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Non-coding RNAs and the acquisition of genomic imprinting in mammals

Science China(Life Sciences) 2009年第3期52卷 195-204页

作者： ZHANG YiJun & QU LiangHu key laboratory of gene engineering of the ministry of education,State key laboratory for Biocontrol,Sun Yan-Sen University,Guangzhou 510275,China key laboratory of gene engineering of the ministry of education State Key Laboratory for Biocontrol Sun Yan-Sen University Guangzhou 510275 China

Genomic imprinting,representing parent-specific expression of alleles at a locus,is mainly evident in flowering plants and placental *** imprinted genes,including numerous non-coding RNAs,are located in clusters regulated by imprinting control regions(ICRs).The acquisition and evolution of genomic imprinting is among the most fundamental genetic *** about the transition of mammalian imprinted gene domains from their non-imprinted ancestors,especially recent studies undertaken on the most ancient mammalian clades-the marsupials and monotremes from which model species genomes have recently been sequenced,are of high *** reviewing and analyzing these studies,a close connection between non-coding RNAs and the acquisition of genomic imprinting in mammals is *** evidence comes from two observations accompanied with the acquisition of the imprinting:(i) many novel non-coding RNA genes emerged in imprinted regions;(ii) the expressions of some conserved non-coding RNAs have changed ***,a systematical analysis of imprinted snoRNA(small nucleolar RNA) genes from 15 vertebrates suggests that the origination of imprinted snoRNAs occurred after the divergence between eutherians and marsupials,followed by a rapid expansion leading to the fixation of major gene families in the eutherian ancestor prior to the radiation of modern placental *** in the regulation of imprinted silencing and mediating the chromatins epigenetic modification may be the major roles that non-coding RNAs play during the acquisition of genomic imprinting in mammals.

关键词： genomic imprinting mammals non-coding RNAs

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tRNAs as regulators in gene expression

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Science China(Life Sciences) 2009年第3期52卷 245-252页

作者： LI Yan & ZHOU Hui key laboratory of gene engineering of the ministry of education,State key laboratory for Biocontrol,Sun Yan-Sen University Guangzhou 510275,China 1. key laboratory of gene engineering of the ministry of education State Key Laboratory for Biocontrol Sun Yan-Sen University Guangzhou 510275 China

Transfer RNAs(tRNAs) hold a central place in protein synthesis by interpreting the genetic information stored in DNA into the amino acid sequence of protein,thus functioning as "adaptor" *** recent years,however,various studies have shown that tRNAs have additional functions beyond participating in protein *** suffering from certain nutritional stresses,tRNAs change the level of aminoacylation to became uncharged,and these uncharged tRNAs act as effector molecules to regulate global gene expression,so that the stressed organism copes with the adverse environmental *** budding yeast and certain mammalian cells,the retrograde movement of mature tRNAs from cytoplasm to nucleus serves as a mechanism for the surveillance system within the nucleus to continue monitoring the integrity of *** the other hand,this retrograde action effectively reduces the global protein synthesis level under conditions of nutritional *** recently,various publications have shown that tRNAs are not stable molecules in an absolute *** certain physiological or environmental stresses,they are specifically cleaved into fragments of different lengths in the anticodon loop or anticodon left *** cleavages are not a meaningless random degradation ***,a novel class of signal molecules such as tRNA halves or sitRNAs may be produced,which are closely correlated with the modulation of global gene *** of the regulatory functions of tRNAs is a frontier,which seeks to reveal the structural and functional diversity of tRNAs as well as their vital functions during the expression of genetic information.

关键词： tRNA sitRNA gene expression regulation stress response

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Computational RNomics:Structure identification and functional prediction of non-coding RNAs in silico

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Science China(Life Sciences) 2010年第5期53卷 548-562页

作者： ZHENG LingLing & QU LiangHu key laboratory of gene engineering of the ministry of education,State key laboratory for Biocontrol,Sun Yat-sen University,Guangzhou 510275,China 1. key laboratory of gene engineering of the ministry of education State Key Laboratory for Biocontrol Sun Yat-sen University Guangzhou 510275 China

The eukaryotic genome contains varying numbers of non-coding RNA(ncRNA) genes."Computational RNomics" takes a multidisciplinary approach,like information science,to resolve the structure and function of ***,we review the main issues in "Computational RNomics" of data storage and management,ncRNA gene identification and characterization,ncRNA target identification and functional prediction,and we summarize the main methods and current content of "computational RNomics".

