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Jiang Z, Cinti C, Taranta M, Mattioli E, Schena E, Singh S, Khurana R, Lattanzi G, Tsinoremas NF, Capobianco E. Network assessment of demethylation treatment in melanoma: Differential transcriptome-methylome and antigen profile signatures. PLoS One 2018; 13:e0206686. [PMID: 30485296 PMCID: PMC6261551 DOI: 10.1371/journal.pone.0206686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023] Open
Abstract
Background In melanoma, like in other cancers, both genetic alterations and epigenetic underlie the metastatic process. These effects are usually measured by changes in both methylome and transcriptome profiles, whose cross-correlation remains uncertain. We aimed to assess at systems scale the significance of epigenetic treatment in melanoma cells with different metastatic potential. Methods and findings Treatment by DAC demethylation with 5-Aza-2’-deoxycytidine of two melanoma cell lines endowed with different metastatic potential, SKMEL-2 and HS294T, was performed and high-throughput coupled RNA-Seq and RRBS-Seq experiments delivered differential profiles (DiP) of both transcriptomes and methylomes. Methylation levels measured at both TSS and gene body were studied to inspect correlated patterns with wide-spectrum transcript abundance levels quantified in both protein coding and non-coding RNA (ncRNA) regions. The DiP were then mapped onto standard bio-annotation sources (pathways, biological processes) and network configurations were obtained. The prioritized associations for target identification purposes were expected to elucidate the reprogramming dynamics induced by the epigenetic therapy. The interactomic connectivity maps of each cell line were formed to support the analysis of epigenetically re-activated genes. i.e. those supposedly silenced by melanoma. In particular, modular protein interaction networks (PIN) were used, evidencing a limited number of shared annotations, with an example being MAPK13 (cascade of cellular responses evoked by extracellular stimuli). This gene is also a target associated to the PANDAR ncRNA, therapeutically relevant because of its aberrant expression observed in various cancers. Overall, the non-metastatic SKMEL-2 map reveals post-treatment re-activation of a richer pathway landscape, involving cadherins and integrins as signatures of cell adhesion and proliferation. Relatively more lncRNAs were also annotated, indicating more complex regulation patterns in view of target identification. Finally, the antigen maps matched to DiP display other differential signatures with respect to the metastatic potential of the cell lines. In particular, as demethylated melanomas show connected targets that grow with the increased metastatic potential, also the potential target actionability seems to depend to some degree on the metastatic state. However, caution is required when assessing the direct influence of re-activated genes over the identified targets. In light of the stronger treatment effects observed in non-metastatic conditions, some limitations likely refer to in silico data integration tools and resources available for the analysis of tumor antigens. Conclusion Demethylation treatment strongly affects early melanoma progression by re-activating many genes. This evidence suggests that the efficacy of this type of therapeutic intervention is potentially high at the pre-metastatic stages. The biomarkers that can be assessed through antigens seem informative depending on the metastatic conditions, and networks help to elucidate the assessment of possible targets actionability.
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Affiliation(s)
- Zhijie Jiang
- Center for Computational Science, University of Miami, Miami, FL, United States of America
| | | | | | - Elisabetta Mattioli
- CNR Institute of Molecular Genetics, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
| | - Elisa Schena
- CNR Institute of Molecular Genetics, Bologna, Italy
- Endocrinology Unit, Department of Medical & Surgical Sciences, Alma Mater Studiorum University of Bologna, S Orsola-Malpighi Hospital, Bologna, Italy
| | - Sakshi Singh
- Institute of Clinical Physiology, CNR, Siena, Italy
| | - Rimpi Khurana
- Center for Computational Science, University of Miami, Miami, FL, United States of America
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
| | - Nicholas F. Tsinoremas
- Center for Computational Science, University of Miami, Miami, FL, United States of America
- Department of Medicine, University of Miami, Miami, FL, United States of America
| | - Enrico Capobianco
- Center for Computational Science, University of Miami, Miami, FL, United States of America
- * E-mail:
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Raju HB, Tsinoremas NF, Capobianco E. Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data. Front Neurol 2016; 7:168. [PMID: 27803687 PMCID: PMC5067702 DOI: 10.3389/fneur.2016.00168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein-protein interaction networks, other connectivity paths were identified between proteins already investigated in studies on disorders, such as Parkinson, Down syndrome, Huntington disease, and Alzheimer. Our findings suggest the importance of reusing gene expression data by meta-analysis approaches.
