BMC Molecular Biology最新文献

{"title":"Gene expression profiling of the venom gland from the Venezuelan mapanare (Bothrops colombiensis) using expressed sequence tags (ESTs)","authors":"Montamas Suntravat,&nbsp;Néstor L. Uzcategui,&nbsp;Chairat Atphaisit,&nbsp;Thomas J. Helmke,&nbsp;Sara E. Lucena,&nbsp;Elda E. Sánchez,&nbsp;A. Rodríguez Acosta","doi":"10.1186/s12867-016-0059-7","DOIUrl":"https://doi.org/10.1186/s12867-016-0059-7","url":null,"abstract":"<p>\u0000 <i>Bothrops colombiensis</i> is a highly dangerous pit viper and responsible for over 70?% of snakebites in Venezuela. Although the composition in <i>B. colombiensis</i> venom has been identified using a proteome analysis, the venom gland transcriptome is currently lacking.</p><p>We constructed a cDNA library from the venom gland of <i>B. colombiensis</i>, and a set of 729 high quality expressed sequence tags (ESTs) was identified. A total number of 344 ESTs (47.2?% of total ESTs) was related to toxins. The most abundant toxin transcripts were metalloproteinases (37.5?%), phospholipases A₂s (PLA₂, 29.7?%), and serine proteinases (11.9?%). Minor toxin transcripts were linked to waprins (5.5?%), C-type lectins (4.1?%), ATPases (2.9?%), cysteine-rich secretory proteins (CRISP, 2.3?%), snake venom vascular endothelium growth factors (svVEGF, 2.3?%), L-amino acid oxidases (2?%), and other putative toxins (1.7?%). While 160 ESTs (22?% of total ESTs) coded for translation proteins, regulatory proteins, ribosomal proteins, elongation factors, release factors, metabolic proteins, and immune response proteins. Other proteins detected in the transcriptome (87 ESTs, 11.9?% of total ESTs) were undescribed proteins with unknown functions. The remaining 138 (18.9?%) cDNAs had no match with known GenBank accessions.</p><p>This study represents the analysis of transcript expressions and provides a physical resource of unique genes for further study of gene function and the development of novel molecules for medical applications.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-016-0059-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4220370","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":"Knockdown of SALL4 inhibits the proliferation and reverses the resistance of MCF-7/ADR cells to doxorubicin hydrochloride","authors":"Yuan-Yuan Chen,&nbsp;Zhi-Zhen Li,&nbsp;Yuan-Yuan Ye,&nbsp;Feng Xu,&nbsp;Rui-Jie Niu,&nbsp;Hong-Chen Zhang,&nbsp;Yi-Jian Zhang,&nbsp;Ying-Bin Liu,&nbsp;Bao-San Han","doi":"10.1186/s12867-016-0055-y","DOIUrl":"https://doi.org/10.1186/s12867-016-0055-y","url":null,"abstract":"<p>Breast cancer is the most frequent malignancy in women and drug resistance is the major obstacle for its successful chemotherapy. In the present study, we analyzed the involvement of an oncofetal gene, sal-like 4 (SALL4), in the tumor proliferation and drug resistance of human breast cancer.</p><p>Our study showed that SALL4 was up-regulated in the drug resistant breast cancer cell line, MCF-7/ADR, compared to the other five cell lines. We established the lentiviral system expressing short hairpin RNA to knockdown SALL4 in MCF-7/ADR cells. Down-regulation of SALL4 inhibited the proliferation of MCF-7/ADR cells and induced the G1 phase arrest in cell cycle, accompanied by an obvious reduction of the expression of cyclinD1 and CDK4. Besides, down-regulating SALL4 can re-sensitize MCF-7/ADR to doxorubicin hydrochloride (ADMh) and had potent synergy with ADMh in MCF-7/ADR cells. Depletion of SALL4 led to a decrease in IC50 for ADMh and an inhibitory effect on the ability to form colonies in MCF-7/ADR cells. With SALL4 knockdown, ADMh accumulation rate of MCF-7/ADR cells was increased, while the expression of BCRP and c-myc was significantly decreased. Furthermore, silencing SALL4 also suppressed the growth of the xenograft tumors and reversed their resistance to ADMh in vivo.</p><p>SALL4 knockdown inhibits the growth of the drug resistant breast cancer due to cell cycle arrest and reverses tumor chemo-resistance through down-regulating the membrane transporter, BCPR. Thus, SALL4 has potential as a novel target for the treatment of breast cancer.