Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear ...Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear parings is proposed. Moreover, the effectiveness of the new scheme is analyzed, and it is proved that the new scheme can prevent from all kinds of known attack. The one-way hash function is effective in the new scheme. The new scheme is proved that it has high effectiveness and fast convergence speed. Moreover, the ap- plication of the new scheme is easy and operational.展开更多
A single mammalian transcript normally encodes one protein, but the transcript of GNAS (G-protein u-subunit) contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other conf...A single mammalian transcript normally encodes one protein, but the transcript of GNAS (G-protein u-subunit) contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF (open reading frame), position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD (nonsense-mediated mRNA decay) rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.展开更多
MicroRNAs (miRNAs) are endogenous, small, non-coding RNAs, which are capable of silencing gene expression at the post-transcriptional level. In this study, we report that miR-205 is significantly underexpressed in b...MicroRNAs (miRNAs) are endogenous, small, non-coding RNAs, which are capable of silencing gene expression at the post-transcriptional level. In this study, we report that miR-205 is significantly underexpressed in breast tumor compared to the matched normal breast tissue. Similarly, breast cancer cell lines, including MCF-7 and MDA-MB- 231, express a lower level miR-205 than the non-malignant MCF-10A cells. Of interest, ectopic expression of miR-205 significantly inhibits cell proliferation and anchorage independent growth, as well as cell invasion. Furthermore, miR- 205 was shown to suppress lung metastasis in an animal model. Finally, western blot combined with the luciferase reporter assays demonstrate that ErbB3 and vascular endothelial growth factor A (VEGF-A) are direct targets for miR-205, and this miR-205-mediated suppression is likely through the direct interaction with the putative miR-205 binding site in the 3'-untranslated region (3'-UTR) of ErbB3 and VEGF-A. Together, these results suggest that miR- 205 is a tumor suppressor in breast cancer.展开更多
We cast vehicle recognition as problem of feature representation and classification, and introduce a sparse learning based framework for vehicle recognition and classification in this paper. After objects captured wit...We cast vehicle recognition as problem of feature representation and classification, and introduce a sparse learning based framework for vehicle recognition and classification in this paper. After objects captured with a GMM background subtraction program, images are labeled with vehicle type for dictionary learning and decompose the images with sparse coding (SC), a linear SVM trained with the SC feature for vehicle classification. A simple but efficient active learning stategy is adopted by adding the false positive samples into previous training set for dictionary and SVM model retraining. Compared with traditional feature representation and classification realized with SVM, SC method achieves dramatically improvement on classification accuracy and exhibits strong robustness. The work is also validated on real-world surveillance video.展开更多
MicroRNAs (miRNAs), which are small noncoding RNA molecules, play important roles in the post-transcriptional regulation process. The microRNA-21 gene (miR-21) has been reported to be highly expressed in various s...MicroRNAs (miRNAs), which are small noncoding RNA molecules, play important roles in the post-transcriptional regulation process. The microRNA-21 gene (miR-21) has been reported to be highly expressed in various solid tumors, including breast cancer. Bone morphogenetic protein-6 (BMP-6) has been identified as an inhibitor of breast cancer epithelial-mesenchymal transition (EMT) through rescuing E-cadherin expression. We initiated experi- ments to identify the relationships between miR-21 and BMP-6 in breast cancer progression. Real-time PCR analysis showed that miR-21 expression was very high in MDA-MB-231 cells that expressed little BMP-6. A reverse correla- tion between BMP-6 and miR-21 was also determined in breast cancer tissue samples. Moreover, BMP-6 inhibited miR-21 transcription in MDA-MB-231 cells. In order to investigate how BMP-6 inhibited the miR-21 promoter (miPPR-21), we constructed a series of miPPR-21 reporters. Luciferase assay results indicated that BMP-6 inhibited miPPR-21 activity through the E2-box and AP-l-binding sites. We also demonstrated that both δEF1 and TPA in- duced miR-21 expression. Using site-directed mutation and CHIP assay, we found that δEF1 induced miPPR-21 ac- tivity by binding to the E2-box on miPPR-21. Moreover, TPA triggered miPPR-21 activity through the AP-I binding sites. BMP-6 treatment significantly reduced the binding of these factors to miPPR-21 by decreasing the expression of δEF1 and c-Fos/c-Jun. We also demonstrated that BMP-6-induced downregulation of miR-21 modified the activ- ity of PDCD4 3'UTR and inhibited MDA-MB-231 cell invasion. δEF1 overexpression and TPA induction blocked this inhibitory effect of BMP-6. In conclusion, BMP-6-induced inhibition of miR-21 suggests that BMP-6 may function as an anti-metastasis factor by a mechanism involving transcriptional repression of miR-21 in breast cancer.展开更多