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Affiliation(s)
- Hemalatha B Raju
- Center for Computational Science, University of Miami Miller School of Medicine, Miami, FL, USA; Human Genetics and Genomic Graduate Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicholas F Tsinoremas
- Center for Computational Science, University of Miami Miller School of Medicine, Miami, FL, USA; Human Genetics and Genomic Graduate Program, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Capobianco
- Center for Computational Science, University of Miami Miller School of Medicine , Miami, FL , USA
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Abstract
The majority of studies on human cancers published to date focus on coding genes. More recently, however, non-coding RNAs (ncRNAs) are gaining growing recognition as important regulatory components. Here we characterise the ncRNA landscape in 442 head and neck squamous cell carcinomas (HNSCs) from the cancer genome atlas (TCGA). HNSCs represent an intriguing case to study the potential role of ncRNA as a function of viral presence, especially as HPV is potentially oncogenic. Thus, we identify HPV16-positive (HPV16+) and HPV-negative (HPV−) tumours and study the expression of ncRNAs on both groups. Overall, the ncRNAs comprise 36% of all differentially expressed genes, with antisense RNAs being the most represented ncRNA type (12.6%). Protein-coding genes appear to be more frequently downregulated in tumours compared with controls, whereas ncRNAs show significant upregulation in tumours, especially in HPV16+ tumours. Overall, expression of pseudogenes, antisense and short RNAs is elevated in HPV16+ tumours, while the remaining long non-coding RNA types are more active in all HNSC tumours independent of HPV status. In addition, we identify putative regulatory targets of differentially expressed ncRNAs. Among these ‘targets’ we find several well-established oncogenes, tumour suppressors, cytokines, growth factors and cell differentiation genes, which indicates the potential involvement of ncRNA in the control of these key regulators as a direct consequence of HPV oncogenic activity. In conclusion, our findings establish the ncRNAs as crucial transcriptional components in HNSCs. Our results display the great potential for the study of ncRNAs and the role they have in human cancers.
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Affiliation(s)
- Daria Salyakina
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Nicholas F Tsinoremas
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Medicine, Miller School of Medicine, University of Miami, Coral Gables, FL, USA
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Issac B, Tsinoremas NF, Capobianco E. Abstract B1-04: Co-expression profiling and transcriptional network evidences from RNA-Seq data reveal specific molecular subtype features in breast cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b1-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Expression profiling is regarded as the gold standard for breast cancer subtypes, but the recent advent of integrative multi-omics is challenging the validity of findings based on clustering approaches, the stability of the identified groups, the overall reproducibility of the molecular subtypes associated to clusters, and the impacts in both diagnostic practice and therapy. The purpose of the study is to elucidate the relevance of method integration, moving from the limitations of co-expression dynamics revealed by clustering to the high potential of transcriptional network analysis aimed to merge gene expression signatures with oncogenic pathway activity, and better define distinct disease features, such as molecular subtypes.
106 solid normal and 124 solid tumor breast cancer paired-end RNA-Seq data were obtained from The Cancer Genome Atlas (TCGA). Tissue type for all samples is infiltrating ductal carcinoma from female patients. Median age of patients is 57 yrs for normal samples and 52.5 yrs for tumor samples. All samples were sequenced on Illumina Hi-Seq 2000 and each sample contains on average ~100 million reads. Only reads with mapping quality (MAQ) score >=20 were used and mapping rate for these reads was above 90% against repeat masked human transcriptome (build hg19). Fragment Per Kilobase per Million reads (FPKM) values were computed using TopHat and Cufflinks software. Comparison between normal and tumor samples generated 2344 significantly differentially expressed genes (DEGs; p-values≤0.05; fold-change≥2).
The data cascade delivered several expression biotype categories, following ENSEMBL classification. Our focus was initially directed to the identification of molecular subtypes associated to clusters. The clusters were treated as seed classes informing on the target phenotypes, but needing refinement. We explored typical associations formed through hierarchical clustering, tested the robustness of the approach, and assessed the accuracy of sample assignment to clusters. Then, we analyzed transcriptional modularity and by constraining the search space of the problem we identified a list of candidate modules to reflect molecular subtype signatures. We annotated such modules and found distinctive features at both functional enrichment and pathway levels by using several software tools and visualization framework (ClueGO, EnrichmentMap, Cytoscape, etc).
We demonstrate that limitations of hierarchical clustering methods for molecular subtyping can in part be bypassed by complementing the expression profiles with transcriptional modules that allow for multiple annotation and useful visualizations. Therefore, it is important to stress a general aspect - that integrative analysis is a key factor relying not just on increasing data dimensionality (i.e., multi-omics into play), but also relying on a refinement of the data cross-fertilization and analysis fusion performed at intra-omic scale, before dealing with inter-omics harmonization.
Citation Format: Biju Issac, Nicholas F. Tsinoremas, Enrico Capobianco. Co-expression profiling and transcriptional network evidences from RNA-Seq data reveal specific molecular subtype features in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-04.
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Raju HB, Englander Z, Capobianco E, Tsinoremas NF, Lerch JK. Identification of potential therapeutic targets in a model of neuropathic pain. Front Genet 2014; 5:131. [PMID: 24904634 PMCID: PMC4033210 DOI: 10.3389/fgene.2014.00131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/24/2014] [Indexed: 01/18/2023] Open
Abstract
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in dysfunction and aberrant pain. The cellular functions (e.g., peripheral neuron spinal cord innervation, neuronal excitability) associated with NP often develop over time and are likely associated with gene expression changes. Gene expression studies on the cells involved in NP (e.g., sensory dorsal root ganglion neurons) are publically available; the mining of these studies may enable the identification of novel targets and the subsequent development of therapies that are essential for improving quality of life for the millions of individuals suffering with NP. Here we analyzed a publically available microarray dataset (GSE30165) in order to identify new RNAs (e.g., messenger RNA (mRNA) isoforms and non-coding RNAs) underlying NP. GSE30165 profiled gene expression in dorsal root ganglion neurons (DRG) and in sciatic nerve (SN) after resection, a NP model. Gene ontological analysis shows enrichment for sensory and neuronal processes. Protein network analysis demonstrates DRG upregulated genes typical to an injury and NP response. Of the top changing genes, 34 and 36% are associated with more than one protein coding isoform in the DRG and SN, respectively. The majority of genes are receptor and enzymes. We identified 15 long non-coding RNAs (lncRNAs) targeting these genes in LNCipedia.org, an online comprehensive lncRNA database. These RNAs represent new therapeutic targets for preventing NP development and this approach demonstrates the feasibility of data reanalysis for their identification.
