33 research outputs found
Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in ‘Rutgers’ tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage, (ii) early symptoms, (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3,000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis
Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression
ATP-dependent chromatin remodeling complexes
are important regulators of gene expression in Eukaryotes.
In plants, SWI/SNF-type complexes have
been shown critical for transcriptional control of
key developmental processes, growth and stress responses.
To gain insight into mechanisms underlying
these roles, we performed whole genome mapping
of the SWI/SNF catalytic subunit BRM in Arabidopsis
thaliana, combined with transcript profiling
experiments. Our data showthatBRM occupies thousands
of sites in Arabidopsis genome, most of which
located within or close to genes. Among identified direct
BRM transcriptional targets almost equal numbers
were up- and downregulated upon BRM depletion,
suggesting that BRM can act as both activator
and repressor of gene expression. Interestingly,
in addition to genes showing canonical pattern of
BRM enrichment near transcription start site, many
other genes showed a transcription termination sitecentred
BRM occupancy profile. We found that BRMbound
3� gene regions have promoter-like features,
including presence of TATA boxes and high H3K4me3
levels, and possess high antisense transcriptional
activity which is subjected to both activation and
repression by SWI/SNF complex. Our data suggest
that binding to gene terminators and controlling transcription
of non-coding RNAs is another way through
which SWI/SNF complex regulates expression of its
targets
Myogenic Differentiation of Mouse Embryonic Stem Cells That Lack a Functional Pax7 Gene
The transcription factor Pax7 plays a key role during embryonic myogenesis and sustains the proper function of
satellite cells, which serve as adult skeletal muscle stem cells. Overexpression of Pax7 has been shown to
promote the myogenic differentiation of pluripotent stem cells. However, the effects of the absence of functional
Pax7 in differentiating embryonic stem cells (ESCs) have not yet been directly tested. Herein, we studied
mouse stem cells that lacked a functional Pax7 gene and characterized the differentiation of these stem cells
under conditions that promoted the derivation of myoblasts in vitro. We analyzed the expression of myogenic
factors, such as myogenic regulatory factors and muscle-specific microRNAs, in wild-type and mutant cells.
Finally, we compared the transcriptome of both types of cells and did not find substantial differences in the
expression of genes related to the regulation of myogenesis. As a result, we showed that the absence of
functional Pax7 does not prevent the in vitro myogenic differentiation of ESCs
Stem cells migration during skeletal muscle regeneration - the role of Sdf-1/Cxcr4 and Sdf-1/ Cxcr7 axis
The skeletal muscle regeneration occurs due to the presence of tissue specific stem cells - satellite
cells. These cells, localized between sarcolemma and basal lamina, are bound to muscle fibers and
remain quiescent until their activation upon muscle injury. Due to pathological conditions, such as
extensive injury or dystrophy, skeletal muscle regeneration is diminished. Among the therapies
aiming to ameliorate skeletal muscle diseases are transplantations of the stem cells. In our previous
studies we showed that Sdf-1 (stromal derived factor ¡1) increased migration of stem cells and
their fusion with myoblasts in vitro. Importantly, we identified that Sdf-1 caused an increase in the
expression of tetraspanin CD9 - adhesion protein involved in myoblasts fusion. In the current study
we aimed to uncover the details of molecular mechanism of Sdf-1 action. We focused at the Sdf-1
receptors - Cxcr4 and Cxcr7, as well as signaling pathways induced by these molecules in primary
myoblasts, as well as various stem cells - mesenchymal stem cells and embryonic stem cells, i.e. the
cells of different migration and myogenic potential. We showed that Sdf-1 altered actin
organization via FAK (focal adhesion kinase), Cdc42 (cell division control protein 42), and Rac-1 (Ras-
Related C3 Botulinum Toxin Substrate 1). Moreover, we showed that Sdf-1 modified the