In order to study the seismic performance of typical approach bridge for port project, the seismic vulnerability model was created. 100 of the earthquake motion records are selected from the database of Pacific Earthq...In order to study the seismic performance of typical approach bridge for port project, the seismic vulnerability model was created. 100 of the earthquake motion records are selected from the database of Pacific Earthquake Research Centre, In order to obtain the maximum responses of structure dynamic response, the model was calculated by using non-linear time history analysis. Then reliability analysis method was used to generate the fragility curves of bridge components. And compared two kinds of bearing made differences to structure' s vulnerability. Researches show that bearing is easy to breakdown with earthquake action. Isolation bearing has good effect, and significantly reduces failure probability, fmaUy the fragility curves obtained can be used to evaluate the seismic performance of continuous beam bridge for port project, and provide the basis for seismic design of bridges for port project.展开更多
RNA helicases of the DEAD-box and related families are involved in various cellular processes including DNA replication, DNA repair, and RNA processing. However, the function of DEAD-box proteins in aquaculture specie...RNA helicases of the DEAD-box and related families are involved in various cellular processes including DNA replication, DNA repair, and RNA processing. However, the function of DEAD-box proteins in aquaculture species is poorly understood at molecular level. We obtained the full-length cDNA sequences of two genes encoding helicase-related proteins, Fc-vasa and Fc-PL10a, from the testes of Chinese shrimp, Fenneropenaeus chinensis. The two predicted amino acid sequences contain all the conserved motifs characterized by the DEAD-box family and several RGG repeats in the N-terminal regions. Homology and phylogenetic analyses indicate that they belong to the vasa and PLIO subfamilies. The three-dimensional structures of the two proteins were predicted with a homology modeling approach. Both core proteins consist of two tandem RecA-like domains similar to those of the DEAD-box RNA helicase. Using reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR we found that Fc-vasa was expressed specifically in the adult gonads. Transcription decreased in the ovary but increased in the testis during gonadal development. Fc-PL10a expression was widely distributed in the tissues we examined. Using in situ hybridization, we demonstrated that the Fc-vasa transcript is localized to the cytoplasm of the spermatogonia and oocytes. Thus, our results suggest that Fc-wasa plays an important role in germ-line development, and has utility as a germ cell lineage marker which will help to generate new insight into the origin and differentiation of germ cells as well as the regulation of reproduction in F. chinensis.展开更多
Once thought to be transcriptional noise, large non-coding RNAs (IncRNAs) have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcri...Once thought to be transcriptional noise, large non-coding RNAs (IncRNAs) have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically. Using a custom-designed microarray, here we examine the expression profile of IncRNAs in embryonic stem (ES) cells, lineage-restricted neuronal progenitor cells, and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methyla- tion patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3. Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these IncRNAs in ES cells. Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of the protein-coding genes.展开更多
