Gene Expression Patterns最新文献

{"title":"Expression patterns and biological function of Specc1 during mouse preimplantation development","authors":"Seulah Lee,&nbsp;Inchul Choi","doi":"10.1016/j.gep.2021.119196","DOIUrl":"10.1016/j.gep.2021.119196","url":null,"abstract":"<div><p>Two unique features occur during preimplantation embryo<span> development: 1) initiation of calcium-dependent adhesion and establishment of apicobasal polarity in the morula<span>, and 2) formation of the blastocoel by establishment of tight junctions (TJs), ion channels, and water channels in the outer blastomeres<span><span><span>. Although several key genes involved in morula and blastocyst formation have been identified, most remain unknown. </span>Sperm antigen<span> with calponin<span> homology and coiled-coil domains 1(SPECC1) is highly expressed in testis and tumor cells, and is involved in diverse cellular processes such as ribosome biogenesis, rRNA transcription, mitosis, cell growth, and apoptosis in tumor cells. However, spatiotemporal expressions of Specc1 during mouse </span></span></span>preimplantation<span> development have not yet been investigated. Here, we examined the expression patterns of Specc1 using qRT-PCR and immunocytochemistry<span><span>, and its biological function using siRNA injection into 1-cell zygotes. Specc1 was detectable throughout preimplantation development and markedly increased from the morula stage onwards. It was particularly observed in trophectoderm cells, rather than the </span>inner cell mass of blastocyst. Maternal and zygotic Specc1 transcripts were abolished using RNA interference. There were no significant differences in development between Specc1 knock down (KD) and control embryos until the morula stage, but was significantly reduced blastocyst development and increased tight junction permeability in KD embryos, as assessed by FITC uptake. In summary, elevated expression of Specc1 in the morula and blastocyst may affect blastocyst formation, including tight junction complex during the morula to blastocyst transition.</span></span></span></span></span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39103815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oscillatory expression of Ascl1 in oligodendrogenesis","authors":"Risa Sueda ,&nbsp;Ryoichiro Kageyama","doi":"10.1016/j.gep.2021.119198","DOIUrl":"10.1016/j.gep.2021.119198","url":null,"abstract":"<div><p>The proneural gene <em>Ascl1</em> promotes formation of both neurons and oligodendrocytes from neural stem cells (NSCs), but it remains to be analyzed how its different functions are coordinated. It was previously shown that Ascl1 enhances proliferation of NSCs when its expression oscillates but induces differentiation into transit-amplifying precursor cells and neurons when its expression is up-regulated and sustained. By time-lapse imaging and immunohistological analyses, we found that Ascl1 expression oscillated in proliferating oligodendrocyte precursor cells (OPCs) at lower levels than in transit-amplifying precursor cells and was repressed when OPCs differentiated into mature oligodendrocytes. Induction of sustained overexpression of Ascl1 reduced oligodendrocyte differentiation and promoted neuronal differentiation. These results suggest that oscillatory expression of Ascl1 plays an important role in proliferating OPCs during oligodendrocyte formation.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39109989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model” [Gene Expr. Patterns 37, 119125]","authors":"Chunpeng He ,&nbsp;Tingyu Han ,&nbsp;Xin Liao ,&nbsp;Rui Guan ,&nbsp;J.