Disruption of a Large Intergenic Noncoding RNA in Subjects with Neurodevelopmental Disabilities

Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders.     

Inactivation of the Host Lipin Gene Accelerates RNA Virus Replication through Viral Exploitation of the Expanded Endoplasmic Reticulum Membrane

RNA viruses take advantage of cellular resources, such as membranes and lipids, to assemble viral replicase complexes (VRCs) that drive viral replication. The host lipins (phosphatidate phosphatases) are particularly interesting because these proteins play key roles in cellular decisions about membrane biogenesis versus lipid storage. Therefore, we examined the relationship between host lipins and tombusviruses, based on yeast model host. We show that deletion of PAH1 (phosphatidic acid phosphohydrolase), which is the single yeast homolog of the lipin gene family of phosphatidate phosphatases, whose inactivation is responsible for proliferation and expansion of the endoplasmic reticulum (ER) membrane, facilitates robust RNA virus replication in yeast. We document increased tombusvirus replicase activity in pah1Δ yeast due to the efficient assembly of VRCs. We show that the ER membranes generated in pah1Δ yeast is efficiently subverted by this RNA virus, thus emphasizing the connection between host lipins and RNA viruses. Thus, instead of utilizing the peroxisomal membranes as observed in wt yeast and plants, TBSV readily switches to the vastly expanded ER membranes in lipin-deficient cells to build VRCs and support increased level of viral replication. Over-expression of the Arabidopsis Pah2p in Nicotiana benthamiana decreased tombusvirus accumulation, validating that our findings are also relevant in a plant host. Over-expression of AtPah2p also inhibited the ER-based replication of another plant RNA virus, suggesting that the role of lipins in RNA virus replication might include several more eukaryotic viruses.     

水稻条纹病毒RNA4基因间隔区的分子变异

应用反转录－聚合酶链式反应（RT－PCR）和单链构象多态性（single-strand conformation polymorphism,SSCP)技术快速检测我国水稻条纹病毒（RSV）RNA4基因间隔区（intergenic region,IR)的分子变异,结果表明,我国RSV RNA4 IR存在分子变异。供试的7个分离物共有4种泳动带型,其中YL、BS、JD、LY分离物完全一致,而YL、BS、YL及JD4个分离物序列完全一致;JN、PJ、SQ3个分离各不一样,序列之间的同源性均在92％－94％之间.IR序列内部具有两个重要的结构特征：（1）有两处反向重复序列,可形成两个明显的发夹结构,其中一个序列比较保守,形成的发夹结构稳定;但中一个发夹结构由于碱基变异导致其稳定性在各个分离物中差异较大;（2）具有插入序列,相对于日本M分离物,我国7个分离物都有一段长19bp的插入序列,这段插入序列比较保守,各分离物之间仅有1－2个碱基的差异。     

Regulation of Herpesvirus Reactivation by Host MicroRNAs

The interplay between latent and lytic modes of infection is central to successful infection of all herpesviruses, yet knowledge of the determinants that govern reactivation of these viruses from latent to lytic infection is limited. Recently, several studies have identified roles for specific cellular microRNAs in inhibiting reactivation of various herpesviruses, thereby promoting latent infections. These studies are discussed in the context of current knowledge on mechanisms of regulation of reactivation of specific herpesviruses.     

水稻条纹病毒两个分离物RNA4基因间隔区的序列比较

通过ＲＴ－ＰＣＲ扩增了我国水稻秫纹病毒（ＲＳＶ）山东济宁（ＪＮ）、云南宜良（ＹＬ）两个分离物ＲＮＡ４基因间隔区（ｉｎｔｅｒｇｅｎｉｃ ｒｅｇｉｏｎ,ＩＲ）序列,并克隆于ｐＧＥＭ－Ｔ ｅａｓｙ载体上。序列分析结果表明：ＪＮ、ＹＬ两分离物ＲＮＡ４ ＩＲ均由６５４个核苷酸组成,两者之间的同源率为９２％。ＪＮ、ＹＬ两个分离物ＲＮＡ４ ＩＲ在ＡＵ碱基富集处可形成上明显的结构,其中一个序列比较保守,形成的发夹     

水稻条纹病毒两个分离物RNA4基因间隔区的序列比较

通过RT-PCR扩增了我国水稻条纹病毒(RSV)山东济宁(JN)、云南宜良(YL)两个分离物RNA4基因间隔区(intergenic region,IR)序列,并克隆于pGEM-T easy载体上.序列分析结果表明:JN、YL两分离物RNA4 IR均由654个核苷酸组成,两者之间的同源率为92%.JN、YL两个分离物RNA4 IR在AU碱基富集处可形成两个明显的发夹结构,其中一个序列比较保守,形成的发夹结构稳定;但另一个由于碱基变异导致所形成的发夹结构的稳定性在各个分离物中差异较大.这些结果说明了我国水稻条纹病毒存在明显的分子变异.     

Selective Degradation of Newly Synthesized Nonmessenger Simian Virus 40 Transcripts

By pretreating simian virus 40-infected BSC-1 cells with glucosamine, [(3)H]uridine labeling of both cellular and viral RNA can be halted instantaneously by addition of cold uridine. We have studied the fate of pulse-labeled viral RNA from cells at 45 h postinfection under these conditions. During a 5-min period of labeling, both the messenger and nonmessenger regions of the late strand were transcribed. After various chase periods, nuclear viral species which sediment at 19, 17.5, and 16S were observed. Nuclear viral RNA decays in a multiphasic manner. Of the material present at the beginning of the chase period, 50% was degraded rapidly with a half-life of 8 min (initial processing). This rapidly degraded material was that fraction of the late strand which did not give rise to stable late mRNA species. Forty percent was transported to the cytoplasm, and 10% remained in the nucleus as material which sedimented in the 2 to 4S region. These 2 to 4S viral RNAs had a half-life of 3 h, and hybridization studies suggest that they are in part coded for by the late-strand nonmessenger region and are derived from the initial nuclear processing step. Another part is coded for by the late-strand messenger region and may be generated by some subsequent nuclear cleavages of 19S RNA into 17.5 and 16S RNAs. Transport of nuclear viral RNA into the cytoplasm was detected after a 5-min pulse and a 7-min chase. The maximum amount of labeled viral RNA was accumulated in the cytoplasm after a 30-min to 1-h chase. At least two viral cytoplasmic species were observed. Kinetic data suggest that 19S RNA is transported directly from the nucleus. Whether cytoplasmic 16S is formed by cleavage of 19S RNA in the cytoplasm is not clear. The half-lives of cytoplasmic 19 and 16S RNAs can be approximated as 2 and 5 h, respectively.