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Affiliation(s)
- Hemalatha B Raju
- Center for Computational Science, Department of Medicine, University of Miami Miller School of Medicine Miami, FL, USA ; Human Genetics and Genomics Graduate Program, University of Miami Miller School of Medicine Miami, FL, USA
| | - Zoe Englander
- Department of Biomedical Engineering, Duke University Durham, NC, USA
| | - Enrico Capobianco
- Center for Computational Science, Department of Medicine, University of Miami Miller School of Medicine Miami, FL, USA ; Laboratory of Integrative Systems Medicine, National Research Council (CNR) Pisa, Italy
| | - Nicholas F Tsinoremas
- Center for Computational Science, Department of Medicine, University of Miami Miller School of Medicine Miami, FL, USA
| | - Jessica K Lerch
- Department of Neuroscience, Center for Brain and Spinal Cord Repair, The Ohio State University Columbus, OH, USA
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Jiang Z, Jones DH, Khuri S, Tsinoremas NF, Wyss T, Jander G, Wilson ACC. Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbion of the green peach aphid, Myzus persicae. BMC Genomics 2013; 14:917. [PMID: 24365332 PMCID: PMC3890641 DOI: 10.1186/1471-2164-14-917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/19/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Myzus persicae, the green peach aphid, is a polyphagous herbivore that feeds from hundreds of species of mostly dicot crop plants. Like other phloem-feeding aphids, M. persicae rely on the endosymbiotic bacterium, Buchnera aphidicola (Buchnera Mp), for biosynthesis of essential amino acids and other nutrients that are not sufficiently abundant in their phloem sap diet. Tobacco-specialized M. persicae are typically red and somewhat distinct from other lineages of this species. To determine whether the endosymbiotic bacteria of M. persicae could play a role in tobacco adaptation, we sequenced the Buchnera Mp genomes from two tobacco-adapted and two non-tobacco M. persicae lineages. RESULTS With a genome size of 643.5 kb and 579 predicted genes, Buchnera Mp is the largest Buchnera genome sequenced to date. No differences in gene content were found between the four sequenced Buchnera Mp strains. Compared to Buchnera APS from the well-studied pea aphid, Acyrthosiphon pisum, Buchnera Mp has 21 additional genes. These include genes encoding five enzymes required for biosynthesis of the modified nucleoside queosine, the heme pathway enzyme uroporphyrinogen III synthase, and asparaginase. Asparaginase, which is also encoded by the genome of the aphid host, may allow Buchnera Mp to synthesize essential amino acids from asparagine, a relatively abundant phloem amino acid. CONCLUSIONS Together our results indicate that the obligate intracellular symbiont Buchnera aphidicola does not contribute to the adaptation of Myzus persicae to feeding on tobacco.
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Affiliation(s)
- Zhijie Jiang
- Center for Computational Science, Miller School of Medicine, University of Miami, Coral Gables 33146, FL, USA
| | - Derek H Jones
- Department of Biology, University of Miami, Coral Gables 33146, FL, USA
| | - Sawsan Khuri
- Center for Computational Science, Miller School of Medicine, University of Miami, Coral Gables 33146, FL, USA
- Department of Computer Science, University of Miami, Coral Gables 33146, FL, USA
| | - Nicholas F Tsinoremas
- Center for Computational Science, Miller School of Medicine, University of Miami, Coral Gables 33146, FL, USA
- Department of Medicine, Miller School of Medicine, University of Miami, Miami 33136, FL, USA
| | - Tania Wyss
- Department of Biology, University of Miami, Coral Gables 33146, FL, USA
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca 14853, NY, USA
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables 33146, FL, USA
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Salyakina D, Tsinoremas NF. Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data. Hum Genomics 2013; 7:23. [PMID: 24279398 PMCID: PMC3906926 DOI: 10.1186/1479-7364-7-23] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/07/2013] [Indexed: 12/15/2022] Open
Abstract
Background Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori suspected viruses in one cancer type. To our knowledge, there have not been many broad screening approaches to address this problem more comprehensively. Methods In this study, we performed a comprehensive screening for viruses in nine common cancers using a multistep computational approach. Tumor transcriptome and genome sequencing data were available from The Cancer Genome Atlas (TCGA). Nine hundred fifty eight primary tumors in nine common cancers with poor prognosis were screened against a non-redundant database of virus sequences. DNA sequences from normal matched tissue specimens were used as controls to test whether each virus is associated with tumors. Results We identified human papilloma virus type 18 (HPV-18) and four human herpes viruses (HHV) types 4, 5, 6B, and 8, also known as EBV, CMV, roseola virus, and KSHV, in colon, rectal, and stomach adenocarcinomas. In total, 59% of screened gastrointestinal adenocarcinomas (GIA) were positive for at least one virus: 26% for EBV, 21% for CMV, 7% for HHV-6B, and 20% for HPV-18. Over 20% of tumors were co-infected with multiple viruses. Two viruses (EBV and CMV) were statistically significantly associated with colorectal cancers when compared to the matched healthy tissues from the same individuals (p = 0.02 and 0.03, respectively). HPV-18 was not detected in DNA, and thus, no association testing was possible. Nevertheless, HPV-18 expression patterns suggest viral integration in the host genome, consistent with the potentially oncogenic nature of HPV-18 in colorectal adenocarcinomas. The estimated counts of viral copies were below one per cell for all identified viruses and approached the detection limit. Conclusions Our comprehensive screening for viruses in multiple cancer types using next-generation sequencing data clearly demonstrates the presence of viral sequences in GIA. EBV, CMV, and HPV-18 are potentially causal for GIA, although their oncogenic role is yet to be established.