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-016-0055-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4434498","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":"Annual acknowledgement of reviewers","authors":"Timothy R. Sands","doi":"10.1186/s12867-016-0058-8","DOIUrl":"https://doi.org/10.1186/s12867-016-0058-8","url":null,"abstract":"<p>The editors of <i>BMC Molecular Biology</i> would like to thank all our reviewers who have contributed to the journal in Volume 16 (2015).</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-016-0058-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5044965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What is normal? Next generation sequencing-driven analysis of the human circulating miRNAOme","authors":"D. P. Tonge,&nbsp;T. W. Gant","doi":"10.1186/s12867-016-0057-9","DOIUrl":"https://doi.org/10.1186/s12867-016-0057-9","url":null,"abstract":"<p>\u0000MicroRNAs (miRNAs) are short non-protein-coding RNA species that have a regulatory function in modulating protein translation and degradation of specific mRNAs. MicroRNAs are estimated to target approximately 60?% of all human mRNAs and are associated with the regulation of all physiological processes. Similar to many messenger RNAs (mRNA), miRNAs exhibit marked tissue specificity, and appear to be dysregulated in response to specific pathological conditions. Perhaps, one of the most significant findings is that miRNAs are detectable in various biological fluids and are stable during routine clinical processing, paving the way for their use as novel biomarkers. Despite an increasing number of publications reporting individual miRNAs or miRNA signatures to be diagnostic of disease or indicative of response to therapy, there is still a paucity of baseline data necessary for their validation. To this end, we utilised state of the art sequencing technologies to determine the global expression of all circulating miRNAs within the plasma of 18 disease-free human subjects.</p><p>In excess of 500 miRNAs were detected in our study population with expression levels across several orders of magnitude. Ten highly expressed miRNAs accounted for 90?% of the total reads that mapped showing that despite the range of miRNAs present, the total miRNA load of the plasma was predominated by just these few species (50?% of which are blood cell associated). Ranges of expression were determined for all miRNA detected (&gt;500) and a set of highly stable miRNAs identified. Finally, the effects of gender, smoking status and body mass index on miRNA expression were determined.</p><p>The data contained within will be of particular use to researchers performing miRNA-based biomarker screening in plasma and allow shortlisting of candidates a priori to expedite discovery or reduce costs as required.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-016-0057-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4374227","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":"TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint","authors":"Sanket Awate,&nbsp;Arrigo De Benedetti","doi":"10.1186/s12867-016-0056-x","DOIUrl":"https://doi.org/10.1186/s12867-016-0056-x","url":null,"abstract":"<p>The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. In this work we investigated the significance of this mechanism by overexpressing mutant TLK1B in which the inhibitory phosphorylation site was eliminated.</p><p>These cells expressing TLK1B resistant to DNA damage showed constitutive phosphorylation of Rad9 S328 that occurred even in the presence of hydroxyurea (HU), and this resulted in a delayed checkpoint recovery. One possible explanation was that premature phosphorylation of Rad9 caused its dissociation from 9-1-1 at stalled replication forks, resulting in their collapse and prolonged activation of the S-phase checkpoint. We found that phosphorylation of Rad9 at S328 results in its dissociation from chromatin and redistribution to the cytoplasm. This results in double stranded breaks formation with concomitant activation of ATM and phosphorylation of H2AX. Furthermore, a Rad9 (S328D) phosphomimic mutant was exclusively localized to the cytoplasm and not the chromatin. Another Rad9 phosphomimic mutant (T355D), which is also a site phosphorylated by TLK1, localized normally. In cells expressing the mutant TLK1B treated with HU, Rad9 association with Hus1 and WRN was greatly reduced, suggesting again that its phosphorylation causes its premature release from stalled forks.