AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expr...AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expression level of HOTAIR in GC tissues. The correlation of its expression with clinicopathological features was analyzed. Area under receiver operating characteristic curve(AUCROC) was constructed to evaluate the diagnostic value of HOTAIR. Wound-healing assay and Transwell assay were performed to detect the biological effects of HOTAIR in GC cells. qp CR,western blot and immunohistochemistry were used to evaluate the m RNA and protein expression of E-cadherin. RNAbinding protein immunoprecipitation was used for the analysis of EZH2 interactions with HOTAIR. Chromatin immunoprecipitation assay was performed to investigate direct interactions between EZH2 and E-cadherin.RESULTS The expression of HOTAIR was up-regulated in GC tumorous tissues compared with the para-tumorous tissues(p < 0.001). Its over-expression was correlated with tumor-node-metastasis(TNM) stage(p = 0.024),tumor invasion(p = 0.018),lymph node metastasis(p = 0.023),and poor prognosis(p < 0.001). Multivariate Cox regression analysis confirmed expression of HOTAIR as an independent predictor of overall survival(p = 0.033),together with TNM stage(p = 0.002) and lymph node metastasis(p = 0.002). The AUCROC was up to 0.709(95%CI: 0.623-0.785,p < 0.001). Knockdown of HOTAIR by si RNA in GC cells suppressed the migration and invasion of GC cells. Significantly negative correlation between HOTAIR and E-cadherin was found in GC tissues and cell lines,and HOTAIR contributed to the regulation of E-cadherin through binding to EZH2 with the E-cadherin promoter. CONCLUSION HOTAIR may play a pivotal role in tumor cell migration and invasion. It can be used as a potential diagnostic and prognostic biomarker for GC.展开更多
Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS...Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.展开更多
Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identifi...Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identification of pati-ents at risk for progressive disease is crucial for managing NAFLD.Recent studies have identified long noncoding RNAs(lncRNAs),circular RNAs,and microRNAs as playing important roles in the pathogenesis of NAFLD.These noncoding RNAs are involved in modulating several metabolic pathways such as hepatic glucose and lipid metabolism,oxidative stress,and even carcinogenesis.Elevated levels of lncARSR and lncRNA nuclear-enriched abundant transcript 1 have been found in patients with NAFLD.In addition,lncRNAs such as PRYP4-3 and RP11-128N14.5 can distinguish patients with NAFLD from healthy indi-viduals.Increased MEG3 expression has been observed in both NAFLD and non-alcoholic steatohepatitis,suggesting that it may help predict patients at risk for disease progression.With advances in transcriptomics,we may discover additional targets to help in the identification and prognostication of NAFLD.展开更多
Endometriosis refers to as an estrogen-dependent disease.Estrogen receptorβ(ERB),the main estrogen receptor subtype which is encoded by the estrogen receptor 2(ESR2)gene,can mediate the action of estrogen in endometr...Endometriosis refers to as an estrogen-dependent disease.Estrogen receptorβ(ERB),the main estrogen receptor subtype which is encoded by the estrogen receptor 2(ESR2)gene,can mediate the action of estrogen in endometriosis.Although selective estrogen receptor modulators can target the ERβ,they are not specific due to the wide distribution of ERβ.Recently,long noncoding RNAs have been implicated in endometriosis.Therefore,we aim to explore and validate the downstream regulatory mechanism of ERβ,and to investigate the potential role of long intergenic noncoding RNA 1018(LINC01018)as a nonhormonal treatment for endometriosis.Our study demonstrates that the expression levels of ESR2 and LINCo1018 are increased in ectopic endometrial tissues and reveals a significant positive correlation between the ESR2 and LINCo1018 expression.Mechanistically,ERβdirectly binds to an estrogen response element located in the LINCO1018 promoter region and activates LINC01018 transcription.Functionally,ERβcan regulate the CDC25C/CDK1/CyclinB1 pathway and promote ectopic endometrial stromal cell proliferation via LINC01018 in vitro.Consistent with these findings,the knockdown of LINC01018 inhibits endometriotic lesion proliferation in vivo.In summary,our study demonstrates that the ERβ/LINC01018/CDC25C/CDK1/CyclinB1 signaling axis regulates endometriosis progression.展开更多
