Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.     

Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services

Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180 K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio = 1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n = 20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n = 8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.     

人类锌指结构新基因ZNF18的克隆和表达谱分析

在很多转录因子中发现的锌指结构,被认为在人类心脏的发育和相关疾病的发生过程中发挥重要的作用。本文报道了克隆和表达分析人类新的锌指蛋白基因ZNF18。该基因cDNA长2 767 bp,编码一个有549个氨基酸的蛋白,这一蛋白含有一个SCAN结构域,一个KRAB结构域和5个连续的C2H2型锌指结构域。ZNF18蛋白与小鼠Zfp535有77％的同源性。ZNF18基因定位于人染色体17p12~p13,包含9个外显子和8个内含子。以ZNF18全长编码区为探针进行Northern杂交,结果显示ZNF18在成体小鼠各组织中广泛表达,但在心脏中低丰度表达。整体原位杂交结果显示,ZNF18基因在小鼠胚胎的表达有很高的动态性。ZNF18主要在E7.5小鼠胚胎的胚外组织表达,E8.5出现了胚胎躯干前端表达。ZNF18从E9.0开始在胚胎的心脏和尾部表达,尤其在E10.5胚胎的心脏高丰度表达。这提示ZNF18基因与心脏发育过程可能有密切的关系。     

The Zinc Finger Protein ZNF268 Is Overexpressed in Human Cervical Cancer and Contributes to Tumorigenesis via Enhancing NF-κB Signaling

Cervical cancer is one of the most common tumors affecting women''s health worldwide. Although human papillomavirus can be detected in nearly all cases, the mechanism of cervical carcinogenesis remains to be further addressed. Here, we demonstrated that ZNF268, a Krüppel-associated box-containing zinc finger protein, might contribute to the development of cervical cancer. We found that ZNF268b2, an isoform of ZNF268, was overexpressed in human squamous cervical cancer specimens. Knockdown of ZNF268 in cervical cancer cells caused cell cycle arrest at the G₀/G₁ phase, reduced colony formation, and increased sensitivity to TNFα-induced apoptosis. In addition, HeLa cell growth in xenograft nude mice was suppressed by ZNF268 knockdown, with increased apoptosis. Furthermore, ZNF268b2 was shown to increase NF-κB signaling in vitro and in vivo. Reconstitution of NF-κB activity restored proliferation in ZNF268 knockdown HeLa cells. Of note, we observed a high frequency of NF-κB activation in ZNF268-overexpressing cervical cancer tissues, suggesting a pathological coincidence of ZNF268b2 overexpression and NF-κB activation. Taken together, our results reveal a novel role of ZNF268b2 that contributes to cervical carcinogenesis in part through enhancing NF-κB signaling.     

锌指基因ZNF268两个新的差异剪接本克隆及鉴定

ZNF268是一个典型的KRAB类锌指基因,含有24个C2H2型锌指基序和一个KRAB功能域,它在人胚胎发育早期表达,并与胚胎肝脏的发育相关。本研究通过免疫组化的方法,发现ZNF268在3～5周龄人胚的造血干细胞中有表达;进一步通过RT-PCR的方法检测发现ZNF268在健康成人全血细胞中也有表达,并且表达有4个差异剪接本,从中克隆得到两个新的ZNF268差异剪接本ZNF268c和ZNF268d。推测ZNF268和血细胞生长发育相关。     

ZNF268基因启动子区的克隆及功能分析

锌指基因家族是人体中最大的基因家族,它参与细胞分化、胚胎发育,并与许多疾病的发生相关。人类ZNF268基因是一个在人胚肝中特异性表达的C2H2型锌指基因,并可能在人的早期肝脏发育中起重要作用。为了研究ZNF268基因表达调控的分子机制,以正常人总基因组为模板PCR扩增了ZNF268基因的5′调控区2533bp片段,并将此片段插入启动子缺失的EGFP(增强型绿色荧光蛋白)载体构建了重组质粒pZNF268—EGFP。用脂质体介导的方法将pZNF268—EGFP转染NIH／3T3、COS7、K562、HeLa4个细胞系。在激光共聚焦显微镜下观察绿色荧光的表达,发现在每个细胞系中,转染了重组质粒pZNF268—EGFP的细胞均有荧光表达,但其起始表达时间均晚于转染了阳性对照质粒pEGFP—C1的细胞且荧光较弱。这表明ZNF268基因的5′调控区2．5kb片段是一个有功能的启动子,但该启动子与CMV启动子相比活性较弱。选择易培养的HeLa细胞系用于缺失研究。将一系列5′端—2456bp至—20bp缺失、3′端均为 77bp的缺失片段插入启动子缺失的CAT(氯酶素酰胺转移酶)载体构建了一系列重组质粒。将这些重组质粒转染HeLa细胞系进行缺失分析,并通过共转染pCMV—Sport—βgal质粒校正转染效率。结果表明,ZNF268启动子—2456～—1639bp区域可能含有正调控元件,—1244～—1013bp和—525～—156bp区域可能含有负调控元件,ZNF268启动子激活转录的一个重要区域位于—156～—20bp。     

Generation of cells that ignore the effects of PIP3 on cytoskeleton

Comment on: Tang M, et al. Mol Biol Cell 2011; 22:437-47.