Identification of a Novel PNMA-MS1 Gene in Marsupials Suggests the LTR Retrotransposon-Derived PNMA Genes Evolved Differently in Marsupials and Eutherians

Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.     

Parent-of-Origin Effects Implicate Epigenetic Regulation of Experimental Autoimmune Encephalomyelitis and Identify Imprinted Dlk1 as a Novel Risk Gene

Parent-of-origin effects comprise a range of genetic and epigenetic mechanisms of inheritance. Recently, detection of such effects implicated epigenetic mechanisms in the etiology of multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system. We here sought to dissect the magnitude and the type of parent-of-origin effects in the pathogenesis of experimental neuroinflammation under controlled environmental conditions. We investigated inheritance of an MS-like disease in rat, experimental autoimmune encephalomyelitis (EAE), using a backcross strategy designed to identify the parental origin of disease-predisposing alleles. A striking 37–54% of all detected disease-predisposing loci depended on parental transmission. Additionally, the Y chromosome from the susceptible strain contributed to disease susceptibility. Accounting for parent-of-origin enabled more powerful and precise identification of novel risk factors and increased the disease variance explained by the identified factors by 2-4-fold. The majority of loci displayed an imprinting–like pattern whereby a gene expressed only from the maternal or paternal copy exerts an effect. In particular, a locus on chromosome 6 comprises a well-known cluster of imprinted genes including the paternally expressed Dlk1, an atypical Notch ligand. Disease-predisposing alleles at the locus conferred lower Dlk1 expression in rats and, together with data from transgenic overexpressing Dlk1 mice, demonstrate that reduced Dlk1 drives more severe disease and modulates adaptive immune reactions in EAE. Our findings suggest a significant epigenetic contribution to the etiology of EAE. Incorporating these effects enables more powerful and precise identification of novel risk factors with diagnostic and prognostic implications for complex disease.     

Identification and Epigenetic Analysis of a Maternally Imprinted Gene Qpct

Most imprinted genes are concerned with embryonic development, especially placental development. Here, we identified a placenta-specific imprinted gene Qpct. Our results show that Qpct is widely expressed during early embryonic development and can be detected in the telecephalon, midbrain, and rhombencephalon at E9.5–E11.5. Moreover, Qpct is strikingly expressed in the brain, lung and liver in E15.5. Expression signals for Qpct achieved a peak at E15.5 during placental development and were only detected in the labyrinth layer in E15.5 placenta. ChIP assay results suggest that the modification of histone H3K4me3 can result in maternal activating of Qpct.     

Identification of a Novel Garlic Cellulase Gene

Genes encoding cellulase enzymes have been investigated in various plants due to the importance of cellulase enzymes in industrial applications, especially in the conversion of biomass into biofuels. Although several cellulase genes have been cloned and characterized, little is known about cellulase genes from garlic or enzyme activities of their gene products. In this study, a cellulase gene from garlic was cloned and characterized in gene and protein levels for the first time. The DNA sequence of the garlic cellulase gene showed 81% identity with the sequence of the endo-beta-1,4-glucanase of Pisum sativum. The open reading frame of this gene is 1,506 bp, which corresponds to 501 deduced amino acids. We identified the novel ORF region, which was translated into a 55.2 kDa protein using the protein expression vector, pET28a, in Escherichia coli and we confirmed that this protein has cellulase activity in vitro. Our study demonstrates that garlic is very useful, not only for the culinary and pharmaceutical industries, but also as an excellent natural source of various kinds of important genes and enzymes.     

Identification and Characterization of a Novel Trans-membrane Protein Gene, pdh1, from Schizosaccharomyces pombe

We have cloned a new gene, pdh1, from genomic DNA of fissionyeast Schizosaccharomyces pombe. pdh1 is actively transcribedas 1400-nucleotide mRNA in vegetatively growing cells and cancode for a 226 amino acid polypeptide (pdh1p). Computationalstructural prediction has revealed that the pdh1p is a highlyhydrophobic protein with seven transmembrane domains. The predictionhas also detected a possible C-kinase phosphorylation site withinthe longest hydrophilic loop.     

Identification of CHIP as a Novel Causative Gene for Autosomal Recessive Cerebellar Ataxia

Autosomal recessive cerebellar ataxias are a group of neurodegenerative disorders that are characterized by complex clinical and genetic heterogeneity. Although more than 20 disease-causing genes have been identified, many patients are still currently without a molecular diagnosis. In a two-generation autosomal recessive cerebellar ataxia family, we mapped a linkage to a minimal candidate region on chromosome 16p13.3 flanked by single-nucleotide polymorphism markers rs11248850 and rs1218762. By combining the defined linkage region with the whole-exome sequencing results, we identified a homozygous mutation (c.493CT) in CHIP (NM_005861) in this family. Using Sanger sequencing, we also identified two compound heterozygous mutations (c.389AT/c.441GT; c.621C>G/c.707GC) in CHIP gene in two additional kindreds. These mutations co-segregated exactly with the disease in these families and were not observed in 500 control subjects with matched ancestry. CHIP colocalized with NR2A, a subunit of the N-methyl-D-aspartate receptor, in the cerebellum, pons, medulla oblongata, hippocampus and cerebral cortex. Wild-type, but not disease-associated mutant CHIPs promoted the degradation of NR2A, which may underlie the pathogenesis of ataxia. In conclusion, using a combination of whole-exome sequencing and linkage analysis, we identified CHIP, encoding a U-box containing ubiquitin E3 ligase, as a novel causative gene for autosomal recessive cerebellar ataxia.     