-Y. Chen ,&nbsp;Kimberly D. Tremblay ,&nbsp;Zuhong Lu","doi":"10.1016/j.gep.2021.119186","DOIUrl":"10.1016/j.gep.2021.119186","url":null,"abstract":"","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119186","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39061222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression of R-spondins/Lgrs in development of movable craniofacial organs","authors":"Jun Nihara ,&nbsp;Maiko Kawasaki ,&nbsp;Katsushige Kawasaki ,&nbsp;Akane Yamada ,&nbsp;Fumiya Meguro ,&nbsp;Takehisa Kudo ,&nbsp;Supaluk Trakanant ,&nbsp;Takahiro Nagai ,&nbsp;Isao Saito ,&nbsp;Takeyasu Maeda ,&nbsp;Atsushi Ohazama","doi":"10.1016/j.gep.2021.119195","DOIUrl":"10.1016/j.gep.2021.119195","url":null,"abstract":"<div><p>Wnt signaling plays a critical role in the development of many organs, including the major movable craniofacial organs tongue, lip, and eyelid. Four members of the R-spondin family (<em>Rspo1</em>–<em>4</em>) bind to <em>Lgr4</em>/<em>5</em>/<em>6</em> to regulate the activation of Wnt signaling. However, it is not fully understood how <em>Rspos</em>/<em>Lgrs</em> regulate Wnt signaling during the development of movable craniofacial organs. To address this question, we examined the expression of <em>Rspos</em>, <em>Lgrs</em>, and <em>Axin2</em> (major mediator of canonical Wnt signaling) during tongue, lip, and eyelid development. The expression of <em>Axin2</em>, <em>Rspos</em> and <em>Lgrs</em> was observed in many similar regions, suggesting that <em>Rspos</em> likely activate canonical Wnt signaling through the <em>Lgr</em>-dependent pathway in these regions. <em>Lgr</em> expression was not detected in regions where <em>Axin2</em> and <em>Rspos</em> were expressed, suggesting that <em>Rspos</em> might activate canonical Wnt signaling through the <em>Lgr</em>-independent pathway in these regions. In addition, the expression of <em>Rspos</em> and <em>Lgrs</em> were observed in some other regions where <em>Axin2</em> was not expressed, suggesting the possibility that <em>Rspos</em> and/or <em>Lgrs</em> are involved in non-canonical Wnt signaling or the Wnt-independent pathway. Thus, we identified a dynamic spatiotemporal expression pattern of <em>Rspos</em> and <em>Lgrs</em> during the development of the eyelid, tongue, and lip.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39091717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N,N-dimethyl-hexadecylamine modulates Arabidopsis root growth through modifying the balance between stem cell niche and jasmonic acid-dependent gene expression","authors":"Ernesto Vázquez-Chimalhua,&nbsp;Eduardo Valencia-Cantero,&nbsp;José López-Bucio,&nbsp;León Francisco Ruiz-Herrera","doi":"10.1016/j.gep.2021.119201","DOIUrl":"10.1016/j.gep.2021.119201","url":null,"abstract":"<div><p><em>N,</em><em>N</em><em>-</em><span>dimethyl-hexadecylamine (DMHDA) is released as part of volatile blends emitted by plant probiotic<span> bacteria and affects root architecture, defense and nutrition of plants. Here, we investigated the changes in gene expression of transcription factors responsible of maintenance of the root stem cell niche<span> and jasmonic acid signaling in </span></span></span><span><em>Arabidopsis</em></span><span> seedlings in response to this volatile. Concentrations of DMHDA that repress primary root growth were found to alter cell size and division augmenting cell tissue layers in the meristem and causing root widening. DMHDA triggered the division of quiescent center cells, which correlated with repression of SHORT ROOT (SHR), SCARECROW (SCR), and PLETHORA 1 (PLT1) proteins and induction of WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor. Interestingly, an activation of the expression of the jasmonic acid-related reporter genes </span><em>JAZ1/TIFY10A-GFP</em> and <em>JAZ10pro::JAZ10-GFP</em><span> suggests that the halted growth of the primary root inversely correlated with expression patterns underlying the defense reaction, which may be of adaptive importance to protect roots against biotic stress. Our data help to unravel the gene expression signatures upon sensing of a highly active bacterial volatile in </span><em>Arabidopsis</em> seedlings.