Special Issue on "RNA Epigenetics"

正We are very pleased to announce a special issue,to be published in April 2017,on‘‘RNA Epigenetics’’in the journal Genomics,ProteomicsBioinformatics(GPB).RNAs are life’s essential molecules with diverse functions.The identification and functional studies of multiple types of non-coding RNAs have been a major focus of life science research during the past decade.Moreover,diversified chemical modifications as well as structural     

抗-20诱导的三眠家蚕后丝腺RNA聚合酶和RNA的合成

蚕在4龄期开始的48小时连续取食抗-20,4眠家蚕被诱导成3眠蚕并吐丝结茧。根据对α-鹅膏蕈碱的敏感性,放线菌素D的抑制作用,DNA需要以及[~3H]-UMP掺入酸不可溶物,测定了蚕后丝腺的RNA聚合酶Ⅰ和Ⅱ活力。观察到随着抗-20处理后天数的增加,RNA聚合酶在热变性小牛胸腺DNA和内源DNA上转录活性迅速升高,并伴随着RNA合成的迅速增加;而对照组蚕的酶活力和RNA含量仍保持在相当稳定的低水平。     

Large-scale synthesis of "Cpep" RNA monomers and their application in automated RNA synthesis

Small interfering RNAs (siRNA) are the latest candidates for oligonucleotide-based therapeutics. Should siRNA be successful in clinical trials, a huge demand for synthetic RNA is anticipated. We believe that 1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl (Cpep) is an ideal 2'-protecting group for large-scale syntheses. Unlike 2'-silyl groups, mild acid hydrolysis instead of fluoride ion is used for the 2'-deprotection. The syntheses of 2'-Cpep protected nucleosides (A, C, G, and U) has been accomplished on a 0.5 Kg scale. The 2'-Cpep monomers were transformed into 3'-O-phosphoramidites for conventional automated solid-phase synthesis. Cost-effective processes for large-scale synthesis of Cpep monomers and initial automated solid-phase synthesis are demonstrated.     

"Pseudolysogenization" by RNA phage Q beta.

We isolated fairly stable lysogenic-like bacteria from a lysogenic state established between an amber mutant for the maturation protein gene of RNA phage Q beta (Q beta am 205) and its nonpermissive host BE110. These bacteria contained few mature phages intracellularly (less than 10(-3) plaque forming unit per cell), continued to grow with a potentiality to produce Q beta am 205 spontaneously, and showed an immunity-like response against homologous phage infection. These characteristics were maintained by growth in liquid medium containing anti-Q beta serum. We designated these cells as pseudolysogenic bacteria. The relative amounts of RNA genomes in these pseudolysogenic cells (about 10(2) infectious RNA strands per cell) indicated that the RNA genomes could replicate in nonpermissive cells and be distributed in daughter cells synchronizing well with cell division.     

Relation between the structural, metabolic and "adhesive" properties of nuclear and cytoplasmic non-ribosomal RNA

Nuclear RNAs release from nucleoproteins of isolated nuclei absorbed on a celite column in a wide range of dissociating conditions (from 1 M LiCl--2 M urea at 2 degrees C to 4 M LiCl--8 M urea at 70-80 degrees C) was demonstrated. Such a high "adhesive" heterogeneity of nuclear RNAs (i.e., variations in the tightness of RNA-protein bonds) appears to be due to the association of nuclear matrix proteins. A direct correlation was found to exist between the metabolic turnover of RNA and the tightness of its association with the nuclear matrix. Actually, the pulse label which rapidly incorporates into the RNAt greater than 50 degrees, the RNA fraction being most tenaciously bound to the matrix, could be chased later into RNAs weakly bound to it. As the RNA-matrix binding weakens, the metabolic and structural properties of a given RNA change, e.g., sedimentation coefficients decrease, while the poly(A)+-RNA content and stability increase. The "adhesive" heterogeneity was found to be inherent in not only nuclear RNAs but also in cytoplasmic non-ribosomal RNAs, showing the same correlation, i.e., the tighter the RNA--protein complex, the higher the rate of RNA turnover. Cytoplasmic RNAs which differ in their adhesiveness may fulfil various intracellular functions, since polyribosomal mRNPs and informosomal mRNPs appear to be enriched in tightly and weakly bound RNA fractions, respectively. The interrelationships between nuclear and cytoplasmic RNAs are discussed.     

Effect of the "RNA control" locus in Escherichia coli on RNA bacteriophage R23 replication.

The effect of the rel gene of Escherichia coli on the RNA synthesis induced by phage R23 was studied. This RNA phage has the property of inhibiting ribosomal RNA formation and completely dominating the RNA synthesis of the host. Phage-specific RNA formation was found to be dependent on the allelic state of the rel gene. Determinations of RNA synthesis were made by both cumulative and short-term incorporations of uracil and adenine. Variations in labeling of nucleotide pools were compensated for by determining specific activities of ATP and UTP and using these values to obtain true, relative rates of RNA synthesis.     

Methylation of Sindbis virus "26S" messenger RNA.

The main virus-specific messenger RNA species of Sindbis virus-infected hamster cells, the “26S” RNA, has been examined with regard to methylation status. Internal methylated residues and terminal methylated residues were present, in approximately equal amounts. The internal methyl groups were almost all in 5-methylcytosine residues and the terminal methyl groups were mainly in 7-methylguanine residues. Evidence is presented that these latter occur in “capped” 5′-termini with the novel structure m⁷G(5′)pppNp.     

Plant noncoding RNA gene discovery by "single-genome comparative genomics"

Plant genomes have undergone multiple rounds of duplications that contributed massively to the growth of gene families. The structure of resulting families has been studied in depth for protein-coding genes. However, little is known about the impact of duplications on noncoding RNA (ncRNA) genes. Here we perform a systematic analysis of duplicated regions in the rice genome in search of such ncRNA repeats. We observe that, just like their protein counterparts, most ncRNA genes have undergone multiple duplications that left visible sequence conservation footprints. The extent of ncRNA gene duplication in plants is such that these sequence footprints can be exploited for the discovery of novel ncRNA gene families on a large scale. We developed an SVM model that is able to retrieve likely ncRNA candidates among the 100,000+ repeat families in the rice genome, with a reasonably low false-positive discovery rate. Among the nearly 4000 ncRNA families predicted by this means, only 90 correspond to putative snoRNA or miRNA families. About half of the remaining families are classified as structured RNAs. New candidate ncRNAs are particularly enriched in UTR and intronic regions. Interestingly, 89% of the putative ncRNA families do not produce a detectable signal when their sequences are compared to another grass genome such as maize. Our results show that a large fraction of rice ncRNA genes are present in multiple copies and are species-specific or of recent origin. Intragenome comparison is a unique and potent source for the computational annotation of this major class of ncRNA.