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81%transposable elements(TEs),while only 57%of the 735-Mb G.raimondii genome is occupied by TEs.In this study,we investi...Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81%transposable elements(TEs),while only 57%of the 735-Mb G.raimondii genome is occupied by TEs.In this study,we investigated whether there were unknown transcripts associated with TE or TE fragments and,if so,how these new transcripts were evolved and regulated.As sequence depths increased from 4 to 100 G,a total of 10,284 novel intergenic transcripts(intergenic genes)were discovered.On average,approximately 84%of these intergenic transcripts possibly overlapped with the long terminal repeat(LTR)insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels.Most of these intergenic transcripts possessed no transcription activation markers,while the majority of the regular genic genes possessed at least one such marker.Genes without transcription activation markers formed their+1 and-1 nucleosomes more closely(only(117±1.4)bp apart),while twice as big spaces(approximately(403.5±46.0)bp apart)were detected for genes with the activation markers.The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content.Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7million years ago(MYA)for all eudicot genomes or 13.7 MYA for the Gossypium family,respectively,while the intergenic transcripts evolved around 1.6 MYA,resultant of the last LTR insertion.The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.展开更多
Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. Th...Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I （ITS1）, rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.展开更多
Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. He...Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed ＂regulatory lincRNAs＂, representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GASS, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.展开更多
The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（...The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（PFS） exhibited stronger degrading abilities and more stable biomass than that of the phenol plus p-cresol-fed system（PCFS）.The microbial community structures were revealed by a modern DNA fingerprint technique,ribosomal intergenic spacer analysis（RISA）.The results indicated that the microbial community of PFS changed obviously when gradually increased phenol concentration,while PCFS showed a little change.16S rRNA sequence analysis of the major bands showed that Alcanivorax sp.genus was predominant species during phenolic compounds degradation.Furthermore,amplified functional DNA restriction analysis（AFDRA） on phenol hydroxylase genes showed that the fingerprints were substantially different in the two systems,and the fingerprints were not the same during the different operational periods.展开更多
Gene fusions are appreciated as ideal cancer biomarkers and therapeutic targets.Chimeric RNAs are traditionally thought to be products of gene fusions,and thus,also cancerspecific.Recent research has demonstrated that...Gene fusions are appreciated as ideal cancer biomarkers and therapeutic targets.Chimeric RNAs are traditionally thought to be products of gene fusions,and thus,also cancerspecific.Recent research has demonstrated that chimeric RNAs can be generated by intergenic splicing in the absence of gene fusion,and such chimeric RNAs are also found in normal physiology.These new findings challenge the traditional theory of chimeric RNAs exclusivity to cancer,and complicates use of chimeric RNAs in cancer detection.Here,we provide an overview of gene fusions and chimeric RNAs,and emphasize their differences.We note that gene fusions are able to generate chimeric RNAs in accordance with the central dogma of biology,and that chimeric RNAs may also be able to influence the generation of the gene fusions per the“horse before the cart”hypothesis.We further expand upon the“horse before the cart”hypothesis,summarizing current evidence in support of the theory and exploring its potential impact on the field.展开更多
Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected co...Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected cotton leaves was used as template, and fragment of LIR was obtained by PCR and inserted into clone vector. The fragment of LIR was fused with gus reporter gene and nos terminator in the orientation of transcription of virion sense and complementary sense respectively, and the plant expression vectors were constructed. GUS activity of Agrobacte-rium-mediated transgenic tobacco was measured. The result indicated that LIR showed strong promoter activity in complementary sense gene orientation. Average GUS activity of the complementary sense promoter was 5-6 times that of CaMV 35S promoter, and the highest GUS activity of individual plant was ten times of that of CaMV 35S promoter. Histochemical localization confirmed its activity in both mesophyll and vascular tissues. Activity of virion sense of LIR was rather low. Thus LIR isolated from CLCuV could be used as a novel strong promoter in plant genetic manipulation.展开更多
One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to e...One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.展开更多