The Fox genes encode a group of transcription factors that contain a forkhead domain, which forms a structure known as a winged helix. These transcription factors play a crucial role in several key biological processe...The Fox genes encode a group of transcription factors that contain a forkhead domain, which forms a structure known as a winged helix. These transcription factors play a crucial role in several key biological processes, including development. High-degree identity in the canonical forkhead domain has been used to divide Fox proteins into 23 families (FoxA to FoxS). We surveyed the genome of three spiralians, the oyster Crassostrea gigas, the limpet Lottia gigantea, and the annelid Capitella teleta. We identified 25 C. gigas fox genes, 21 L. gigantea fox genes, and 25 C. teleta fox genes. The C. gigas fox and L. giganteafox genes represented 19 of the 23 families, whereas FoxI, QI, R, and S were missing. The majority of the Fox families were observed within the C. teletafox genes, with the exception of FoxR and S. In addition, thefoxAB-like gene,foxY-like gene, andfoxH gene were also present in the three genomes. The conserved FoxC-FoxL 1 cluster, observed in mammals, was also found in C. gigas. The diversity of temporal expression patterns observed across the developmental process implies the C. gigasfox genes exert a wide range of functions. Further functional studies are required to gain insight into the evolution of Fox genes in bilaterians.展开更多
Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(...Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.展开更多
The peripheral nervous system is able to regenerate after injury, and regeneration is associated with the expression of many genes and proteins. MicroRNAs are evolutionarily conserved, small, non-coding RNA molecules ...The peripheral nervous system is able to regenerate after injury, and regeneration is associated with the expression of many genes and proteins. MicroRNAs are evolutionarily conserved, small, non-coding RNA molecules that regulate gene expression at the level of translation. In this paper, we focus on the identification and functional annotation of novel microRNAs in the proximal sciatic nerve after rat sciatic nerve transection. Using Solexa sequencing, computational analysis, and quantitative reverse transcription PCR verification, we identified 98 novel microRNAs expressed on days 0, 1, 4, 7, and 14 after nerve transection. Furthermore, we predicted the target genes of these microRNAs and analyzed the biological processes in which they were involved. The identified biological processes were consistent with the known time-frame of peripheral nerve injury and repair. Our data provide an important resource for further study of the role and regulation of microRNAs in peripheral nerve injury and regeneration.展开更多
Viral microRNAs are one component of the RNA interference phenomenon generated during viral infection. They were first identified in the Herpesviridae family, where they were found to regulate viral mRNA translation. ...Viral microRNAs are one component of the RNA interference phenomenon generated during viral infection. They were first identified in the Herpesviridae family, where they were found to regulate viral mRNA translation. In addition, prior work has suggested that Kaposi's sarcoma-associated herpesvirus (KSHV) is capable of regulating cellular gene transcription by miRNA. We demonstrate that a miRNA, hsvl-mir-H27, encoded within the genome of herpes simplex virus 1 (HSV-1), targets the mRNA of the cellular transcriptional repressor Kelch-like 24 (KLHL24) that inhibits transcriptional efficiency of viral imme- diate-early and early genes. The viral miRNA is able to block the expression of KLHL24 in cells infected by HSV-1. Our dis- covery reveals an effective viral strategy for evading host cell defenses and supporting the efficient replication and prolifera- tion of HSV- 1.展开更多
Non-coding RNAs(nc RNAs),such as micro RNAs and large intergenic non-coding RNAs,have been shown to play essential roles in regulating pluripotency.Yet,it is not clear the role of natural antisense transcripts(NATs),a...Non-coding RNAs(nc RNAs),such as micro RNAs and large intergenic non-coding RNAs,have been shown to play essential roles in regulating pluripotency.Yet,it is not clear the role of natural antisense transcripts(NATs),also belonging to nc RNAs,in embryonic stem cells.However,the role of NATs in embryonic stem cells remains unknown.We further confirmed the expression of the NATs of three key pluripotency genes,Oct4,Nanog and Sox2.Moreover,overexpression of Sox2-NAT reduces the expression of Sox2 protein,and slightly enhances the Sox2 m RNA level.Altogether,our data indicated that like other nc RNAs,NATs might be involved in pluripotency maintenance.展开更多
基金Supported by the National Science Foundation for Young Scholars of China(61001091)~~
文摘Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear parings is proposed. Moreover, the effectiveness of the new scheme is analyzed, and it is proved that the new scheme can prevent from all kinds of known attack. The one-way hash function is effective in the new scheme. The new scheme is proved that it has high effectiveness and fast convergence speed. Moreover, the ap- plication of the new scheme is easy and operational.