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Affiliation(s)
- Daria Salyakina
- Center for Computational Science, University of Miami, 1120 NW 14 St, Miami, FL 33136, USA.
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Rodrigues CO, Shehadeh LA, Hoosien M, Otero V, Chopra I, Tsinoremas NF, Bishopric NH. Heterogeneity in SDF-1 expression defines the vasculogenic potential of adult cardiac progenitor cells. PLoS One 2011; 6:e24013. [PMID: 21887363 PMCID: PMC3161114 DOI: 10.1371/journal.pone.0024013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/01/2011] [Indexed: 02/01/2023] Open
Abstract
Rationale The adult myocardium has been reported to harbor several classes of multipotent progenitor cells (CPCs) with tri-lineage differentiation potential. It is not clear whether c-kit+CPCs represent a uniform precursor population or a more complex mixture of cell types. Objective To characterize and understand vasculogenic heterogeneity within c-kit+presumptive cardiac progenitor cell populations. Methods and Results c-kit+, sca-1+ CPCs obtained from adult mouse left ventricle expressed stem cell-associated genes, including Oct-4 and Myc, and were self-renewing, pluripotent and clonogenic. Detailed single cell clonal analysis of 17 clones revealed that most (14/17) exhibited trilineage differentiation potential. However, striking morphological differences were observed among clones that were heritable and stable in long-term culture. 3 major groups were identified: round (7/17), flat or spindle-shaped (5/17) and stellate (5/17). Stellate morphology was predictive of vasculogenic differentiation in Matrigel. Genome-wide expression studies and bioinformatic analysis revealed clonally stable, heritable differences in stromal cell-derived factor-1 (SDF-1) expression that correlated strongly with stellate morphology and vasculogenic capacity. Endogenous SDF-1 production contributed directly to vasculogenic differentiation: both shRNA-mediated knockdown of SDF-1 and AMD3100, an antagonist of the SDF-1 receptor CXC chemokine Receptor-4 (CXCR4), reduced tube-forming capacity, while exogenous SDF-1 induced tube formation by 2 non-vasculogenic clones. CPCs producing SDF-1 were able to vascularize Matrigel dermal implants in vivo, while CPCs with low SDF-1 production were not. Conclusions Clonogenic c-kit+, sca-1+ CPCs are heterogeneous in morphology, gene expression patterns and differentiation potential. Clone-specific levels of SDF-1 expression both predict and promote development of a vasculogenic phenotype via a previously unreported autocrine mechanism.
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Affiliation(s)
- Claudia O. Rodrigues
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Lina A. Shehadeh
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Michael Hoosien
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Valerie Otero
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Ines Chopra
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Nicholas F. Tsinoremas
- Center for Computational Sciences, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
| | - Nanette H. Bishopric
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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Gerzenstein SM, Pletcher MT, Cervino ACL, Tsinoremas NF, Young B, Puliafito CA, Fini ME, Schwartz SG. Glucocorticoid receptor polymorphisms and intraocular pressure response to intravitreal triamcinolone acetonide. Ophthalmic Genet 2008; 29:166-70. [PMID: 19005987 DOI: 10.1080/13816810802320217] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Elevation of intraocular pressure (IOP) following injection of intravitreal triamcinolone acetonide (IVTA) is an important clinical problem. The etiology of the steroid response is poorly understood, although a genetic determinant has long been suspected. We performed a pharmacogenomic association study with glucocorticoid receptor polymorphisms. MATERIALS AND METHODS Fifty-two patients (56 eyes) who underwent treatment with IVTA for various retinal diseases were genotyped for six well-studied glucocorticoid receptor polymorphisms (ER22/23EK, N363S, BclI, N766N, and single nucleotide polymorphisms (SNPs) within introns 3 and 4). RESULTS Three polymorphisms (ER22/23EK, N363S, and the intron 3 SNP) were essentially nonpolymorphic within this population sample and excluded from further analysis. The remaining three polymorphisms (BclI, N766N, and within intron 4) passed the Hardy-Weinberg Equilibrium test, indicating good genotyping quality and normal population distribution of allelic frequency. No statistically significant correlations were found between these three polymorphisms and magnitude of IOP elevation following IVTA, using single point association and haplotype analyses. CONCLUSIONS In this small, pilot study, we found no statistically significant relationship between glucocorticoid receptor polymorphisms and IOP elevation following IVTA. The precise etiology of the steroid response remains obscure. To our knowledge, this is the first published pharmacogenomic study of this common clinical entity.