Jellyfish blooms have increased worldwide, and the outbreaks of jellyfish population not only affect the food web structures via voracious predation but also play an important role in the dynamics of nutrients and oxy...Jellyfish blooms have increased worldwide, and the outbreaks of jellyfish population not only affect the food web structures via voracious predation but also play an important role in the dynamics of nutrients and oxygen in planktonic food webs. However, it remains unclear whether specific carbon compounds released through jellyfish metabolic processes have the potential to shape bacterial community composition. Therefore, in this study, we aimed to investigate the compositional succession of the bacterioplankton community in response to the dissolved organic matter (DOM) released by the live Scyphomedusae Cyanea lamarckii and Chrysaora hysoscella collected from Helgoland Roads of the North Sea. The bacterial community was significantly stimulated by the DOM released form live jellyfish and different dominant phylotypes were observed for these two Scyphomedusae species. Furthermore, the bacterial community structures in the different DOM sources, jellyfish-incubated media, Kabeltonne seawater, and artificial seawater (DOM-free) were significantly different, as revealed by automated ribosomal intergenic spacer analysis fingerprints. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed a rapid species-specific shift in bacterial community composition. Gammaproteobacteria dominated the community instead of the Bacteroidetes community for C. lamarckii, whereas Gammaproteobacteria and Bacteroidetes dominated the community for C. hysoscella. The significant differences in the bacterial community composition and succession indicate that the components of the DOM released by jellyfish might differ with jellyfish species.展开更多
China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and cla...China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and classification among 49 popular cultivated strains. The great majority of the 49 strains possessed two different IGS1 sequences, with distinct lengths and homologies. Based on the length and homology of the IGS1 sequences of the 49 strains, the strains were classified into two groups： A and B. Group A was subdivided into six subgroups. Forty-seven strains were homozygous or heterozygous among these six subgroups in group A, Cr01 was heterozygous between A and B, and Guangxiang 9 was homozygous in group B. An IGS1 polymorphism map of each cultivated L. edodes strain is reported for the first time and could be used as a marker for the initial classification and management of cultivated L. edodes strains in China.展开更多
<span style="font-family:Verdana;">The sequence of the ribosomal RNA gene (rDNA) plays an important role in species identification and phylogenetic analysis. However, the only published </span>&l...<span style="font-family:Verdana;">The sequence of the ribosomal RNA gene (rDNA) plays an important role in species identification and phylogenetic analysis. However, the only published </span><span><span style="font-family:Verdana;">full-length sequence of a ribosomal gene of green algae is that of </span><i><span style="font-family:Verdana;">Ulva mutabilis</span></i><span style="font-family:Verdana;">.</span></span><span style="font-family:Verdana;"> In this study, we </span><a name="_Hlk17805857"></a><span style="font-family:Verdana;">amplified the full-length sequence of each ribosomal gene unit of the ribosomal gene of </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;">. The full-length sequence of the ribosomal gene in </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> is 8676 bp, including the 1759 bp 18S rDNA, 576 bp internal transcribed spacer (ITS) + 5.8S rDNA, 3282 bp 28S </span><span style="font-family:Verdana;">rDNA, and 3059 bp intergenic spacer (IGS) region. We then carried out a series</span><span style="font-family:Verdana;"> of genetic analyses based on the ITS and IGS sequences, to verify whether IGS </span><span><span style="font-family:Verdana;">sequences are useful for studying the genetic diversity of green algae from different locations. We amplified the IGS sequences of </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> from 10 different locations in the Yellow Sea. Multiple alignments of the IGS sequences </span></span><span style="font-family:Verdana;">of samples from these 10 different sites revealed varying degrees of base </span><span><span style="font-family:Verdana;">differences, and comparative analysis of the ITS sequences revealed that our amplified species was classified as </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> and distinct from other green a展开更多
Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys in...Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys intergenic region in mtDNA were amplified and sequenced; sexual hormone assay, oral glucose tolerance test （OGTT） and insulin releasing test were carried out. Then variations found in mtDNA were compared between the two groups, the correlations between variations and clinical indexes were analyzed in all subjects. Results Nucleotide variations found in mtDNA were not different between the two groups, but the mutation of 16 094T/C was found associated with the serum levels ofT and fasting insulin; （303-317）CnTC, associated with the serum levels of A and LH; 195C/T with A level and 491T/C with LH level; （8 272-8 289）（ACCCCCTCT）, was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA perhaps associate with PCOS clinical symptoms and involve in PCOS development.展开更多
Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are ident...Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology （KO） numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http：//bioserver 1 .physics.iisc.ernet.in/psrna/and http：//bicmku.in： 8081/psrna/.展开更多
The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is funda- mental to ecology and conservation. Recent research...The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is funda- mental to ecology and conservation. Recent research on DNA-based inference of trophic associations suggests that the host range of phytophagous insects in the tropics may be wider than previously thought based on traditional observation. However, the reliability of molecular inference of ecological associations, still strongly dependent on PCR and thus exposed to the risk of contamination with environmental DNA, is under debate. Here, we explored alternative procedures to reduce the chance of amplification of external, nondiet DNA, including surface decontamination and analysis of mid/hind guts, comparing the results with those obtained using the standard protocol. We studied 261 specimens in eight species of Neotropical Chrysomelidae that yielded 316 psbA-trnH intergenic spacer sequences （cpDNA marker of putative diets） from unique and multiple-band PCR results. The taxonomic identity of these sequences was inferred using the automated pipeline BAGpipe, yielding results consistent with 31 plant families. Regardless of the proto- col used, a wide taxonomic spectrum of food was inferred for all chrysomelid species. Canonical Correspondence Analysis using these data revealed significant differences at- tributed mainly to species （expectedly, since they represent different ecologies）, but also to treatment （untreated vs. cleaned/gut samples） and PCR results （single vs. multiple bands）. Molecular identification of diets is not straightforward and, regardless of the species＇ niche breadth, combining approaches that reduce external contamination and studying multiple individuals per species may help increasing confidence in results.展开更多
基金Supported by the Shandong Provincial Natural Science Foundation of China,No.ZR2016HQ08Shandong Province Medical Science and Technology Development Projects of China,No.2016WS0151the Jining Municipal Project on Science and Technology Development of China,No.2013jnwk58
文摘AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expression level of HOTAIR in GC tissues. The correlation of its expression with clinicopathological features was analyzed. Area under receiver operating characteristic curve(AUCROC) was constructed to evaluate the diagnostic value of HOTAIR. Wound-healing assay and Transwell assay were performed to detect the biological effects of HOTAIR in GC cells. qp CR,western blot and immunohistochemistry were used to evaluate the m RNA and protein expression of E-cadherin. RNAbinding protein immunoprecipitation was used for the analysis of EZH2 interactions with HOTAIR. Chromatin immunoprecipitation assay was performed to investigate direct interactions between EZH2 and E-cadherin.RESULTS The expression of HOTAIR was up-regulated in GC tumorous tissues compared with the para-tumorous tissues(p < 0.001). Its over-expression was correlated with tumor-node-metastasis(TNM) stage(p = 0.024),tumor invasion(p = 0.018),lymph node metastasis(p = 0.023),and poor prognosis(p < 0.001). Multivariate Cox regression analysis confirmed expression of HOTAIR as an independent predictor of overall survival(p = 0.033),together with TNM stage(p = 0.002) and lymph node metastasis(p = 0.002). The AUCROC was up to 0.709(95%CI: 0.623-0.785,p < 0.001). Knockdown of HOTAIR by si RNA in GC cells suppressed the migration and invasion of GC cells. Significantly negative correlation between HOTAIR and E-cadherin was found in GC tissues and cell lines,and HOTAIR contributed to the regulation of E-cadherin through binding to EZH2 with the E-cadherin promoter. CONCLUSION HOTAIR may play a pivotal role in tumor cell migration and invasion. It can be used as a potential diagnostic and prognostic biomarker for GC.
文摘Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.
文摘Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identification of pati-ents at risk for progressive disease is crucial for managing NAFLD.Recent studies have identified long noncoding RNAs(lncRNAs),circular RNAs,and microRNAs as playing important roles in the pathogenesis of NAFLD.These noncoding RNAs are involved in modulating several metabolic pathways such as hepatic glucose and lipid metabolism,oxidative stress,and even carcinogenesis.Elevated levels of lncARSR and lncRNA nuclear-enriched abundant transcript 1 have been found in patients with NAFLD.In addition,lncRNAs such as PRYP4-3 and RP11-128N14.5 can distinguish patients with NAFLD from healthy indi-viduals.Increased MEG3 expression has been observed in both NAFLD and non-alcoholic steatohepatitis,suggesting that it may help predict patients at risk for disease progression.With advances in transcriptomics,we may discover additional targets to help in the identification and prognostication of NAFLD.