文摘A single mammalian transcript normally encodes one protein, but the transcript of GNAS (G-protein u-subunit) contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF (open reading frame), position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD (nonsense-mediated mRNA decay) rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.
文摘MicroRNAs (miRNAs) are endogenous, small, non-coding RNAs, which are capable of silencing gene expression at the post-transcriptional level. In this study, we report that miR-205 is significantly underexpressed in breast tumor compared to the matched normal breast tissue. Similarly, breast cancer cell lines, including MCF-7 and MDA-MB- 231, express a lower level miR-205 than the non-malignant MCF-10A cells. Of interest, ectopic expression of miR-205 significantly inhibits cell proliferation and anchorage independent growth, as well as cell invasion. Furthermore, miR- 205 was shown to suppress lung metastasis in an animal model. Finally, western blot combined with the luciferase reporter assays demonstrate that ErbB3 and vascular endothelial growth factor A (VEGF-A) are direct targets for miR-205, and this miR-205-mediated suppression is likely through the direct interaction with the putative miR-205 binding site in the 3'-untranslated region (3'-UTR) of ErbB3 and VEGF-A. Together, these results suggest that miR- 205 is a tumor suppressor in breast cancer.
基金the National Natural Science Foundation of China under Grant NO 61472166,NO 61105015,Jiangsu Provincial Natural Science Foundation under Grant NO BK2010366 and Key Laboratory of Cloud Computing and Intelligent Information Processing of Changzhou City under Grand NO CM20123004
文摘We cast vehicle recognition as problem of feature representation and classification, and introduce a sparse learning based framework for vehicle recognition and classification in this paper. After objects captured with a GMM background subtraction program, images are labeled with vehicle type for dictionary learning and decompose the images with sparse coding (SC), a linear SVM trained with the SC feature for vehicle classification. A simple but efficient active learning stategy is adopted by adding the false positive samples into previous training set for dictionary and SVM model retraining. Compared with traditional feature representation and classification realized with SVM, SC method achieves dramatically improvement on classification accuracy and exhibits strong robustness. The work is also validated on real-world surveillance video.
文摘MicroRNAs (miRNAs), which are small noncoding RNA molecules, play important roles in the post-transcriptional regulation process. The microRNA-21 gene (miR-21) has been reported to be highly expressed in various solid tumors, including breast cancer. Bone morphogenetic protein-6 (BMP-6) has been identified as an inhibitor of breast cancer epithelial-mesenchymal transition (EMT) through rescuing E-cadherin expression. We initiated experi- ments to identify the relationships between miR-21 and BMP-6 in breast cancer progression. Real-time PCR analysis showed that miR-21 expression was very high in MDA-MB-231 cells that expressed little BMP-6. A reverse correla- tion between BMP-6 and miR-21 was also determined in breast cancer tissue samples. Moreover, BMP-6 inhibited miR-21 transcription in MDA-MB-231 cells. In order to investigate how BMP-6 inhibited the miR-21 promoter (miPPR-21), we constructed a series of miPPR-21 reporters. Luciferase assay results indicated that BMP-6 inhibited miPPR-21 activity through the E2-box and AP-l-binding sites. We also demonstrated that both δEF1 and TPA in- duced miR-21 expression. Using site-directed mutation and CHIP assay, we found that δEF1 induced miPPR-21 ac- tivity by binding to the E2-box on miPPR-21. Moreover, TPA triggered miPPR-21 activity through the AP-I binding sites. BMP-6 treatment significantly reduced the binding of these factors to miPPR-21 by decreasing the expression of δEF1 and c-Fos/c-Jun. We also demonstrated that BMP-6-induced downregulation of miR-21 modified the activ- ity of PDCD4 3'UTR and inhibited MDA-MB-231 cell invasion. δEF1 overexpression and TPA induction blocked this inhibitory effect of BMP-6. In conclusion, BMP-6-induced inhibition of miR-21 suggests that BMP-6 may function as an anti-metastasis factor by a mechanism involving transcriptional repression of miR-21 in breast cancer.