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Affiliation(s)
- Sabrina M Gerzenstein
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
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Abstract
MOTIVATION Biological samples frequently contain multiple cell-types that each can play a crucial role in the development and/or regulation of adjacent cells or tissues. The search for biomarkers, or expression patterns of, one cell-type in those samples can be a complex and time-consuming process. Ordinarily, extensive laboratory bench work must be performed to separate the mixed cell population into its subcomponents, such that each can be accurately characterized. RESULTS We have developed a methodology to electronically subtract gene expression in one or more components of a mixed cell population from a mixture, to reveal the expression patterns of other minor or difficult to isolate components. Examination of simulated data indicates that this procedure can reliably determine the expression patterns in cell-types that contribute as little as 5% of the total expression in a mixed cell population. We re-analyzed microarray expression data from the viral infection of macrophages and from the T-cells of wild type and Foxp3 deletion mice. Using our subtraction methodology, we were able to substantially improve the identification of genes involved in processes of subcomponent portions of these samples.
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Affiliation(s)
- Mark M Gosink
- Scientific Computing, Scripps Florida, 5353 Parkside Dr Jupiter, FL 33458, USA.
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Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease in which genetics is one of the underlying risk factors. Complicating the analysis of SLE is the fact that the phenotype is heterogeneous, with variations in clinical features, and subgroups are associated with a variety of different autoantibodies. Many association studies of candidate genes as well as linkage studies have generated significant results, highlighting the multigenetic component of the disease. Those findings need to be replicated by independent laboratories and many other genes still remain to be identified. Here, we present our findings on the first genome-wide association study performed in 105 Caucasian patients and controls using the Affymetrix NspI array. The SLE patients studied here were all characterized by the presence of autoantibodies against the U1-6 small nuclear ribonucleoprotein antigen spliceosomal complex. Testing each SNP individually for association with disease, we identified 7 markers with an uncorrected P-value < 0.0001. Of those, three were in reported regions of linkage, namely 20p12, 2q37, and 4p15. To increase the power of our study, we included 60 controls corresponding to the parents from the publicly available CEPH families. The analysis of the 165 cases and controls leads to 28 SNPs being associated with an uncorrected P-value < 0.0001.
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Abstract
In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.
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Cervino ACL, Gosink M, Fallahi M, Pascal B, Mader C, Tsinoremas NF. A comprehensive mouse IBD database for the efficient localization of quantitative trait loci. Mamm Genome 2006; 17:565-74. [PMID: 16783638 DOI: 10.1007/s00335-005-0170-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 01/15/2006] [Indexed: 10/24/2022]
Abstract
Traditional fine-mapping approaches in mouse genetics that go from a linkage region to a candidate gene are very costly and time consuming. Shared ancestry regions, along with the combination of genetics and genomics approaches, provide a powerful tool to shorten the time and effort required to identify a causative gene. In this article we present a novel methodology that predicts IBD (identical by descent) regions between pairs of inbred strains using single nucleotide polymorphism (SNP) maps. We have validated this approach by comparing the IBD regions, estimated using different algorithms, to the results derived using the sequence information in the strains present in the Celera Mouse Database. We showed that based on the current publicly available SNP genotypes, large IBD regions (>1 Mb) can be identified successfully. By assembling a list of 21,514 SNPs in 61 common inbred strains, we inferred IBD regions between all pairs of strains and confirmed, for the first time, that existing quantitative trait genes (QTG) and susceptibility genes all lie outside of IBD regions. We also illustrated how knowledge of IBD structures can be applied to strain selection for future crosses. We have made our results available for data mining and download through a public website ( http://www.mouseibd.florida.scripps.edu ).
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Affiliation(s)
- Alessandra C L Cervino
- Department of Informatics, Scripps Florida, 5353 Parkside Drive, RF-A, Jupiter, FL 33458, USA.
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14
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Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004; 5:R73. [PMID: 15461792 PMCID: PMC545593 DOI: 10.1186/gb-2004-5-10-r73] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 07/07/2004] [Accepted: 08/16/2004] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. RESULTS The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. CONCLUSIONS These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized.
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Affiliation(s)
- Eric E Schadt
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Stephen W Edwards
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | - Dan Holder
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Lisa Ying
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Vladimir Svetnik
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Amy Leonardson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Kyle W Hart
- Rally Scientific, 41 Fayette Street, Suite 1, Watertown, MA 02472, USA
| | - Archie Russell
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guoya Li
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guy Cavet
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - John Castle
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Paul McDonagh
- Amgen Inc, 1201 Amgen Court W, Seattle, WA 98119, USA
| | - Zhengyan Kan
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ronghua Chen
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Andrew Kasarskis
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Mihai Margarint
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ramon M Caceres
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Jason M Johnson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | | | | | - Daniel D Shoemaker
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
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15
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Abstract
Millions of transcript sequences have become available for characterizing the transcriptome of human and mouse. Transcript databases have been extensively mined for extracting alternative splicing information within the same species; but they also represent a potentially valuable resource for the discovery of alternative splice variants in another species. In this study, we have performed analysis of alternative splicing patterns for 7,475 pairs of human and mouse genes. We found that cross-species transcript analysis could accomplish the same level of sensitivity in detecting constitutive splice patterns as EST resource from the same species. In contrast, identifying alternative splice patterns in human genes, mouse transcripts achieved only 50% of the sensitivity of human EST and 70% of the sensitivity of human mRNA. While identifying alternative splice patterns in mouse genes, human transcripts are 38% more sensitive than mouse mRNA, and reach 60% of the sensitivity of mouse EST. Furthermore, using the cross-species approach, we predicted novel alternative splice patterns for 42% of human genes and 51% of mouse genes. Splice site motif analysis suggests that the majority of predicted novel splice patterns are expressed in human. EST-based frequency analysis shows that novel splice patterns are expressed at lower frequency than alternative splice patterns present in the transcript data from both species, possibly explaining why they remain undetected in the transcript data of the same species.
