发育良好,无空泡以及集块现象。模型组肌原纤维排列紊乱,心肌细胞线粒体形态异常,排列不齐,增生明显,有空泡现象形成。卡托普利组及祛痰通阳汤高剂量组电镜肌原纤维排列基本整齐,线粒体未见明显肿胀,线粒体嵴密集,优于中药低剂量组及中剂量组。2.卡托普利组、中药高剂量组大鼠血浆BNP水平较模型组显著降低(P0.01)。3.与模型组相比,中药高剂量组和卡托普利组心脏质量指数均显著降低(P0.05)。4.卡托普利组及祛痰通阳汤高剂量组心肌组织Keap1 m RNA表达与模型组相比显著降低(P0.05);卡托普利组及祛痰通阳汤高剂量组心肌组织Nrf2 m RNA表达与模型组的相比显著提高(P0.05)。结论:高剂量祛痰通阳汤可显著减轻慢性心衰大鼠的心肌损伤,可能与抑制Keap1 m RNA的表达及增强Nrf2 m RNA表达,进而抗心肌氧化损伤有关。     

急性心肌梗死高龄患者心肌灌注水平影响左室重构

为了探讨高龄急性心肌梗死(acute myocardial infarction, AMI)患者心脏超声特点,分析左室重构(left ventricle remodel, LVR)与心肌灌注水平的相关性,本研究选取2016年2月至2017年10月在广西医科大学第一附属医院治疗的高龄AMI患者104例,根据患者年龄分为A组49例(60~79岁)和B组55例(≥80岁),比较两组心脏超声指标,采用声学造影积分指数(contrast score index, CSI)评估两组术后心肌灌注水平。结果表明,B组后下壁心肌梗死比例为27.27%,明显高于A组(p<0.05);B组和A组前壁、下壁、前壁+下壁心肌梗死比例差异无统计学意义(p>0.05);B组左心室射血分数(left ventricular ejection fraction, LVEF)为(45.29±12.14)%,明显低于A组(p<0.05),左心房内径和左心室内径分别为(46.10径和左心室) mm和(57.29径和左心室内) mm,明显高于A组(p<0.05);B组经皮冠状动脉介入治疗(percutaneous coronary intervention,PCI)术后6个月CSI为(0.68±0.20),明显低于A组(p<0.05);B组术后左心房内径和左心室内径分别为(50.01±8.10) mm和(64.10±7.02) mm,明显高于A组(p<0.05);左心室内径与CSI呈负相关(r=-0.312, p<0.05)。综上表明,≥80岁患者与60~79岁患者心脏超声特点有所差异,年龄超过80岁的患者心功能以及PCI术后心肌灌注水平较差;心肌灌注水平与左室重构有一定相关性。