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| 2. |
- Petit, Marleen MR, et al.
(författare)
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Smooth muscle expression of lipoma preferred partner is mediated by an alternative intronic promoter that is regulated by serum response factor/myocardin.
- 2008
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Ingår i: Circulation research. - 1524-4571. ; 103:1, s. 61-9
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Tidskriftsartikel (refereegranskat)abstract
- Lipoma preferred partner (LPP) was recently recognized as a smooth muscle marker that plays a role in smooth muscle cell migration. In this report, we focus on the transcriptional regulation of the LPP gene. In particular, we investigate whether LPP is directly regulated by serum response factor (SRF). We show that the LPP gene contains 3 evolutionarily conserved CArG boxes and that 1 of these is part of an alternative promoter in intron 2. Quantitative RT-PCR shows that this alternative promoter directs transcription specifically to smooth muscle containing tissues in vivo. By using chromatin immunoprecipitation, we demonstrate that 2 of the CArG boxes, including the promoter-associated CArG box, bind to endogenous SRF in cultured aortic smooth muscle cells. Electrophoretic mobility-shift assays show that the conserved CArG boxes bind SRF in vitro. In reporter experiments, we show that the alternative promoter has transcriptional capacity that is dependent on SRF/myocardin and that the promoter associated CArG box is required for that activity. Finally, we show by quantitative RT-PCR that the alternative promoter is strongly downregulated in SRF-deficient embryonic stem cells and in smooth muscle tissues derived from conditional SRF knockout mice. Collectively, our data demonstrate that expression of LPP in smooth muscle is mediated by an alternative promoter that is regulated by SRF/myocardin.
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| 3. |
- Håkansson, Joakim, 1975, et al.
(författare)
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Neural cell adhesion molecule-deficient beta-cell tumorigenesis results in diminished extracellular matrix molecule expression and tumour cell-matrix adhesion
- 2005
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Ingår i: Tumour Biology. - : Springer Science and Business Media LLC. - 1010-4283 .- 1423-0380. ; 26:2, s. 103-112
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Tidskriftsartikel (refereegranskat)abstract
- To understand by which mechanism neural cell adhesion molecule (N-CAM) limits beta tumour cell disaggregation and dissemination, we searched for potential downstream genes of N-CAM during beta tumour cell progression by gene expression profiling. Here, we show that N-CAM-deficient beta-cell tumorigenesis is associated with changes in the expression of genes involved in cell-matrix adhesion and cytoskeletal dynamics, biological processes known to affect the invasive and metastatic behaviour of tumour cells. The extracellular matrix (ECM) molecules emerged as the primary target, i.e. N-CAM deficiency resulted in down-regulated mRNA expression of a broad range of ECM molecules. Consistent with this result, deficient deposition of major ECM stromal components, such as fibronectin, laminin 1 and collagen IV, was observed. Moreover, N-CAM-deficient tumour cells displayed defective matrix adhesion. These results offer a potential mechanism for tumour cell disaggregation during N-CAM-deficient beta tumour cell progression. Prospective consequences of these findings for the role of N-CAM in beta tumour cell dissemination are discussed.
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| 4. |
- Larsson, Erik, 1975, et al.
(författare)
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Do two mutually exclusive gene modules define the phenotypic diversity of mammalian smooth muscle?