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Affiliation(s)
- Z Kan
- Rosetta Inpharmatics, 12040 115th Ave. N.E., Kirkland, WA 98034, USA.
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16
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Tsinoremas NF, Hubbard JA, Evans MC, Allen JF. P-700 photooxidation in state 1 and state 2 in cyanobacteria upon flash illumination with phycobilin- and chlorophyll-absorbed light. FEBS Lett 2002. [DOI: 10.1016/0014-5793(89)81727-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Andersson CR, Tsinoremas NF, Shelton J, Lebedeva NV, Yarrow J, Min H, Golden SS. Application of bioluminescence to the study of circadian rhythms in cyanobacteria. Methods Enzymol 2000; 305:527-42. [PMID: 10812624 DOI: 10.1016/s0076-6879(00)05511-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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18
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Christopher DA, Shen Y, Dudley P, Tsinoremas NF. Expression of a higher-plant chloroplast psbD promoter in a cyanobacterium (Synechococcus sp. strain PCC7942) reveals a conserved cis-element, designated PGT, that differentially interacts with sequence-specific binding factors during leaf development. Curr Genet 1999; 35:657-66. [PMID: 10467011 DOI: 10.1007/s002940050465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chloroplast psbD gene, which encodes the D2 subunit of photosystem II, is regulated by a blue light-responsive promoter (BLRP). We tested the ability of different regions of the barley (Hordeum vulagare) BLRP to drive transcription of the lacZ reporter gene in genomic transformants of Synechococcus sp. strain PCC7942. The barley BLRP was transcribed in Synechococcus from the same initiation sites that are used in plant chloroplasts in vivo. A region of the BLRP, residing between -83 and -112 bp upstream from the transcription initiation sites, functioned as a negative element in Synechococcus. Nucleotide sequences within this region are conserved among the psbD genes of several monocots and dicots, and with the nuclear negative regulatory element GT. Thus this new cis-element was designated Plastid GT, PGT. Proteins from chloroplasts of barley and Arabidopsis thaliana interacted with PGT in a sequence-specific and developmental-dependent manner. The DNA-protein complexes from Arabidopsis chloroplasts are composed of 60- and 38-kDa polypeptides. We postulate that GT and PGT have evolved in the nucleus and chloroplast, respectively, from a common ancestral regulatory element.
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Affiliation(s)
- D A Christopher
- Department of Plant Molecular Physiology, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA.
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19
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Abstract
We generated random mutations in Synechococcus sp. strain PCC 7942 to look for genes of output pathways in the cyanobacterial circadian system. A derivative of transposon Tn5 was introduced into the chromosomes of reporter strains in which cyanobacterial promoters drive the Vibrio harveyi luxAB genes and produce an oscillation of bioluminescence as a function of circadian gene expression. Among low-amplitude mutants, one mutant, tnp6, had an insertion in a 780-bp open reading frame. The tnp6 mutation produced an altered circadian phasing phenotype in the expression rhythms of psbAI::luxAB, psbAII::luxAB, and kaiA::luxAB but had no or little effect on those of psbAIII::luxAB, purF::luxAB, kaiB::luxAB, rpoD2::luxAB, ndhD::luxAB, and conII::luxAB. This suggests that the interrupted gene in tnp6, named cpmA (circadian phase modifier), is part of a circadian output pathway that regulates the expression rhythms of psbAI, psbAII, and kaiA.
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Affiliation(s)
- M Katayama
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
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20
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Tsinoremas NF, Kawakami A, Christopher DA. High-fluence blue light stimulates transcription from a higher plant chloroplast psbA promoter expressed in a cyanobacterium, Synechococcus (sp. strain PCC7942). Plant Cell Physiol 1999; 40:448-452. [PMID: 10394638 DOI: 10.1093/oxfordjournals.pcp.a029562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
High-fluence white and blue light, but not red light, enhanced transcription of the barley chloroplast psbA promoter when heterologously expressed as a lacZ transcriptional fusion in the cyanobacterium, Synechococcus sp. strain PCC7942. Analysis of Arabidopsis thaliana phytochrome mutants, phyAphyB and hy2, indicated that a distinct blue phototransduction pathway stimulates psbA expression. The evolutionary implications of these findings are discussed.