基金the National Natural Science Foundation of China(82271676)for funding support.
文摘Endometriosis refers to as an estrogen-dependent disease.Estrogen receptorβ(ERB),the main estrogen receptor subtype which is encoded by the estrogen receptor 2(ESR2)gene,can mediate the action of estrogen in endometriosis.Although selective estrogen receptor modulators can target the ERβ,they are not specific due to the wide distribution of ERβ.Recently,long noncoding RNAs have been implicated in endometriosis.Therefore,we aim to explore and validate the downstream regulatory mechanism of ERβ,and to investigate the potential role of long intergenic noncoding RNA 1018(LINC01018)as a nonhormonal treatment for endometriosis.Our study demonstrates that the expression levels of ESR2 and LINCo1018 are increased in ectopic endometrial tissues and reveals a significant positive correlation between the ESR2 and LINCo1018 expression.Mechanistically,ERβdirectly binds to an estrogen response element located in the LINCO1018 promoter region and activates LINC01018 transcription.Functionally,ERβcan regulate the CDC25C/CDK1/CyclinB1 pathway and promote ectopic endometrial stromal cell proliferation via LINC01018 in vitro.Consistent with these findings,the knockdown of LINC01018 inhibits endometriotic lesion proliferation in vivo.In summary,our study demonstrates that the ERβ/LINC01018/CDC25C/CDK1/CyclinB1 signaling axis regulates endometriosis progression.
基金supported by the National Key Research and Development Program of China(2022YFF1001400)the National Natural Science Foundation of China(31690090,32200286,32070207)+2 种基金Foundation of Hubei Hongshan Laboratory(2021hszd014)Hubei Provincial Natural Science Foundation of China(2021CFA055,2021BBA102)the China Postdoctoral Science Foundation(2022TQ0240,2022M722470)。
文摘Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81%transposable elements(TEs),while only 57%of the 735-Mb G.raimondii genome is occupied by TEs.In this study,we investigated whether there were unknown transcripts associated with TE or TE fragments and,if so,how these new transcripts were evolved and regulated.As sequence depths increased from 4 to 100 G,a total of 10,284 novel intergenic transcripts(intergenic genes)were discovered.On average,approximately 84%of these intergenic transcripts possibly overlapped with the long terminal repeat(LTR)insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels.Most of these intergenic transcripts possessed no transcription activation markers,while the majority of the regular genic genes possessed at least one such marker.Genes without transcription activation markers formed their+1 and-1 nucleosomes more closely(only(117±1.4)bp apart),while twice as big spaces(approximately(403.5±46.0)bp apart)were detected for genes with the activation markers.The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content.Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7million years ago(MYA)for all eudicot genomes or 13.7 MYA for the Gossypium family,respectively,while the intergenic transcripts evolved around 1.6 MYA,resultant of the last LTR insertion.The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.
基金Partially Supported by the Chinese University of Hong Kong Strategic Research Programme.
文摘Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I （ITS1）, rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.
基金supported by the National Basic Research Program of China (No. 2011CB510100)the National Natural Science Foundation of China (No. 81030015)
文摘Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed ＂regulatory lincRNAs＂, representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GASS, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.
基金supported by the National Natural Science Foundation of China (No. 50608011)
文摘The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（PFS） exhibited stronger degrading abilities and more stable biomass than that of the phenol plus p-cresol-fed system（PCFS）.The microbial community structures were revealed by a modern DNA fingerprint technique,ribosomal intergenic spacer analysis（RISA）.The results indicated that the microbial community of PFS changed obviously when gradually increased phenol concentration,while PCFS showed a little change.16S rRNA sequence analysis of the major bands showed that Alcanivorax sp.genus was predominant species during phenolic compounds degradation.Furthermore,amplified functional DNA restriction analysis（AFDRA） on phenol hydroxylase genes showed that the fingerprints were substantially different in the two systems,and the fingerprints were not the same during the different operational periods.
基金Hao Wu was supported by China Scholarship Council(CSC,No.201706370109).We thank Emily Lin for her help in creating the figure.We thank Justin Elfman for his help with English editing.