关键词： non-coding RNA eukaryote computational RNomics

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Identification,expression and functional analysis of U3 snoRNA genes from Neurospora crassa

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Progress in Natural Science:Materials International 2009年第2期19卷 167-172页

作者： Na Liu,Qiaojuan Huang,Zhou Hui,Yintong Liang,Chunhong Yu,Lianghu Qu key laboratory of gene engineering of the ministry of education,State key laboratory for Biocontrol,Zhongshan University,Guangzhou 510275,China [a]key laboratory of gene engineering of the ministry of education State Key Laboratory for Biocontrol Zhongshan University Guangzhou 510275 China

By screening of a cDNA library constructed with small RNAs from Neurospora crassa and genome analysis,three U3 snoRNAs of 262,270 and 275 nt were identified and named as NcU3A,NcU3B and NcU3C,respectively. Expression of the three U3 snoRNA genes was further analyzed by Northern blot hybridization. Meanwhile,two 50-truncated U3 transcripts with different sizes were also identified,indicating a complex posttranscriptional processing of the U3 snoRNAs. In addition to the known functional elements complementary to 18S rRNA,a novel antisense sequence to 26S rRNA was found in NcU3A. A primer extension assay showed that the antisense sequence did not guide 20-O-ribose methylation of 26S rRNA but probably functioned as an rRNA chaperon. In the N. crassa genome,three U3 snoRNA genes are independently transcribed and each of them contains a small intron. The same intron-inserting site in the U3 snoRNA genes among N. crassa and yeasts shows the ancient origin of the intron in these organisms. Our results provide new insights into the structural and functional diversity of U3 snoRNA family.

关键词： Neurospora crassa U3 snoRNA rRNA processing

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Identification and characterization of two novel box H/ACA snoRNAs from Schizosaccharomyces pombe

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Progress in Natural Science:Materials International 2005年第6期15卷 507-514页

作者： LI Siguang, ZHOU Hui, ZHANG Peng, LUO Yuping and QU Lianghu*(key laboratory of gene engineering of the ministry of education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China) key laboratory of gene engineering of the ministry of education Biotechnology Research Center Zhongshan University Guangzhou 510275 China

Through constructing a specialized cDNA library based on small RNAs isolated from partial purified nuclei of Schizosaccharomyces pombe, two novel noncoding RNAs, termed Sp15-70 and Sp18-61, have been identified. Bioinformatics analysis reveals that both the novel RNAs possess a typical secondary structure of box H/ACA snoRNA and antisense elements to rRNAs. According to the relationship between the structure and function of box H/ACA snoRNA, Sp15-70 was predicted to direct pseudouridylation in 25S rRNA at U2401 and U2298; Sp18-61 was predicted to direct pseudouridylation in 18S rRNA at U208 and 25S rRNA at U2341. The four predicted pseudouridylation sites were all verified experimentally by the CMC-primer extension analysis. Both Sp15-70 and Sp18-61 were encoded by single copies which were located in the intergenic regions between the CDS of two protein-coding genes on chromosome Ⅰ and Ⅲ of S. pombe, respectively. Putative TATA-like elements can be found upstream from the 5′ end of these snoRNA genes, suggesting that they could be transcribed from their own promoters. Comparison of the two snoRNAs and their functional homologues in diverse organisms reveals that extensive recombinations among different snoRNAs have occurred during the evolution from their primitive progenitors.

关键词： box H/ACA snoRNA RNA pseudouridylation gene evolution Schizosaccharomyces pombe.

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Stacking interaction in metal complexes with compositions of DNA and heteroaromatic N-bases

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Chinese Science Bulletin 2002年第1期47卷 1-9页

作者： Jl Liangnian & LE XueyiDepartment of Chemistry, key laboratory for the gene engineering of the ministry of education of China, and State key laboratory of Ultrafast Laser Spectroscopy, Zhongshan University, Guangzhou 510275, China Department of Applied C Department of Chemistry Key Laboratory for the Gene Engineering of the Ministry of Education of China and State Key Laboratory of Ultrafast Laser Spectroscopy Zhongshan University Guangzhou China Department of Applied Chemistry South-China Agricultural University Guangzhou China

