Scaffolding a Caenorhabditis nematode genome with RNA-seq

Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.     

系统性红斑狼疮患者脱氧核糖核酸酶1基因表达研究

目的　研究脱氧核糖核酸酶 1(deoxyribonuclease ,DNASE1)基因表达及 m RNA剪接形式与系统性红斑狼疮 (systemic lupus erythematosus,SL E)的关联性。　方法　以实时荧光定量聚合酶链反应 (real- time PCR)方法检测 DNASE1的 m RNA表达水平 ,以毛细管电泳技术分析 m RNA编码区替代剪接体 ,结合单核苷酸多态性 (single nucleotide polymorphisms,SNPs)单倍型了解基因结构对表达的影响。　结果　SL E患者 DNASE1基因表达水平显著高于正常对照 (P<0 .0 0 1) ,未发现 SL E疾病活动性指数积分与基因表达水平存在相关性 ,但性别分析显示女性患者 DNASE1基因表达水平高于男性患者 (P<0 .0 1)。 8名正常人与 18例患者的毛细管电泳结果显示 ,患者与正常人替代剪接谱系不同 ,且 380 bp处存在明显条带 ,具有不同单倍型的 SL E患者替代剪接谱系亦有差异。　结论　 SL E患者 DNASE1基因表达异常 ,并存在与正常人不同的 m RNA剪接体。 DNASE1基因与 SL E发病相关     

神经母细胞瘤SK-N-SH细胞内DHRS4L2基因一种新选择性剪接亚型S4的克隆和亚细胞定位

目的 神经母细胞瘤SK-N-SH细胞系脱氢酶/还原酶(SDR家族)成员4类2[dehydrogenase/reductase(SDR family)member 4 like 2,DHRS4L2]基因的一种新的选择性剪接亚型克隆、生物信息学分析及其亚细胞定位.方法 以SK-N-SH细胞cDNA为模板,PCR扩增DHRS4基因簇Ea1转录本.将PCR产物A-T克隆至pGEMT-Easy质粒,对质粒进行DNA Sanger测序.将测序所得序列用NCBI ORF finder分析其编码区,用Motif Scan分析预测蛋白氨基酸序列.用Clustal Omega进行蛋白序列比对分析.将新亚型完整编码框cDNA以及删除偶核定位信号的编码框分别插入pEGFP-C1质粒,所得质粒和空质粒分别转染SK-N-SH细胞,在荧光显微镜下观察转染表达蛋白亚细胞定位.结果 用RT-PCR和Sanger测序方法发现,SK-N-SH表达DHRS4L2 Ea1转录本,未检测到其表达脱氢酶/还原酶(SDR家族)成员4类1[dehydrogenase/reductase(SDR family)member 4 like 1,DHRS4L1]的Ea2转录本.DHRS4L2 Ea1表达一个新的选择性剪接亚型DHRS4L2-S4(KU141377),由AY616183基础上在Ea1与E2外显子之间插入新外显子Ej形成,外显子Ej含有新亚型翻译起始密码子ATG.转录本KU141377预测蛋白羧基端具有偶核定位信号(bipartite nuclear localization signal,NLS),提示其可能定位于细胞核.绿色荧光蛋白融合蛋白实验显示,在SK-N-SH细胞该蛋白定位于细胞核.该蛋白还含有一个甘氨酸密集区(glycine-rich region)和阿片样生长因子受体重复(opioid growth factor receptor repeat)序列.结论 研究发现SK-N-SH细胞表达的一种DHRS4L2新选择性剪接亚型KU141377,其预测编码蛋白含有细胞偶核定位信号,融合荧光蛋白实验显示该新亚型定位于细胞核,这为后续研究DHRS4L2在神经母细胞瘤中的潜在功能奠定基础.     

An alternatively-spliced mRNA in the carboxy terminus of the neurofibromatosis type 1 (NF1) gene is expressed in muscle

The gene for neurofibromatosis type 1 (NF1) was identified bypositional cloning and found to contain two alternatively splicedexons. The first described alternatively spliced exon (exon23a) is located within the GAP-related domain of the gene andinserts an additional 63 nucleotides into the NF1 mRNA. Thesecond alternatively spliced exon (exon 48a) is located nearthe extreme carboxy terminus of the gene and inserts an additional54 nucleotides into the mRNA. This second isoform, termed 3'ALT,was originally detected while screening a fetal brain cDNA library.Examination of its expression by reverse-transcribed RNA PCRdemonstrates high level of expression in cardiac muscle, skeletalmuscle and smooth muscle. Trace levels of expression are detectedin brain and nerve. The 3'ALT isoform is expressed in fetalcardiac muscle, adult left ventricle and cardiac Purkinje cells.Further confirmation of the existence of this isoform was obtainedby blotting the PCR products with a radiolabeled oligonucleotideentirely derived from sequences contained within exon 48a andby direct sequencing of the PCR products. Additionally, thisisoform is expressed in muscle tissues from other vertebratespecies. The expression of this isoform in muscle suggests thatthe NF1 gene may play additional tissue-specific roles in muscledevelopment and signal transduction.