</p><p>We propose that normally, the inactivation of TLK1B following replication arrest and genotoxic stress functions to allow the retention of 9-1-1 at the sites of damage or stalled forks. Following reactivation of TLK1B, whose synthesis is concomitantly induced by genotoxins, Rad9 is hyperphosphorylated at S328, resulting in its dissociation and inactivation of the checkpoint that occurs once repair is complete.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-016-0056-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4374228","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":"Erratum to: Temperature-induced variation in gene expression burst size in metazoan cells","authors":"Ophélie Arnaud,&nbsp;Sam Meyer,&nbsp;Elodie Vallin,&nbsp;Guillaume Beslon,&nbsp;Olivier Gandrillon","doi":"10.1186/s12867-015-0054-4","DOIUrl":"https://doi.org/10.1186/s12867-015-0054-4","url":null,"abstract":"","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-015-0054-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4116128","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":"Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays","authors":"Quirino Alves de Lima Neto,&nbsp;Francisco Ferreira Duarte Junior,&nbsp;Paulo Sérgio Alves Bueno,&nbsp;Flavio Augusto Vicente Seixas,&nbsp;Madzia Pauline Kowalski,&nbsp;Eyemen Kheir,&nbsp;Torsten Krude,&nbsp;Maria Aparecida Fernandez","doi":"10.1186/s12867-015-0053-5","DOIUrl":"https://doi.org/10.1186/s12867-015-0053-5","url":null,"abstract":"<p>The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro.</p><p>We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The <i>chY1</i>, <i>chY3</i> and <i>chY5</i> genes were highly conserved with their vertebrate counterparts, whilst the <i>chY4</i> gene showed a relatively high degree of diversification from the other vertebrate <i>Y4</i> genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four <i>Y</i> RNA genes present in the hamster genome, we found that only the <i>chY1</i> and <i>chY3</i> RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the <i>chY4</i> and <i>chY5</i> RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system.</p><p>These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2016-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-015-0053-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4210387","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":"microRNA-150 promotes cervical cancer cell growth and survival by targeting FOXO4","authors":"Jun Li,&nbsp;Lina Hu,&nbsp;Chao Tian,&nbsp;Feng Lu,&nbsp;Jia Wu,&nbsp;Li Liu","doi":"10.1186/s12867-015-0052-6","DOIUrl":"https://doi.org/10.1186/s12867-015-0052-6","url":null,"abstract":"<p>Dysregulation of microRNA-150 (miR-150) is commonly observed in solid tumor and has been reported to be involved in multiple important biological processes, such as cell proliferation, apoptosis, and metastasis. Elevated miR-150 level was also detected in cervical carcinoma, whereas its function in cancer progression has not been studied yet.</p><p>The expression of miRNA-150 in cervical carcinoma was compared with normal cervical tissue and using qRT-PCR. The effects of miR-150 on cell cycle and apoptosis, as well as the expression of cycle- and apoptosis-related genes, were determined using flow cytometry, TUNEL assay, qRT-PCR, and Western blot, respectively. The direct target of miR-150 was confirmed using 3′ untranslated region (UTR) luciferase reporter assay.</p><p>miR-150 promotes cervical cancer cell survival and growth, while the inhibition of miR-150 suppresses these actions. miR-150 also induced the cell cycle progression from G1/G0 to S phase, resulting in an enhancement of growth. Several cell cycle- and apoptosis-related genes, CyclinD1, p27, BIM, and FASL were modulated by miR-150. Moreover, miR-150 directly reduced the expression of FOXO4, which regulates the expression of CyclinD1, p27, BIM, and FASL, by targeting its 3′ UTR.</p><p>Taken together, our data demonstrated that elevated miR-150 targets FOXO4 expression and therefore regulates multiple genes expression, resulting in cervical cancer cell growth and survival.