文摘Gene fusions are appreciated as ideal cancer biomarkers and therapeutic targets.Chimeric RNAs are traditionally thought to be products of gene fusions,and thus,also cancerspecific.Recent research has demonstrated that chimeric RNAs can be generated by intergenic splicing in the absence of gene fusion,and such chimeric RNAs are also found in normal physiology.These new findings challenge the traditional theory of chimeric RNAs exclusivity to cancer,and complicates use of chimeric RNAs in cancer detection.Here,we provide an overview of gene fusions and chimeric RNAs,and emphasize their differences.We note that gene fusions are able to generate chimeric RNAs in accordance with the central dogma of biology,and that chimeric RNAs may also be able to influence the generation of the gene fusions per the“horse before the cart”hypothesis.We further expand upon the“horse before the cart”hypothesis,summarizing current evidence in support of the theory and exploring its potential impact on the field.
基金This work has been registered as national patent (patent applying number: 99103044.3).theMomentous Project of Chinese Academy of Sciences, National High Science and Technology Program, National Special Program for Research and Industrialization of Tran
文摘Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected cotton leaves was used as template, and fragment of LIR was obtained by PCR and inserted into clone vector. The fragment of LIR was fused with gus reporter gene and nos terminator in the orientation of transcription of virion sense and complementary sense respectively, and the plant expression vectors were constructed. GUS activity of Agrobacte-rium-mediated transgenic tobacco was measured. The result indicated that LIR showed strong promoter activity in complementary sense gene orientation. Average GUS activity of the complementary sense promoter was 5-6 times that of CaMV 35S promoter, and the highest GUS activity of individual plant was ten times of that of CaMV 35S promoter. Histochemical localization confirmed its activity in both mesophyll and vascular tissues. Activity of virion sense of LIR was rather low. Thus LIR isolated from CLCuV could be used as a novel strong promoter in plant genetic manipulation.
基金The National Natural Science Foundation of China under contract Nos 30640015 and 30771644the Major Program of Zhejiang Province of China under contract No. 2005C23085
文摘One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.
基金Project at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (Germany)the funding from the China Scholarship Council+1 种基金Jutta Niggemann and Thorsten Dittmar (ICBM COU Oldenburg) who supported the preparation of the DOM free seawater strongly with material and technical supportthe crew of the AADE research vessel for providing samples as well as the entire team of the AWI Food Web Project
文摘Jellyfish blooms have increased worldwide, and the outbreaks of jellyfish population not only affect the food web structures via voracious predation but also play an important role in the dynamics of nutrients and oxygen in planktonic food webs. However, it remains unclear whether specific carbon compounds released through jellyfish metabolic processes have the potential to shape bacterial community composition. Therefore, in this study, we aimed to investigate the compositional succession of the bacterioplankton community in response to the dissolved organic matter (DOM) released by the live Scyphomedusae Cyanea lamarckii and Chrysaora hysoscella collected from Helgoland Roads of the North Sea. The bacterial community was significantly stimulated by the DOM released form live jellyfish and different dominant phylotypes were observed for these two Scyphomedusae species. Furthermore, the bacterial community structures in the different DOM sources, jellyfish-incubated media, Kabeltonne seawater, and artificial seawater (DOM-free) were significantly different, as revealed by automated ribosomal intergenic spacer analysis fingerprints. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed a rapid species-specific shift in bacterial community composition. Gammaproteobacteria dominated the community instead of the Bacteroidetes community for C. lamarckii, whereas Gammaproteobacteria and Bacteroidetes dominated the community for C. hysoscella. The significant differences in the bacterial community composition and succession indicate that the components of the DOM released by jellyfish might differ with jellyfish species.
基金supported by the earmarked fund for China Agriculture Research System (CARS-20)the Youth Talent Development Plan of Shanghai Municipal Agricultural System, China (20160113)the Agriculture Research System of Shanghai, China (201809)
文摘China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and classification among 49 popular cultivated strains. The great majority of the 49 strains possessed two different IGS1 sequences, with distinct lengths and homologies. Based on the length and homology of the IGS1 sequences of the 49 strains, the strains were classified into two groups： A and B. Group A was subdivided into six subgroups. Forty-seven strains were homozygous or heterozygous among these six subgroups in group A, Cr01 was heterozygous between A and B, and Guangxiang 9 was homozygous in group B. An IGS1 polymorphism map of each cultivated L. edodes strain is reported for the first time and could be used as a marker for the initial classification and management of cultivated L. edodes strains in China.