Comparative Oncogenomics Implicates the Neurofibromin 1 Gene (NF1) as a Breast Cancer Driver

Identifying genomic alterations driving breast cancer is complicated by tumor diversity and genetic heterogeneity. Relevant mouse models are powerful for untangling this problem because such heterogeneity can be controlled. Inbred Chaos3 mice exhibit high levels of genomic instability leading to mammary tumors that have tumor gene expression profiles closely resembling mature human mammary luminal cell signatures. We genomically characterized mammary adenocarcinomas from these mice to identify cancer-causing genomic events that overlap common alterations in human breast cancer. Chaos3 tumors underwent recurrent copy number alterations (CNAs), particularly deletion of the RAS inhibitor Neurofibromin 1 (Nf1) in nearly all cases. These overlap with human CNAs including NF1, which is deleted or mutated in 27.7% of all breast carcinomas. Chaos3 mammary tumor cells exhibit RAS hyperactivation and increased sensitivity to RAS pathway inhibitors. These results indicate that spontaneous NF1 loss can drive breast cancer. This should be informative for treatment of the significant fraction of patients whose tumors bear NF1 mutations.     

Identification of an Imprinted Gene Cluster in the X-Inactivation Center

Mammalian development is strongly influenced by the epigenetic phenomenon called genomic imprinting, in which either the paternal or the maternal allele of imprinted genes is expressed. Paternally expressed Xist, an imprinted gene, has been considered as a single cis-acting factor to inactivate the paternally inherited X chromosome (Xp) in preimplantation mouse embryos. This means that X-chromosome inactivation also entails gene imprinting at a very early developmental stage. However, the precise mechanism of imprinted X-chromosome inactivation remains unknown and there is little information about imprinted genes on X chromosomes. In this study, we examined whether there are other imprinted genes than Xist expressed from the inactive paternal X chromosome and expressed in female embryos at the preimplantation stage. We focused on small RNAs and compared their expression patterns between sexes by tagging the female X chromosome with green fluorescent protein. As a result, we identified two micro (mi)RNAs–miR-374-5p and miR-421-3p–mapped adjacent to Xist that were predominantly expressed in female blastocysts. Allelic expression analysis revealed that these miRNAs were indeed imprinted and expressed from the Xp. Further analysis of the imprinting status of adjacent locus led to the discovery of a large cluster of imprinted genes expressed from the Xp: Jpx, Ftx and Zcchc13. To our knowledge, this is the first identified cluster of imprinted genes in the cis-acting regulatory region termed the X-inactivation center. This finding may help in understanding the molecular mechanisms regulating imprinted X-chromosome inactivation during early mammalian development.     

Identification of Rictor as a Novel Substrate of Polo-like kinase 1

Plk1 has been essentially described as a critical regulator of many mitotic events. However, increasing evidence supports the notion that its molecular functions are not restricted to the cell cycle. In particular, recent reports suggest the existence of a molecular and functional link between Plk1 and the mammalian target of rapamycin (mTOR) pathway, which controls cell growth and proliferation via the raptor-mTOR (TORC1) and rictor-mTOR (TORC2) protein complexes. Herein, we have identified rapamycin-insensitive companion of mTOR (Rictor), a core component of mTORC2, as a new Plk1 substrate and have shown that Plk1 phosphorylates Rictor at Ser1162 in vitro and in vivo. Surprisingly, cells expressing the unphosphorylatable mutant (S1162A) of Rictor did not show any effect on well characterized canonical PI3K-mTOR pathway. However, we found that cells expressing the unphosphorylatable form of Rictor have an elevated level of mSin1 isoform (mSin1.5). Considering that mSin1.5-containing mTORC2 was reported to associate with stress signaling, we propose that phosphorylation of Rictor at Ser1162 by Plk1 might be involved in a novel signaling pathway by regulating the mSin1.5-defined mTORC2.     