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"16 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2015-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-015-0052-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5111599","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":"Transfection of Sertoli cells with androgen receptor alters gene expression without androgen stimulation","authors":"D. Fietz,&nbsp;M. Markmann,&nbsp;D. Lang,&nbsp;L. Konrad,&nbsp;J. Geyer,&nbsp;S. Kliesch,&nbsp;T. Chakraborty,&nbsp;H. Hossain,&nbsp;M. Bergmann","doi":"10.1186/s12867-015-0051-7","DOIUrl":"https://doi.org/10.1186/s12867-015-0051-7","url":null,"abstract":"<p>Androgens play an important role for the development of male fertility and gained interest as growth and survival factors for certain types of cancer. Androgens act via the androgen receptor (AR/<i>Ar</i>), which is involved in various cell biological processes such as sex differentiation. To study the functional mechanisms of androgen action, cell culture systems and AR-transfected cell lines are needed. Transfection of AR into cell lines and subsequent gene expression analysis after androgen treatment is well established to investigate the molecular biology of target cells. However, it remains unclear how the transfection with AR itself can modulate the gene expression even without androgen stimulation. Therefore, we transfected <i>Ar</i>-deficient rat Sertoli cells 93RS2 by electroporation using a full length human AR.</p><p>Transfection success was confirmed by Western Blotting, immunofluorescence and RT-PCR. AR transfection-related gene expression alterations were detected with microarray-based genome-wide expression profiling of transfected and non-transfected 93RS2 cells without androgen stimulation. Microarray analysis revealed 672 differentially regulated genes with 200 up- and 472 down-regulated genes. These genes could be assigned to four major biological categories (development, hormone response, immune response and metabolism). Microarray results were confirmed by quantitative RT-PCR analysis for 22 candidate genes.</p><p>We conclude from our data, that the transfection of <i>Ar</i>-deficient Sertoli cells with AR has a measurable effect on gene expression even without androgen stimulation and cause Sertoli cell damage. Studies using AR-transfected cells, subsequently stimulated, should consider alterations in AR-dependent gene expression as off-target effects of the AR transfection itself.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"16 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2015-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-015-0051-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5600557","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":"Conserved and highly expressed tRNA derived fragments in zebrafish","authors":"Ana Raquel Soares,&nbsp;Noémia Fernandes,&nbsp;Marisa Reverendo,&nbsp;Hugo Rafael Araújo,&nbsp;José Luís Oliveira,&nbsp;Gabriela M. R. Moura,&nbsp;Manuel A. S. Santos","doi":"10.1186/s12867-015-0050-8","DOIUrl":"https://doi.org/10.1186/s12867-015-0050-8","url":null,"abstract":"<p>Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire.</p><p>Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish. The tRFs identified are 18–30 nt long, are derived from specific 5′ and 3′ processing of mature tRNAs and are differentially expressed during development and in differentiated tissues, suggesting that they are likely produced by specific processing rather than random degradation of tRNAs. We further show that a highly expressed tRF (5′tRF-Pro^CGG) is cleaved in vitro by Dicer and has silencing ability, indicating that it can enter the RNAi pathway. A computational analysis of zebrafish tRFs shows that they are conserved among vertebrates and mining of publicly available datasets reveals that some 5′tRFs are differentially expressed in disease conditions, namely during infection and colorectal cancer.</p><p>tRFs constitute a class of conserved regulatory RNAs in vertebrates and may be involved in mechanisms of genome regulation and in some diseases.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"16 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2015-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-015-0050-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4850142","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}