文摘<span style="font-family:Verdana;">The sequence of the ribosomal RNA gene (rDNA) plays an important role in species identification and phylogenetic analysis. However, the only published </span><span><span style="font-family:Verdana;">full-length sequence of a ribosomal gene of green algae is that of </span><i><span style="font-family:Verdana;">Ulva mutabilis</span></i><span style="font-family:Verdana;">.</span></span><span style="font-family:Verdana;"> In this study, we </span><a name="_Hlk17805857"></a><span style="font-family:Verdana;">amplified the full-length sequence of each ribosomal gene unit of the ribosomal gene of </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;">. The full-length sequence of the ribosomal gene in </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> is 8676 bp, including the 1759 bp 18S rDNA, 576 bp internal transcribed spacer (ITS) + 5.8S rDNA, 3282 bp 28S </span><span style="font-family:Verdana;">rDNA, and 3059 bp intergenic spacer (IGS) region. We then carried out a series</span><span style="font-family:Verdana;"> of genetic analyses based on the ITS and IGS sequences, to verify whether IGS </span><span><span style="font-family:Verdana;">sequences are useful for studying the genetic diversity of green algae from different locations. We amplified the IGS sequences of </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> from 10 different locations in the Yellow Sea. Multiple alignments of the IGS sequences </span></span><span style="font-family:Verdana;">of samples from these 10 different sites revealed varying degrees of base </span><span><span style="font-family:Verdana;">differences, and comparative analysis of the ITS sequences revealed that our amplified species was classified as </span><i><span style="font-family:Verdana;">Blidingia minima</span></i><span style="font-family:Verdana;"> and distinct from other green a
基金supported by a grant from the Foundation of Ministry of Education of China (No. JHG06-7-03)
文摘Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys intergenic region in mtDNA were amplified and sequenced; sexual hormone assay, oral glucose tolerance test （OGTT） and insulin releasing test were carried out. Then variations found in mtDNA were compared between the two groups, the correlations between variations and clinical indexes were analyzed in all subjects. Results Nucleotide variations found in mtDNA were not different between the two groups, but the mutation of 16 094T/C was found associated with the serum levels ofT and fasting insulin; （303-317）CnTC, associated with the serum levels of A and LH; 195C/T with A level and 491T/C with LH level; （8 272-8 289）（ACCCCCTCT）, was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA perhaps associate with PCOS clinical symptoms and involve in PCOS development.
基金funded by the Department of Biotechnology (DBT), Government of India
文摘Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology （KO） numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http：//bioserver 1 .physics.iisc.ernet.in/psrna/and http：//bicmku.in： 8081/psrna/.
文摘The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is funda- mental to ecology and conservation. Recent research on DNA-based inference of trophic associations suggests that the host range of phytophagous insects in the tropics may be wider than previously thought based on traditional observation. However, the reliability of molecular inference of ecological associations, still strongly dependent on PCR and thus exposed to the risk of contamination with environmental DNA, is under debate. Here, we explored alternative procedures to reduce the chance of amplification of external, nondiet DNA, including surface decontamination and analysis of mid/hind guts, comparing the results with those obtained using the standard protocol. We studied 261 specimens in eight species of Neotropical Chrysomelidae that yielded 316 psbA-trnH intergenic spacer sequences （cpDNA marker of putative diets） from unique and multiple-band PCR results. The taxonomic identity of these sequences was inferred using the automated pipeline BAGpipe, yielding results consistent with 31 plant families. Regardless of the proto- col used, a wide taxonomic spectrum of food was inferred for all chrysomelid species. Canonical Correspondence Analysis using these data revealed significant differences at- tributed mainly to species （expectedly, since they represent different ecologies）, but also to treatment （untreated vs. cleaned/gut samples） and PCR results （single vs. multiple bands）. Molecular identification of diets is not straightforward and, regardless of the species＇ niche breadth, combining approaches that reduce external contamination and studying multiple individuals per species may help increasing confidence in results.
