BMC Molecular Biology最新文献

{"title":"Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939","authors":"Jun Yang,&nbsp;Yan Liu,&nbsp;Bing Wang,&nbsp;Hongzhen Lan,&nbsp;Ying Liu,&nbsp;Fei Chen,&nbsp;Ju Zhang,&nbsp;Jian Luo","doi":"10.1186/s12867-017-0100-5","DOIUrl":"https://doi.org/10.1186/s12867-017-0100-5","url":null,"abstract":"<p>Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation potential to cholangiocarcinoma cell line QBC939 and this process is mediated by crm-1. However, no other post-transcriptional regulation was found in this process including sumoylation in cholangiocarcinoma.</p><p>In this study, we explored the role of sumoylation in the nuclear-cytoplasmic translocation of p27kip1 and its involvement of QBC939 cells’ proliferation. First, we identified K73 as the sumoylation site in p27kip1. By utilizing plasmid flag-p27kip1, HA-RanBP2, GST-RanBP2 and His-p27kip1 and immunoprecipitation assay, we validated that p27kip1 can serve as the sumoylation target of RanBP2 in QBC939. Furthermore, we confirmed crm-1’s role in promoting nuclear-cytoplasmic translocation of p27kip1 and found that RanBP2’s function relies on crm-1. However, K73R mutated p27kip1 can’t be identified by crm-1 or RanBP2 in p27kip1 translocation process, suggesting sumoylation of p27kip1 via K73 site is necessary in this process by RanBP2 and crm-1. Phenotypically, the overexpression of either RanBP2 or crm-1 can partially rescue the anti-proliferative effect brought by p27kip1 overexpression in both the MTS and EdU assay. For the first time, we identified and validated the K73 sumoylation site in p27kip1, which is critical to RanBP2 and crm-1 in p27kip1 nuclear-cytoplasmic translocation process.</p><p>Taken together, targeted inhibition of sumoylation of p27kip1 may serve as a potentially potent therapeutic target in the eradication of cholangiocarcinoma development and relapses.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0100-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4319729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing","authors":"Parisa Amini,&nbsp;Julia Ettlin,&nbsp;Lennart Opitz,&nbsp;Elena Clementi,&nbsp;Alexandra Malbon,&nbsp;Enni Markkanen","doi":"10.1186/s12867-017-0099-7","DOIUrl":"https://doi.org/10.1186/s12867-017-0099-7","url":null,"abstract":"<p>Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA–protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult.</p><p>We excised matched cancer-associated stroma (CAS) and normal stroma from clinical specimen of FFPE canine mammary tumours using LCM, and compared the commonly used protease-based RNA isolation procedure with an adapted novel technique that additionally incorporates a focused ultrasonication step.</p><p>We successfully adapted a protocol that uses focused ultrasonication to isolate RNA from small amounts of deparaffinised, stained, clinical LCM samples. Using this approach, we found that total RNA yields could be increased by 8- to 12-fold compared to a commonly used protease-based extraction technique. Surprisingly, RNA extracted using this new approach was qualitatively at least equal if not superior compared to the old approach, as Cq values in RT-qPCR were on average 2.3-fold lower using the new method. Finally, we demonstrate that RNA extracted using the new method performs comparably in NGS as well.</p><p>We present a successful isolation protocol for extraction of RNA from difficult and limiting FFPE tissue samples that enables successful analysis of small sections of clinically relevant specimen. The possibility to study gene expression signatures in specific small sections of archival FFPE tissue, which often entail large amounts of highly relevant clinical follow-up data, unlocks a new dimension of hitherto difficult-to-analyse samples which now become amenable for investigation.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0099-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5184514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries","authors":"Gorantla Venkata Raghuram,&nbsp;Deepika Gupta,&nbsp;Siddharth Subramaniam,&nbsp;Ashwini Gaikwad,&nbsp;Naveen Kumar Khare,&nbsp;Malcolm Nobre,&nbsp;Naveen Kumar Nair,&nbsp;Indraneel Mittra","doi":"10.1186/s12867-017-0098-8","DOIUrl":"https://doi.org/10.1186/s12867-017-0098-8","url":null,"abstract":"<p>We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA.</p><p>To test this hypothesis, we generated small DNA fragments by sonicating high molecular weight DNA (HMW DNA) to mimic circulating cfDNA. Sonication of HMW DNA isolated from cancerous and non-cancerous human cells, bacteria and plant generated fragments 300–3000?bp in size which are similar to that reported for circulating cfDNA. We show here that while HMW DNAs were incapable of entering into cells, sonicated DNA (sDNA) from different sources could do so indiscriminately without heed to species or kingdom boundaries. Thus, sDNA from human cells and those from bacteria and plant could enter into nuclei of mouse cells and sDNA from human, bacterial and plant sources could spontaneously enter into bacteria. The intracellular sDNA associated themselves with host cell chromosomes and integrated into their genomes. Furthermore, sDNA, but not HMW DNA, from all four sources could phosphorylate H2AX and activate the pro-inflammatory transcription factor NFκB in mouse cells, indicating that sDNAs had acquired biological activities.</p><p>Our results show that small fragments of DNA from different sources can indiscriminately enter into other cells across species and kingdom boundaries to integrate into their genomes and activate biological processes. This raises the possibility that fragmented DNA that are generated following organismal cell-death may have evolutionary implications by acting as mobile genetic elements that are involved in horizontal gene transfer.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0098-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4374326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t","authors":"Manuela Malsy,&nbsp;Bernhard Graf,&nbsp;Katrin Almstedt","doi":"10.1186/s12867-017-0097-9","DOIUrl":"https://doi.org/10.1186/s12867-017-0097-9","url":null,"abstract":"<p>Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. NFAT proteins are found in several types of tumors, for instance, pancreatic carcinoma. The role of NFATs in carcinogenesis is regulating central genes in cell differentiation and cell growth. NFAT proteins are primarily located in cytoplasm and only transported to the cell nucleus after activation. Here, they interact with other transcription factors cooperating with NFAT proteins, thus influencing the selection and regulation of NFAT-controlled genes. To identify and characterize possible interaction partners of the transcription factor NFATc2 in pancreatic carcinoma cells PaTu 8988t.</p><p>NFATc2 expression and the mode of action of Ionomycin in the pancreatic tumor cell lines PaTu 8988t were shown with Western blotting and immunofluorescence tests. Potential partner proteins were verified by means of immunoprecipitation and binding partners, their physical interactions with DNA pull-down assays, siRNA technologies, and GST pull-down assays. Functional evidence was complemented by reporter–promoter analyses.</p><p>NFATc2 and Sp1 are co-localized in cell nuclei and physically interact at the NFAT target sequence termed NFAT-responsive promotor construct. Sp1 increases the functional activity of its binding partner NFATc2. This interaction is facilitated by Ionomycin in the early stimulation phase (up to 60?min).</p><p>Oncological therapy concepts are becoming more and more specific, aiming at the efficient modulation of specific signal and transcription pathways. The oncogenic transcription partner Sp1 is important for the transcriptional and functional activity of NFATc2 in pancreatic carcinoma. The binding partners interact in cells. Further studies are necessary to identify the underlying mechanisms and establish future therapeutic options for treating this aggressive type of tumor.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0097-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4110658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA","authors":"Leslie C. Sutherland,&nbsp;Philippe Thibault,&nbsp;Mathieu Durand,&nbsp;Elvy Lapointe,&nbsp;Jose M. Knee,&nbsp;Ariane Beauvais,&nbsp;Irina Kalatskaya,&nbsp;Sarah C. Hunt,&nbsp;Julie J. Loiselle,&nbsp;Justin G. Roy,&nbsp;Sarah J. Tessier,&nbsp;Gustavo Ybazeta,&nbsp;Lincoln Stein,&nbsp;Rashmi Kothary,&nbsp;Roscoe Klinck,&nbsp;Benoit Chabot","doi":"10.1186/s12867-017-0096-x","DOIUrl":"https://doi.org/10.1186/s12867-017-0096-x","url":null,"abstract":"<p>RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. To accomplish this, we downregulated RBM10 in human cell lines, using small interfering RNAs, then monitored alternative splicing, using a reverse transcription-PCR screening platform.