The current development in the intramolecular aromatic-ring stacking interactions in the complexes with compositions of DNA and heteroaromatic N-bases has been reviewed to a great extent, especially the significant contributions in several important systems about ternary mixed-ligand complexes, including nucleotide-metal ion-po-lyaromatic amine, amino acid-metal ion-polyaromatic amine, nucleotide-metal ion-pyridine-like aromatic amine, nucleo-tide-metal ion-amino acid, nucleotide-metal ion-nucleic acid base, nucleic acid base-metal ion, and the important factors affecting the intramolecular aromatic-ring stacking interac-tions in the complexes. Based on the study of stacking inter-action in the complexes, the mechanism of interaction be-tween DNA molecules and complexes of heteroaromatic N-bases has been established, which is crucial for the design and synthesis of the complexes acting as molecular devices of DNA.

关键词： ternary mixed-ligand complexes stacking interaction transition metal ion heteroaromatic N-base nucleotide amino acid.

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Identification and functional analysis of a novel box C/D snoRNA from Schizosaccharomyces pombe

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Chinese Science Bulletin 2004年第18期49卷 1929-1936页

作者： LUO Yuping, ZHUO Hui, LI Siguang & QU Lianghu key laboratory of gene engineering of the ministry of education, Bio-technology Research Center Zhongshan University, Guangzhou 510275, China Correspondence should be addressed to Qu Lianghu (e-mil: lsbrc04@***) key laboratory of gene engineering of the ministry of education Biotechnology Research Center Zhongshan University Guangzhou 510275 China

By constructing and screening the Schizosac-charomyces pombe nuclear cDNA library, a novel small nu-cleolar RNAs (snoRNA) was identified. The novel snoRNAdisplays structural features typical of C/D box snoRNA fam-ily and possesses a 10-nt-long rRNA antisense element whichis predicted to guide the 2’-O-methylation of the fission yeast 25S rRNA at G940. As expected, the rRNA ribose-methyla-tion site predicted by the novel snoRNA was preciselymapped by a deoxynucleoside triphosphate concentration-dependent primer extension assay. The comparison of func-tional element of guide snoRNAs among eukaryotes reveals that the novel snoRNA is a partial counterpart of the bud-ding yeast snR60 and was termed snR60-II. snR60-II genenested in the intron of a non-coding RNA gene with an un-known function, which is the first example of a yeastsnoRNA encoded in an intron of a non-coding RNA ***, a number of yeast snR60 homologues were also identified from other fungi and fly. Our results reveal thatsnR60 exhibits diverse genomic organization in eukaryotes, implying the high mobility of snR60 gene in the course ofevolution.

关键词：功能分析 C/DsnoRNA 人体酵母菌探针 rRNA 甲基化核酸分析

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Identification and functional analysis of 23 novel box C/D snoRNAs from Oryza sativa

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Chinese Science Bulletin 2003年第19期48卷 2077-2082页

作者： ZHUO Min, ZHOU Hui, HUANG Zhanpeng, LIANG Dan, CHEN Chunlong, CHEN Yueqin & QU Lianghu key laboratory of gene engineering of the ministry of education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China key laboratory of gene engineering of the ministry of education Biotechnology Research Center Zhongshan University Guangzhou 510275 China Yarmouk University Irbid - Jordan

In a cDNA library generated from rice small nuclear RNAs, 30 box C/D small nucleolar RNAs (snoRNAs) were identified through preliminary screen. Except 7 known snoRNAs such as U14, all snoRNAs were identified in rice for the first time experimentally. Among the 23 novel snoRNAs, 11 snoRNAs appear rice-specific, 6 snoRNAs are unique to plants, the remaining 6 snoRNAs have their counterparts in both Arabidopsis and yeast or mammals according to the conserved antisense sequences that guide 2′-O-ribose methylation of rRNA. 17 of the 23 novel snoRNAs were predicted to guide 24 2′-O-ribose methylations at the specific sites of rice 5.8S, 18S, 25S rRNAs, among which 19 methylated sites were determined by primer extension at low dNTP concentrations. The remaining 6 snoRNAs devoid of rRNA antisense elements may represent novel snoRNA species in rice. The results show that constructing a cDNA library from small nuclear RNAs is an effective experimental approach for novel snoRNA identification. The novel snoRNAs are important in elucidating the genomic organization and expression of plant snoRNA genes and the mechanism through which 2’-O-ribose methylations took place in rRNAs.