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39259788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and initial characterization of a vasa homolog in Cynops cyanurus","authors":"Yinjiao Zhao ,&nbsp;Pingfan Wei ,&nbsp;Dan Wang ,&nbsp;Wenrui Han ,&nbsp;Hanyu Mao ,&nbsp;Shu Wei ,&nbsp;Fang Yan","doi":"10.1016/j.gep.2021.119180","DOIUrl":"10.1016/j.gep.2021.119180","url":null,"abstract":"<div><p>The <em>vasa</em><span> mRNA encodes a putative RNA helicase that belongs to the DEAD-box protein family. Vasa protein is a conserved germ cell marker ranging from fruit fly to human. In this study, we cloned the full-length </span><em>vasa</em> cDNA from the ovary of newt <span><em>Cynops</em><em> cyanurus</em></span> and examined its expression in embryos and adult tissues. The predictive <em>C. cyanurus</em><span> Vasa protein sequence shares eight conserved regions with Vasa proteins from other vertebrates. The </span><em>C. cyanurus vasa</em><span> mRNA expression is restricted to testis and ovary. During oogenesis, </span><em>vasa</em><span> mRNA shows highest expression in the early stages of oocytes. However, it rapidly down-regulates during embryogenesis. These findings suggest that Vasa may be involved in early germ cell specification/initiation in </span><em>C. cyanurus.</em></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25538761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TBX3 induces biased differentiation of human induced pluripotent stem cells into cardiac pacemaker-like cells","authors":"Ying Yan ,&nbsp;Feng Liu ,&nbsp;Xitong Dang ,&nbsp;Rui Zhou ,&nbsp;Bin Liao","doi":"10.1016/j.gep.2021.119184","DOIUrl":"10.1016/j.gep.2021.119184","url":null,"abstract":"<div><h3>Background</h3><p><span>TBX3<span> plays a critical role in the formation of the sinoatrial node (SAN) during </span></span>embryonic heart<span> development. However, the contribution of TBX3 in driving the differentiation of human induced pluripotent stem cells (hiPSC)into pacemaker cells remains to be explored.</span></p></div><div><h3>Results</h3><p>Using the pan-cardiomyocyte differentiation protocol of human induced pluripotent stem cells (hiPSC)，TBX3 gene was introduced into the differentiating hiPSC on day 5 post-differentiation, and the differentiation of pacemaker-like cardiomyocytes was evaluated on day 21. The results showed that TBX3 significantly induced biased differentiation of hiPSC into pacemaker-like cells as judged by significantly increased expression of SAN-specific marker gene, SHOX2, and slightly decreased expression of SAN-detrimental transcription factor, NKX2-5.</p></div><div><h3>Conclusion</h3><p>Our results suggest that TBX3 plays an important role in driving the differentiation of hiPSC into pacemaker-like cells, and manipulation of TBX3 expression during pan-cardiomyocyte differentiation may lead to the development of therapeutic pacemaker cells.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38889188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De novo assembly and Transcriptome Analysis of the Momordica charantia Seedlings Responding to methyl jasmonate using 454 pyrosequencing","authors":"Shanyong Yi ,&nbsp;Xiangwen Song ,&nbsp;Wangyang Yu ,&nbsp;Rongfei Zhang ,&nbsp;Wei Wang ,&nbsp;Yucheng Zhao ,&nbsp;Bangxing Han ,&nbsp;Yanan Gai","doi":"10.1016/j.gep.2020.119160","DOIUrl":"10.1016/j.gep.2020.119160","url":null,"abstract":"<div><p><em>Momordica charantia</em>, a medicinal and edible species of the Cucurbitaceae family, has been widely used as a vegetable around the world. Hundreds of pharmacological compounds isolated from the <em>M. charantia</em> have been reported. However, the mechanism of action of the secondary metabolites has not been fully elucidated. In this study, 118,590 unigenes were gained by <em>de novo</em> assembly based on the raw data from high-throughput sequencing of mRNA (RNA-Sequencing) upon systemic analysis, among which, 51,860 (43.73%) could be annotated to the public sequence databases such as Nr, GO, Swiss-Prot, KEGG and KOG. The transcriptomic changes of <em>M. charantia</em> seedlings treated with or without methyl jasmonate (MeJA) were analyzed to identify key genes involved in MeJA treatment. Additionally, 554 differentially expressed genes (DEGs), including 328 up-regulated ones and 226 down-regulated genes, have been identified. Most DEGs were associated with secondary metabolism and stress responses. Meanwhile, six DEGs were further confirmed by quantitative