</p><p>RBM10 knockdown (KD) provoked alterations in splicing events in 10–20% of the pre-mRNAs, most of which had not been previously identified as RBM10 targets. Hierarchical clustering of the genes affected by RBM10 KD revealed good conservation of alternative exon inclusion or exclusion across cell lines. Pathway annotation showed <i>RAS</i> signaling to be most affected by RBM10 KD. Of particular interest was the finding that splicing of <i>SMN</i> pre-mRNA, encoding the survival of motor neuron (SMN) protein, was influenced by RBM10 KD. Inhibition of RBM10 resulted in preferential expression of the full-length, exon 7 retaining, <i>SMN</i> transcript in four cancer cell lines and one normal skin fibroblast cell line. SMN protein is expressed from two genes, <i>SMN1</i> and <i>SMN2</i>, but the <i>SMN1</i> gene is homozygously disrupted in people with spinal muscular atrophy; as a consequence, all of the SMN that is expressed in people with this disease is from the <i>SMN2</i> gene. Expression analyses using primary fibroblasts from control, carrier and spinal muscle atrophy donors demonstrated that RBM10 KD resulted in preferential expression of the full-length, exon 7 retaining, <i>SMN2</i> transcript. At the protein level, upregulation of the full-length SMN2 was also observed. Re-expression of RBM10, in a stable RBM10 KD cancer cell line, correlated with a reversion of the KD effect, demonstrating specificity.</p><p>Our work has not only expanded the number of pre-mRNA targets for RBM10, but identified RBM10 as a novel regulator of <i>SMN2</i> alternative inclusion.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0096-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4789372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Growth arrest specific gene 2 in tilapia (Oreochromis niloticus): molecular characterization and functional analysis under low-temperature stress","authors":"ChangGeng Yang,&nbsp;Fan Wu,&nbsp;Xing Lu,&nbsp;Ming Jiang,&nbsp;Wei Liu,&nbsp;Lijuan Yu,&nbsp;Juan Tian,&nbsp;Hua Wen","doi":"10.1186/s12867-017-0095-y","DOIUrl":"https://doi.org/10.1186/s12867-017-0095-y","url":null,"abstract":"<p>Growth arrest specific 2 (<i>gas2</i>) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, little information is available on fish <i>gas2</i>. In this study, the tilapia (<i>Oreochromis niloticus</i>) <i>gas2</i> gene was cloned and characterized for the first time.</p><p>The open reading frame was 1020?bp, encoding 340 amino acids; the 5′-untranslated region (UTR) was 140?bp and the 3′-UTR was 70?bp, with a poly (A) tail. The highest promoter activity occurred in the regulatory region (–3000 to –2400?bp). The Gas2-GFP fusion protein was distributed within the cytoplasm. Quantitative reverse transcription-polymerase chain reaction and western blot analyses revealed that <i>gas2</i> gene expression levels in the liver, muscle, and brain were clearly affected by low temperature stress. The results of <i>gas2</i> RNAi showed decreased expression of the <i>gas2</i> and P53 genes.</p><p>These results suggest that the tilapia <i>gas2</i> gene may be involved in low temperature stress-induced apoptosis.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0095-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4680379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands","authors":"Daniyah H. Bay,&nbsp;Annika Busch,&nbsp;Fred Lisdat,&nbsp;Keisuke Iida,&nbsp;Kazunori Ikebukuro,&nbsp;Kazuo Nagasawa,&nbsp;Isao Karube,&nbsp;Wataru Yoshida","doi":"10.1186/s12867-017-0094-z","DOIUrl":"https://doi.org/10.1186/s12867-017-0094-z","url":null,"abstract":"<p>G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay.</p><p>When G-quadruplex-forming sequences from the <i>Dele</i> and <i>Cdc6</i> genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When <i>Dele</i> and <i>Cdc6</i> CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on <i>Dele</i> G-quadruplex; however, increased by mutation on <i>Cdc6</i> G-quadruplex.</p><p>\u0000 <i>Dele</i> and <i>Cdc6</i> G-quadruplex formation is significant in the transcriptional regulation. <i>Dele</i> and <i>Cdc6</i> G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands <i>Dele</i> G-quadruplex also demonstrates promotor activity, whereas <i>Cdc6</i> G-quadruplex may possess a dual function of transcriptional regulation.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0094-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5480946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial RNA processing in absence of tRNA punctuations in octocorals","authors":"Gaurav G. Shimpi,&nbsp;Sergio Vargas,&nbsp;Angelo Poliseno,&nbsp;Gert Wörheide","doi":"10.1186/s12867-017-0093-0","DOIUrl":"https://doi.org/10.1186/s12867-017-0093-0","url":null,"abstract":"<p>Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals.</p><p>We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus <i>Sinularia</i> (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5′ and/or 3′ untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the <i>mtMutS</i>, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the <i>ATP6</i> gene (lnc<i>ATP6</i>) potentially involved in antisense regulation was detected.