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Affiliation(s)
- N F Tsinoremas
- Department of Plant Molecular Physiology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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21
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Liu Y, Tsinoremas NF. An unusual gene arrangement for the putative chromosome replication origin and circadian expression of dnaN in Synechococcus sp. strain PCC 7942. Gene 1996; 172:105-9. [PMID: 8654968 DOI: 10.1016/0378-1119(96)00160-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In eubacteria, the clustering of DnaA boxes around the dnaN (beta subunit of DNA polymerase III) and dnaA genes usually defines the chromosome replication origin (oriC). In this study, the dnaN locus from the cyanobacterium Synechococcus sp. strain PCC 7942 was sequenced. The gene order in this region is cbbZp-dnaN-orf288-purL-purF which contrasts with other eubacteria. A cluster of eleven DnaA boxes (consensus sequence: TTTTCCACA) was found in the intergenic region between dnaN and cbbZp. We also found a 41-bp sequence within this region that is 80% identical to the proposed oriC of Streptomyces coelicolor. Therefore, we propose that this intergenic region may serve as an oriC in Synechococcus. Using bacterial luciferase as a reporter, we also showed that dnaN is rhythmically expressed, suggesting that DNA replication could be under circadian control in this organism.
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Affiliation(s)
- Y Liu
- Department of Biology, Vanderbilt University, Nashville, TN 37235, USA
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22
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Liu Y, Tsinoremas NF, Golden SS, Kondo T, Johnson CH. Circadian expression of genes involved in the purine biosynthetic pathway of the cyanobacterium Synechococcus sp. strain PCC 7942. Mol Microbiol 1996; 20:1071-81. [PMID: 8809759 DOI: 10.1111/j.1365-2958.1996.tb02547.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Extensive circadian (daily) control over gene expression in the cyanobacterium Synechococcus sp. strain PCC 7942 is programmed into at least two differentially phased groups. The transcriptional activity of the smaller group of genes is maximal at about dawn and minimal at about dusk. We identified one of the genes belonging to this latter group as purF, which encodes the key regulatory enzyme in the de novo purine synthetic pathway, glutamine PRPP amidotransferase (also known as amidophosphoribosyltransferase). Its expression pattern as a function of circadian time was confirmed by both luminescence from a purF::luxAB reporter strain and the abundance of purF mRNA. By fusing sequences upstream of the purF coding region to promoterless luxAB genes, we identified a limited upstream region, which potentially regulates purF circadian expression patterns in vivo. We also identified the purL gene immediately upstream of purF. The purL gene encodes FGAM synthetase, the fourth enzyme in the purine nucleotide biosynthesis pathway. Although these genes are expressed as part of a larger operon in other bacteria, reporter gene fusions revealed that purF and purL are transcribed independently in Synechococcus and that they are expressed at different phases of the circadian cycle. This differential expression pattern may be related to the oxygen sensitivity of amidophosphoribosyltransferase.
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Affiliation(s)
- Y Liu
- Department of Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
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23
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Tsinoremas NF, Ishiura M, Kondo T, Andersson CR, Tanaka K, Takahashi H, Johnson CH, Golden SS. A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO J 1996; 15:2488-95. [PMID: 8665856 PMCID: PMC450181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We isolated mutants affected in the circadian expression of the psbAI gene in Synechococcus sp. strain PCC 7942 using a strategy that tags the genomic locus responsible for the mutant phenotype. The search identified one short period (22 h) mutant (M2) and two low amplitude mutants, one of which showed apparent arhythmia (M11) and one that was still clearly rhythmic (M16). We characterized the disrupted locus of the low amplitude but still rhythmic mutant (M16) as the rpoD2 gene, a member of a gene family that encodes sigma70-like transcription factors in Synechococcus. We also inactivated rpoD2 in a number of reporter strains and showed that the circadian expression of some genes is not modified by the loss of this sigma factor. Therefore, we conclude that rpoD2 is a component of an output pathway of the biological clock that affects the circadian expression of a subset of genes in Synechococcus. This work demonstrates a direct link between a transcription factor and the manifestation of circadian gene expression.
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Affiliation(s)
- N F Tsinoremas
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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24
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Abstract
We wanted to identify genes that are controlled by the circadian clock in the prokaryotic cyanobacterium Synechococcus sp. strain PCC 7942. To use luciferase as a reporter to monitor gene expression, bacterial luciferase genes (luxAB) were inserted randomly into the Synechococcus genome by conjugation with Escherichia coli and subsequent homologous recombination. The resulting transformed clones were then screened for bioluminescence using a new developed cooled-CCD camera system. We screened approximately 30,000 transformed Synechococcus colonies and recovered approximately 800 clones whose bioluminescence was bright enough to be easily monitored by the screening apparatus. Unexpectedly, the bioluminescence expression patterns of almost all of these 800 colonies clearly manifested circadian rhythmicity. These rhythms exhibited a range of waveforms and amplitudes, and they also showed a variety of phase relationships. We also found bioluminescence rhythms expressed by cyanobacterial colonies in which the luciferase gene set was coupled to the promoters of several known genes. Together, these results indicate that control of gene expression by circadian clocks may be more widespread than expected thus far. Moreover, our results show that screening organisms in which promoterless luciferase genes have been inserted randomly throughout the genome by homologous recombination provides an extremely sensitive method to explore differential gene expression.