- 2008
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Ingår i: Molecular genetics and genomics : MGG. - : Springer Science and Business Media LLC. - 1617-4615 .- 1617-4623. ; 280:2, s. 127-37
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Tidskriftsartikel (refereegranskat)abstract
- Smooth muscle cells (SMCs) are key components of all hollow organs, where they perform contractile, synthetic and other functions. Unlike other muscle cells, SMCs are not terminally differentiated, but exhibit considerable phenotypic variation. Such variation is manifested both across disease states such as asthma and atherosclerosis, and physiological states such as pregnancy and wound healing. While there has been considerable investigation into the diversity of SMCs at the level of morphology and individual biomarkers, less is known about the diversity of SMCs at the level of the transcriptome. To explore this question, we performed an extensive statistical analysis that integrates 200 transcriptional profiles obtained in different SMC phenotypes and reference tissues. Our results point towards a non-trivial hypothesis: that transcriptional variation in different SMC phenotypes is characterized by coordinated differential expression of two mutually exclusive (anti-correlating) gene modules. The first of these modules (C) encodes 19 co-transcribed cell cycle associated genes, whereas the other module (E) encodes 41 co-transcribed extra-cellular matrix components. We propose that the positioning of smooth muscle cells along the C/E axis constitutes an important determinant of SMC phenotypes. In conclusion, our study introduces a new approach to assess phenotypic variation in smooth muscle cells, and is relevant as an example of how integrative bioinformatics analysis can shed light on not only terminal differentiated states but also subtler details in phenotypic variability. It also raises the broader question whether coordinated expression of gene modules is a common mechanism underlying phenotypic variability in mammalian cells.
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| 5. |
- Nelander, Sven, 1974
(författare)
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A genomic approach to smooth muscle differentiation and diversity
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Smooth muscle cells (SMCs) are a broad class of contractile cells that are found in a number of organs systems, including the vasculature, the urogenital system, the bronchi and the gastrointestinal tract. The two main functions exerted by SMCs are to provide contractile force and to synthesize structural components of the extracellular matrix. SMCs are not terminally differentiated, but have a capacity to adjust their cellular phenotype to meet crucial physiological needs. Examples include repair of blood vessels, and uterine growth during pregnancy. In addition, SMC plasticity may be important in human diseases such as asthma, pre-term delivery, atherosclerosis, and hypertension. A great challenge in smooth muscle biology is therefore to identify molecular mechanisms that mediate SMC phenotypic differences. The aim of the present study is to examine SMC differentiation and diversity in terms of global gene expression. In general terms, we ask how genome sequences and large-scale observations of gene expression patterns together can be used to define and understand SMC differentiation and diversity. Three lines of investigation are followed. First, we examine gene expression patterns of SMC subpopulations using gene chip technology, which results in a transcription atlas of SMC diversity (I, IV). Second, we propose a general approach to the functional and regulatory interpretation of such data, based on the biological concept of gene batteries defined as sets of genes that are co-regulated and functionally linked (II, III). This approach is general, and applicable beyond SMC biology. Third, we use this framework to interpret our exploration of SMC phenotypes, and to postulate regulators of SMC phenotypic diversity (III, IV). We find evidence that that several gene batteries are synchronously regulated during vascular SMC maturation and neointima formation, suggesting that distinct features of the vascular SMC phenotype are encoded by individual gene batteries (IV). Among regulated gene batteries, a lipid metabolism battery and a vascular-selective extracellular matrix battery are found. Regulatory sequence analysis was performed on a whole-genome scale with respect to 266 DNA-binding transcription factors, and results were used to predict cis regulatory elements of importance for gene batteries and vascular SMC marker genes (III, IV). Specific findings include novel SMC differentiation markers, including LPP, a potential SMC-selective transcriptional regulator (II). In summary, the work provides a genomic formulation of the SMC differentiation and diversity problem, and proposes a model for the SMC phenotype which is based on explicitly defined groups of genes.
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| 6. |
- Nelander, Sven, 1974, et al.
(författare)
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Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals
- 2005
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Ingår i: BMC genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. RESULTS: In a screen that covered approximately 40 percent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously described cases of gene battery-like regulation, (ii) previously unreported cases of gene battery-like regulation with some support in a limited number of genes, and (iii) predicted cases that currently lack experimental support. The novel predictions include for example Sox 17 and RFX transcription factor binding sites that were detected in approximately 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in approximately 30% of all kidney specific genes respectively. The results are publicly available at http://www.wlab.gu.se/lindahl/genebatteries. CONCLUSION: 21 co-expressed gene clusters were enriched for a total of 66 shared cis-regulatory sequence elements. A majority of these predictions represent novel cases of potential co-regulation of functionally coupled proteins. Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design.
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