关键词：功能分析 cDNA snoRNAs 水稻基因表达

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Characterization of three novel snoRNAs from Schizosaccharomyces pombe implies the structural and functional diversity of box H/ACA snoRNA family

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Chinese Science Bulletin 2003年第21期48卷 2320-2327页

作者： QU Guosheng, ZHOU Hui, YU Chuanhe, CHEN Xiao & QU Lianghu key laboratory of gene engineering of the ministry of education, Bio-technology Research Center, Zhongshan University, Guangzhou 510275, China Correspondence should be addressed to Qu Lianghu (e-mail: lsbrc04@ ***) key laboratory of gene engineering of the ministry of education Biotechnology Research Center Zhongshan University China

Site-specific pseudouridylations of rRNAs and snRNAs are directed by small guide RNAs that usually pos-sess conserved H and ACA motifs and the consensus secon-dary structure consisting of hairpin-hinge-hairpin-tail. In this study, through screening cDNA library, three novel box H/ACA snoRNAs, termed SP12, SP16 and SP20, have been identified from fisson yeast Schizosacchromyces pombe. Each of the small RNAs possesses an ACA-like motif and exhibits secondary structures containing two or three large hairpin- like domains. Although the box H is noncanonical, SP20 can be potentially folded into a typical box H/ACA snoRNA-like structure and is predicted to guide two pseudouridylations, U1208 and U1053, on 18S rRNA. In contrast, SP12 and SP16 display different structures from SP20 and have no antisense elements to rRNAs or snRNAs. Obviously, they are new members of orphan guide snoRNAs whose functions remain elusive. The genes encoded for SP12 and SP16 are both lo-cated in long intergenic regions between protein-coding genes. A post-transcriptional processing for SP16 precursor was demonstrated. Interestingly, SP20 gene is nested inside a very hypothetical ORF, but transcribed in a reverse sense. Northern and RT-PCR analyses could not detect the tran-script from the hypothetical ORF, and therefore exclude the expression of the spurious gene. This is the first example that a genetic locus predicted for protein-coding gene actually encodes a small non-messenger RNA in S. pombe.

关键词： RNA 核糖核酸脱氧核糖核酸 DNA 蛋白质

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Promoter polymorphism of MRP1 associated with reduced survival in hepatocellular carcinoma

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World Journal of Gastroenterology 2010年第48期16卷 6104-6110页

作者： Jing Zhao,Bing-Yun Yu,Jin-E Yang,key laboratory of gene engineering of the ministry of education,School of Life Sciences,Sun Yat-sen (Zhongshan) University,Guangzhou 510275,Guangdong Province,China Dao-Yuan Wang,Department of Medical Oncology,The First Affiliated Hospital of Guangzhou Medical College,Guangzhou 510120,Guangdong Province,China key laboratory of gene engineering of the ministry of education School of Life Sciences Sun Yat-sen (Zhongshan) University Xin Gang Xi Road 135# Guangzhou 510275 Guangdong Province China. lssyje@***

AIM:To investigate the effect of the G-1666A polymorphism in the multidrug resistance related protein-1 (MRP1) on outcome of hepatocellular carcinoma (HCC). METHODS:A cohort of 162 patients with surgically resected HCC who received no postsurgical treatment until relapse was studied. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism analysis. Electrophoretic mobility shift assay (EMSA) was used to evaluate the influence of the G-1666A polymorphism on the binding affinity of the MRP1 promoter with its putative transcription factors. RESULTS:Kaplan-Meier analysis showed that patients with GG homologues had a reduced 4-year disease-free survival compared with those carrying at least one A allele (P = 0.011). Multivariate Cox regression analysis indicated that the-1666GG genotype represented an independent predictor of poorer disease-free survival [hazard ratio (HR) = 3.067,95% confidence interval (CI):1.587-5.952,P = 0.001],and this trend became worse in men (HR = 3.154,95% CI:1.604-6.201,P = 0.001). A similar association was also observed between 4-year overall survival and the polymorphism in men (HR = 3.342,95% CI:1.474-7.576,P = 0.004). Moreover,EMSA suggested that the G allele had a stronger binding affinity to nuclear proteins. CONCLUSION:The MRP1-1666GG genotype predicted a worse outcome and was an independent predictor of poor survival in patients with HCC from Southeast China.

关键词： Multidrug resistance related protein-1 Single nucleotide polymorphism Hepatocellular carcinoma Prognosis

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