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Affiliation(s)
- Y Liu
- Department of Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
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25
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Abstract
A diverse set of circadian clock mutants was isolated in a cyanobacterial strain that carries a bacterial luciferase reporter gene attached to a clock-controlled promoter. Among 150,000 clones of chemically mutagenized bioluminescent cells, 12 mutants were isolated that exhibit a broad spectrum of periods (between 16 and 60 hours), and 5 mutants were found that show a variety of unusual patterns, including arrhythmia. These mutations appear to be clock-specific. Moreover, it was demonstrated that in this cyanobacterium it is possible to clone mutant genes by complementation, which provides a means to genetically dissect the circadian mechanism.
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Affiliation(s)
- T Kondo
- National Institute for Basic Biology, Okazaki, Japan
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26
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Tsinoremas NF, Kutach AK, Strayer CA, Golden SS. Efficient gene transfer in Synechococcus sp. strains PCC 7942 and PCC 6301 by interspecies conjugation and chromosomal recombination. J Bacteriol 1994; 176:6764-8. [PMID: 7961432 PMCID: PMC197036 DOI: 10.1128/jb.176.21.6764-6768.1994] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We developed a versatile, efficient genetic transfer method for Synechococcus sp. strains PCC 7942 and PCC 6301 that exceeds natural transformation efficiencies by orders of magnitude. As a test case, we complemented a histidine auxotroph and identified a hisS homolog of PCC 7942 as the complementing gene.
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Affiliation(s)
- N F Tsinoremas
- Department of Biology, Texas A&M University, College Station 77843-3258
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27
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Tsinoremas NF, Schaefer MR, Golden SS. Blue and red light reversibly control psbA expression in the cyanobacterium Synechococcus sp. strain PCC 7942. J Biol Chem 1994; 269:16143-7. [PMID: 8206914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The three psbA genes encoding the photosystem II D1 protein in Synechococcus sp. strain PCC 7942 respond differentially to an increase in intensity of white light through transcriptional induction of psbAII and psbAIII and accelerated degradation of psbAI and psbAIII messages. We report that the genes exhibit a novel photoreversible response involving blue and red light that is almost indistinguishable from the high-white light response. Transfer of cells from white to low-fluence blue light caused a decrease in the level of the psbAI message and increased levels of psbAII and psbAIII messages, whereas transfer to red or far-red light had little effect. Five min of blue light was sufficient to trigger psbAII and psbAIII induction; five min of subsequent red irradiation attenuated this response, whereas subsequent green or far-red light (or darkness) had no effect. Response to both high and blue light was insensitive to inhibitors of photosynthetic electron transport. We propose that Synechococcus modulates photosystem II biosynthesis in a variable light environment through a photoreception signal pathway, which is independent of photosystem II activity and which is distinct from red/green-reversible control of chromatically adapting cyanobacteria and the red/far-red-reversible phytochrome of plants.
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Affiliation(s)
- N F Tsinoremas
- Department of Biology, Texas A & M University, College Station 77843-3258
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28
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Tsinoremas NF, Castets AM, Harrison MA, Allen JF, Tandeau de Marsac N. Photosynthetic electron transport controls nitrogen assimilation in cyanobacteria by means of posttranslational modification of the glnB gene product. Proc Natl Acad Sci U S A 1991; 88:4565-9. [PMID: 1905010 PMCID: PMC51705 DOI: 10.1073/pnas.88.11.4565] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A glnB gene is identified in the cyanobacterium Synechococcus sp. PCC 7942, and its gene product is found to be covalently modified as a result of imbalance in electron transfer in photosynthesis, where photosystem II is favored over photosystem I. The gene was cloned and sequenced and found to encode a polypeptide of 112 amino acid residues, whose sequence shows a high degree of similarity to the Escherichia coli regulatory protein, PII. In E. coli, PII is involved in signal transduction in transcriptional and post-translational regulation of nitrogen assimilation. Increase in ammonium ion concentration is shown to decrease covalent modification of the Synechococcus PII protein, as in enteric bacteria. We therefore propose that the photosynthetic electron transport chain may regulate the pathway of nitrogen assimilation in cyanobacteria by means of posttranslational, covalent modification of the glnB gene product. The existence of the glnB gene in different strains of cyanobacteria is demonstrated and its implications are discussed.
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Affiliation(s)
- N F Tsinoremas
- Département de Biochimie et Génétique Moléculaire, Institut Pasteur, Paris, France
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29
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Harrison MA, Tsinoremas NF, Allen JF. Cyanobacterial thylakoid membrane proteins are reversibly phosphorylated under plastoquinone-reducing conditions in vitro. FEBS Lett 1991; 282:295-9. [PMID: 1903715 DOI: 10.1016/0014-5793(91)80499-s] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Reversible, light-dependent protein phosphorylation was observed in isolated thylakoid membranes of the cyanobacterium Synechococcus 6301. A polypeptide of 15 kDa in particular was phosphorylated under plastoquinone-reducing conditions and was not phosphorylated under plastoquinone-oxidising conditions. Phosphorylation and dephosphorylation reactions involving this and several other membrane polypeptides showed sensitivity to inhibitors of protein kinases and phosphatases. Changes in phosphorylation state correlated with changes in low temperature fluorescence emission characteristic of changes in excitation energy distribution between the photosystems. The 15 kDa phosphopolypeptide is likely to be involved directly in light state adaptations in cyanobacteria.
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Affiliation(s)
- M A Harrison
- Department of Pure and Applied Biology, University of Leeds, UK
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