Identification and Characteristics of a Novel E1 Like Gene nUBE1l in Human test

The selective degradation of many short一lived or abnormal Proteins in eukaryotic cells 15 carried out by the ubiquitin system.In this Pathway,Proteins are targeted for degradation by covalent ligation to ubiquitin,a highly conserved 76一resid…     

印记基因DLK1的研究进展

在哺乳动物中,有一部分特别的基因,它们由于受到印迹而只表达单一亲本的基因,这种表观遗传的修饰现象就是基因组印记,这有别于经典的孟德尔遗传学定律。DNA甲基化是一种重要的表观遗传修饰,主要的修饰部位发生在DNA的CpG岛,它参与了细胞分化,基因组稳定性、基因印记等多种细胞生物学过程,基因印迹的建立和维持是胚胎正常发育的基础,这一过程的实现有赖于各种DNA甲基化转移酶的精确表达和密切的配合。已发现在哺乳动物的基因组中存在着许多的印记基因,DLK1基因为父系表达母源沉默的印记基因,它的表达同样受到DNA甲基化的调节,它首先在神经母细胞瘤发现并克隆,定位于人类染色体14q32,属于表皮生长因子样超家族的成员之一,约有6个外显子。研究表明,DLK1基因在胚胎肝、早期肌肉组织以及造血干细胞等组织中均有表达,人DLK1基因全长1557bp,编码序列含有1152核苷酸,编码383个氨基酸残基,在人、小鼠、绵羊都存在保守序列,它参与多种细胞的增殖、分化并且与相关肿瘤的发生发展有着密切的关系,印迹基因的印迹异常与肿瘤的易感性及发生发展有重要的关系,本文就国内外DLK1基因的研究进展做一综述。     

鼻咽癌下调新基因NOR1相互作用蛋白的筛选和鉴定

NOR1基因是新的鼻咽癌相关基因,该基因在鼻咽癌细胞系HNE1和鼻咽癌组织中表达下调．在鼻咽癌细胞HNE1中恢复NOR1基因表达抑制了鼻咽癌细胞的生长和增殖能力．为了探讨NOR1基因的生物学功能,以NOR1基因为诱饵运用酵母双杂交技术在人胎脑文库中筛选其交互作用蛋白,挑选阳性克隆,进行DNA序列分析和同源检索,阳性克隆编码7个不同的蛋白质,其中一个阳性克隆编码线粒体ATP合成酶亚基OSCP蛋白．瞬时转染pCMV-myc-NOR1质粒进入鼻咽癌5-8F细胞,通过密度梯度离心法分离线粒体蛋白,Western blot检测表明myc-NOR1蛋白分布于线粒体与胞浆．免疫荧光检测表明在鼻咽正常上皮细胞NP69中内源性NOR1蛋白与线粒体存在明显共定位．随后采用特异性酵母双杂交、免疫荧光共定位、免疫共沉淀技术证实了NOR1与OSCP在线粒体内存在交互作用．提示,NOR1是一个新的线粒体蛋白,可能通过结合OSCP蛋白调控细胞能量代谢,为深入探讨其功能提供了重要线索．     

Identification and Functional Expression of HCx31.9, a Novel Gap Junction Gene

By combining in silico and bench molecular biology methods we have identified a novel human gap junction gene that encodes a protein designated HCx31.9. We have determined its human chromosomal location and gene structure, and we have identified a putative mouse ortholog, mCx30.2. We have observed the presence of HCx31.9 in human cerebral cortex, liver, heart, spleen, lung, and kidney and the presence of mCx30.2 in mouse cerebral cortex, liver and lung. Moreover, preliminary data on the electrophysiological properties of HCx31.9 have been obtained by functional expression in paired Xenopus oocytes and in transfected N2A cells.     

鼻咽癌相关基因NAP1的克隆及鉴定

从UniGene库中选取编号为BG231197,来自人鼻咽组织的EST序列.利用Blast检索GenBank的nr数据库和EST数据库,构建EST重叠群.利用人类基因组草图搜索法从成人正常鼻咽组织中PCR扩增获得该基因全长cDNA,命名为NAP1,GenBank登录号为AY190326.NAP1基因cDNA序列全长为573 bp,编码由85个氨基酸组成,相对分子质量为9 700的多肽.用α-³²P-dCTP标记NAP1基因片段,与含15种正常成人组织的多组织RNA印迹膜杂交,结果表明NAP1基因在淋巴结和气管中高表达,转录本大小约为0.6 kb,在其他组织中不表达.NAP1蛋白质与滤泡树突状细胞（follicular dendritic cell, FDC）的一种分泌肽前体（FDC -SP）（AF435080）同源,与其他已知蛋白质无明显同源性.NAP1基因定位在染色体4q13,基因组跨越9 179 bp,含5个外显子和4个内含子.采用差异RT-PCR检测了40例经病理诊断为低分化鳞状上皮癌的鼻咽活检组织及其对侧相应部位的正常鼻咽组织中该基因的表达差异.在40例鼻咽癌中,NAP1基因表达下调的有17例（42.5%）,表达上调的有6例（15%）,无明显表达差异的有17例（42.5%）.原位杂交和免疫组化结果显示该基因在正常鼻咽和鼻咽癌组织间质中的树突状细胞中表达,在其他间质细胞和鼻咽上皮中均不表达.以上结果表明,NAP1为树突状细胞的一种新的多肽,该基因在鼻咽癌组织中表达下调的原因,及其与鼻咽癌发生、发展的关系值得进一步探讨.