</p><p>Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0093-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4686980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis","authors":"Bingying Deng,&nbsp;Xiang Cheng,&nbsp;Haoming Li,&nbsp;Jianbing Qin,&nbsp;Meiling Tian,&nbsp;Guohua Jin","doi":"10.1186/s12867-017-0091-2","DOIUrl":"https://doi.org/10.1186/s12867-017-0091-2","url":null,"abstract":"<p>The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate neurogenesis in the hippocampus are reported. The present study aimed to perform microarray expression profiling to identify long noncoding RNAs (lncRNAs) that might participate in the hippocampal neurogenesis, and investigate the potential roles of identified lncRNAs in the hippocampal neurogenesis.</p><p>In this study, the profiling suggested that 74 activated and 29 repressed (|log fold-change|&gt;1.5) lncRNAs were differentially expressed between the denervated and the normal hippocampi. Furthermore, differentially expressed lncRNAs associated with neurogenesis were found. According to the tissue-specific expression profiles, and a novel lncRNA (lncRNA2393) was identified as a neural regulator in the hippocampus in this study. The expression of lncRNA2393 was activated in the denervated hippocampus. FISH showed lncRNA2393 specially existed in the subgranular zone of the dentate gyrus in the hippocampus and in the cytoplasm of neural stem cells (NSCs). The knockdown of lncRNA2393 depletes the EdU-positive NSCs. Besides, the increased expression of lncRNA2393 was found to be triggered by the change in the microenvironment.</p><p>We concluded that expression changes of lncRNAs exists in the microenvironment of denervated hippocampus, of which promotes hippocampal neurogenesis. The identified lncRNA lncRNA2393 expressed in neural stem cells, located in the subgranular zone of the dentate gyrus, which can promote NSCs proliferation in vitro. Therefore, the question is exactly which part of the denervated hippocampus induced the expression of lncRNA2393. Further studies should aim to explore the exact molecular mechanism behind the expression of lncRNA2393 in the hippocampus, to lay the foundation for the clinical application of NSCs in treating diseases of the central nervous system.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0091-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4259871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early growth response protein 1 regulates promoter activity of α-plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system","authors":"Rebecca R. Minich,&nbsp;Jin Li,&nbsp;Bruce L. Tempel","doi":"10.1186/s12867-017-0092-1","DOIUrl":"https://doi.org/10.1186/s12867-017-0092-1","url":null,"abstract":"<p>Along with sodium/calcium (Ca²⁺) exchangers, plasma membrane Ca²⁺ ATPases (ATP2Bs) are main regulators of intracellular Ca²⁺ levels. There are four ATP2B paralogs encoded by four different genes. <i>Atp2b2</i> encodes the protein pump with the fastest activation, ATP2B2. In mice, the <i>Atp2b2</i> transcript has several alternate transcriptional start site variants: <i>α</i>, <i>β</i>, <i>μ</i> and <i>δ</i>. These variants are expressed in developmental and tissue specific manners. The <i>α</i> and <i>β Atp2b2</i> transcripts are equally expressed in the brain. <i>αAtp2b2</i> is the only transcript found in the outer hair cells of young mice (Silverstein RS, Tempel BL. in Neuroscience 141:245–257, 2006). Mutations in the coding region of the mouse <i>Atp2b2</i> gene indicate a narrow window for tolerated dysfunction of the ATP2B2 protein, specifically in the auditory system. This highlights the necessity of tight regulation of this gene for normal cell physiology.</p><p>Although ATP2Bs are important regulators of Ca²⁺ in many cell types, little is known about their transcriptional regulation. This study identifies the proximal promoter of the <i>αAtp2b2</i> transcript. Further investigations indicate that ATOH1 and EGR1 modulate promoter activity. Additionally, we report that EGR1 increases endogenous expression of <i>Atp2b2</i> transcript in two cell lines. Electrophoretic mobility shift assays (EMSA) indicate that EGR1 binds to a specific site in the CpG island of the <i>αAtp2b2</i> promoter.</p><p>This study furthers our understanding of <i>Atp2b2</i> regulation by: (I) elucidating transcriptional regulatory mechanisms for <i>Atp2b2,</i> and (II) identifying transcription factors that modulate expression of <i>Atp2b2</i> in the brain and peripheral auditory system and (III) allows for future studies modulating gene expression of <i>Atp2b2.</i>\u0000 </p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2017-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-017-0092-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4867858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}