real-time RT-PCR (qRT-PCR) analysis, resulting in similar expression patterns as compared to those of RNA-Sequencing. Nine significantly enriched pathways including 11 DEGs were identified to be possibly involved in the MeJA-responsive biosynthesis of secondary metabolites based on the transcriptome sequencing analysis. Among them, 4 DEGs, encoding two peroxidases, one cinnamyl alcohol dehydrogenase and one hypothetical protein Csa, might play important roles in the process of phenylpropanoid biosynthesis. In addition, 9 transcription factors (TFs) were also detected as DEGs from 1899 unigenes. Most of them up-regulated by MeJA treatment might be potentially involved in regulating secondary metabolites biosynthesis. This work is the first research on the large-scale assessment of <em>M. charantia</em> transcriptomic resources and the analysis of DEGs and TFs in secondary metabolites biosynthesis of <em>M. charantia</em> seedings treated with or without MeJA, which will be conducive to the further applications of <em>M. charantia</em>.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2020.119160","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38654607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hes1 oscillation frequency correlates with activation of neural stem cells","authors":"Takashi Kaise ,&nbsp;Ryoichiro Kageyama","doi":"10.1016/j.gep.2021.119170","DOIUrl":"10.1016/j.gep.2021.119170","url":null,"abstract":"<div><p><span><span>Quiescent neural stem cells (NSCs) are occasionally activated to undergo proliferation and subsequent </span>neuronal differentiation<span><span>. It was previously shown that the transcriptional repressor Hes1 is involved in both active and quiescent states of NSCs: when Hes1 expression oscillates, it periodically represses the </span>proneural gene </span></span><em>Ascl1</em>, thereby driving Ascl1 oscillations, which regulate the active state, while sustained Hes1 expression continuously suppresses Ascl1, promoting quiescence. However, it remains to be analyzed how the transition from quiescent to active states of NSCs is controlled. Here, we found that overexpression of the active form of Notch1 significantly activates NSCs in both <em>in-vitro</em> and <em>in-vivo</em> conditions and that its levels are proportional to NSC activation. The active form of Notch1 induces a burst of Hes1 oscillations in quiescent NSCs, and the frequency of Hes1 oscillations, rather than the Hes1 peak levels, correlates with the efficiency of NSC activation. These results raised the possibility that bursting Hes1 oscillations could increase the chance of Ascl1 oscillations in quiescent NSCs, suggesting that Notch1-induced Hes1 oscillation is a cue for a transition from quiescent to active states of NSCs.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119170","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25442819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens","authors":"Zengrong Zhang ,&nbsp;Mohan Qiu ,&nbsp;Huarui Du ,&nbsp;Qingyun Li ,&nbsp;Chunlin Yu ,&nbsp;Wu Gan ,&nbsp;Han Peng ,&nbsp;Bo Xia ,&nbsp;Xia Xiong ,&nbsp;Xiaoyan Song ,&nbsp;Li Yang ,&nbsp;Chenming Hu ,&nbsp;Jialei Chen ,&nbsp;Chaowu Yang ,&nbsp;Xiaosong Jiang","doi":"10.1016/j.gep.2021.119181","DOIUrl":"10.1016/j.gep.2021.119181","url":null,"abstract":"<div><h3>Background</h3><p><span>The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a </span>biological model<span> to search for genetic diversity of hypoxia adaption.</span></p></div><div><h3>Methods</h3><p>The whole genome re-sequencing technology was conducted to investigate the genetic diversity.</p></div><div><h3>Results</h3><p><span>In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including </span>HIF1A<span><span><span>, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF </span>signaling pathway, MAPK signaling pathway, </span>PPAR<span> signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs.</span></span></p></div><div><h3>Conclusions</h3><p>This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38994649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}