文摘In order to study the seismic performance of typical approach bridge for port project, the seismic vulnerability model was created. 100 of the earthquake motion records are selected from the database of Pacific Earthquake Research Centre, In order to obtain the maximum responses of structure dynamic response, the model was calculated by using non-linear time history analysis. Then reliability analysis method was used to generate the fragility curves of bridge components. And compared two kinds of bearing made differences to structure' s vulnerability. Researches show that bearing is easy to breakdown with earthquake action. Isolation bearing has good effect, and significantly reduces failure probability, fmaUy the fragility curves obtained can be used to evaluate the seismic performance of continuous beam bridge for port project, and provide the basis for seismic design of bridges for port project.
基金Supported by the Specialized Research Fund for the Doctoral Program of Higher Education,China (No. 200804230015)the National High Technology Research and Development Program of China (863 Program) (No. 2006AA10A401)
文摘RNA helicases of the DEAD-box and related families are involved in various cellular processes including DNA replication, DNA repair, and RNA processing. However, the function of DEAD-box proteins in aquaculture species is poorly understood at molecular level. We obtained the full-length cDNA sequences of two genes encoding helicase-related proteins, Fc-vasa and Fc-PL10a, from the testes of Chinese shrimp, Fenneropenaeus chinensis. The two predicted amino acid sequences contain all the conserved motifs characterized by the DEAD-box family and several RGG repeats in the N-terminal regions. Homology and phylogenetic analyses indicate that they belong to the vasa and PLIO subfamilies. The three-dimensional structures of the two proteins were predicted with a homology modeling approach. Both core proteins consist of two tandem RecA-like domains similar to those of the DEAD-box RNA helicase. Using reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR we found that Fc-vasa was expressed specifically in the adult gonads. Transcription decreased in the ovary but increased in the testis during gonadal development. Fc-PL10a expression was widely distributed in the tissues we examined. Using in situ hybridization, we demonstrated that the Fc-vasa transcript is localized to the cytoplasm of the spermatogonia and oocytes. Thus, our results suggest that Fc-wasa plays an important role in germ-line development, and has utility as a germ cell lineage marker which will help to generate new insight into the origin and differentiation of germ cells as well as the regulation of reproduction in F. chinensis.
文摘Once thought to be transcriptional noise, large non-coding RNAs (IncRNAs) have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically. Using a custom-designed microarray, here we examine the expression profile of IncRNAs in embryonic stem (ES) cells, lineage-restricted neuronal progenitor cells, and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methyla- tion patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3. Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these IncRNAs in ES cells. Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of the protein-coding genes.
基金Supported by the National Basic Research Program of China(973 Program)(No.2010CB126401)the National Natural Science Foundation of China(No.31402285)+3 种基金the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A405)the Earmarked Fund for Modern Agro-Industry Technology Research System(No.CARS-48)the Taishan Scholars Climbing Program of Shandong Provincethe Oversea Taishan Scholars Program of Shandong Province
文摘The Fox genes encode a group of transcription factors that contain a forkhead domain, which forms a structure known as a winged helix. These transcription factors play a crucial role in several key biological processes, including development. High-degree identity in the canonical forkhead domain has been used to divide Fox proteins into 23 families (FoxA to FoxS). We surveyed the genome of three spiralians, the oyster Crassostrea gigas, the limpet Lottia gigantea, and the annelid Capitella teleta. We identified 25 C. gigas fox genes, 21 L. gigantea fox genes, and 25 C. teleta fox genes. The C. gigas fox and L. giganteafox genes represented 19 of the 23 families, whereas FoxI, QI, R, and S were missing. The majority of the Fox families were observed within the C. teletafox genes, with the exception of FoxR and S. In addition, thefoxAB-like gene,foxY-like gene, andfoxH gene were also present in the three genomes. The conserved FoxC-FoxL 1 cluster, observed in mammals, was also found in C. gigas. The diversity of temporal expression patterns observed across the developmental process implies the C. gigasfox genes exert a wide range of functions. Further functional studies are required to gain insight into the evolution of Fox genes in bilaterians.
基金supported by grants from Natural Science Foundation of China (31271385)Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-R-01-04)
文摘Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.
基金supported by the National High Technology Research and Development Program of China (Grant No. 2006AA02A128)the National Natural Science Foundation of China (Grant No. 30870811)+1 种基金the Jiangsu Provincial Natural Science Foundation (Grant No. BK2008010)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)
文摘The peripheral nervous system is able to regenerate after injury, and regeneration is associated with the expression of many genes and proteins. MicroRNAs are evolutionarily conserved, small, non-coding RNA molecules that regulate gene expression at the level of translation. In this paper, we focus on the identification and functional annotation of novel microRNAs in the proximal sciatic nerve after rat sciatic nerve transection. Using Solexa sequencing, computational analysis, and quantitative reverse transcription PCR verification, we identified 98 novel microRNAs expressed on days 0, 1, 4, 7, and 14 after nerve transection. Furthermore, we predicted the target genes of these microRNAs and analyzed the biological processes in which they were involved. The identified biological processes were consistent with the known time-frame of peripheral nerve injury and repair. Our data provide an important resource for further study of the role and regulation of microRNAs in peripheral nerve injury and regeneration.
基金supported by the National Natural Science Foundation of China (30670094, 30700028)National Basic Research Program of China (2012CB518901, 2011CB504903)
文摘Viral microRNAs are one component of the RNA interference phenomenon generated during viral infection. They were first identified in the Herpesviridae family, where they were found to regulate viral mRNA translation. In addition, prior work has suggested that Kaposi's sarcoma-associated herpesvirus (KSHV) is capable of regulating cellular gene transcription by miRNA. We demonstrate that a miRNA, hsvl-mir-H27, encoded within the genome of herpes simplex virus 1 (HSV-1), targets the mRNA of the cellular transcriptional repressor Kelch-like 24 (KLHL24) that inhibits transcriptional efficiency of viral imme- diate-early and early genes. The viral miRNA is able to block the expression of KLHL24 in cells infected by HSV-1. Our dis- covery reveals an effective viral strategy for evading host cell defenses and supporting the efficient replication and prolifera- tion of HSV- 1.
基金supported by the National Natural Science Foundation of China(31271547)the Natural Science Foundation of Tianjin,China(14JYBJC23600)+3 种基金the National Key Basic Research and Development Program of China(2010CB833603)the Program for New Century Excellent Talents(NCET-13-0293)the 111 Project Grant(B08011)the Funds for National Basic Science Personnel Training(J1103503)
文摘Non-coding RNAs(nc RNAs),such as micro RNAs and large intergenic non-coding RNAs,have been shown to play essential roles in regulating pluripotency.Yet,it is not clear the role of natural antisense transcripts(NATs),also belonging to nc RNAs,in embryonic stem cells.However,the role of NATs in embryonic stem cells remains unknown.We further confirmed the expression of the NATs of three key pluripotency genes,Oct4,Nanog and Sox2.Moreover,overexpression of Sox2-NAT reduces the expression of Sox2 protein,and slightly enhances the Sox2 m RNA level.Altogether,our data indicated that like other nc RNAs,NATs might be involved in pluripotency maintenance.