transcription profile of genes encoding factors engaged in cells adhesion and migration. As the
result, cells such as primary myoblasts or embryonic stem cells, became characterized by more
effective migration when transplanted into regenerating muscle
The miR151 and miR5100 Transfected Bone Marrow Stromal Cells Increase Myoblast Fusion in IGFBP2 Dependent Manner
BACKGROUND: Bone marrow stromal cells (BMSCs) form a perivascular cell population in the bone marrow. These cells do not present naïve myogenic potential. However, their myogenic identity could be induced experimentally in vitro or in vivo. In vivo, after transplantation into injured muscle, BMSCs rarely fused with myofibers. However, BMSC participation in myofiber reconstruction increased if they were modified by NICD or PAX3 overexpression. Nevertheless, BMSCs paracrine function could play a positive role in skeletal muscle regeneration. Previously, we showed that SDF-1 treatment and coculture with myofibers increased BMSC ability to reconstruct myofibers. We also noticed that SDF-1 treatment changed selected miRNAs expression, including miR151 and miR5100. METHODS: Mouse BMSCs were transfected with miR151 and miR5100 mimics and their proliferation, myogenic differentiation, and fusion with myoblasts were analyzed. RESULTS: We showed that miR151 and miR5100 played an important role in the regulation of BMSC proliferation and migration. Moreover, the presence of miR151 and miR5100 transfected BMSCs in co-cultures with human myoblasts increased their fusion. This effect was achieved in an IGFBP2 dependent manner. CONCLUSIONS: Mouse BMSCs did not present naïve myogenic potential but secreted proteins could impact myogenic cell differentiation. miR151 and miR5100 transfection changed BMSC migration and IGFBP2 and MMP12 expression in BMSCs. miR151 and miR5100 transfected BMSCs increased myoblast fusion in vitro. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12015-022-10350-y
Cell cycle regulation of embryonic stem cells and mouse embryonic fibroblasts lacking functional Pax7
The transcription factor Pax7 plays a key role during embryonic myogenesis and in adult organisms in that
it sustains the proper function of satellite cells, which serve as adult skeletal muscle stem cells. Recently
we have shown that lack of Pax7 does not prevent the myogenic differentiation of pluripotent stem cells.
In the current work we show that the absence of functional Pax7 in differentiating embryonic stem cells
modulates cell cycle facilitating their proliferation. Surprisingly, deregulation of Pax7 function also
positively impacts at the proliferation of mouse embryonic fibroblasts. Such phenotypes seem to be
executed by modulating the expression of positive cell cycle regulators, such as cyclin E
Regulation of Sulfur Assimilation Pathways in Burkholderia cenocepacia: Identification of Transcription Factors CysB and SsuR and Their Role in Control of Target Genes
Two genes encoding transcriptional regulators involved in sulfur assimilation pathways in Burkholderia cenocepacia strain 715j have been identified and characterized functionally. Knockout mutations in each of the B. cenocepacia genes were constructed and introduced into the genome of 715j by allelic replacement. Studies on the utilization of various sulfur sources by 715j and the obtained mutants demonstrated that one of the B. cenocepacia regulators, designated CysB, is preferentially involved in the control of sulfate transport and reduction, while the other, designated SsuR, is required for aliphatic sulfonate utilization. Using transcriptional promoter-lacZ fusions and DNA-binding experiments, we identified several target promoters for positive control by CysB and/or SsuR—sbpp (preceding the sbp cysT cysW cysA ssuR cluster), cysIp (preceding the cysI cysD1 cysN cysH cysG cluster), cysD2p (preceding a separate cluster, cysD2 cysNC), and ssuDp (located upstream of the ssuDCB operon)—and we demonstrated overlapping functions of CysB and SsuR at particular promoters. We also demonstrated that the cysB gene is negatively controlled by both CysB and SsuR but the ssuR gene itself is not significantly regulated as a separate transcription unit. The function of B. cenocepacia CysB (in vivo and in vitro) appeared to be independent of the presence of acetylserine, the indispensable coinducer of the CysB regulators of Escherichia coli and Salmonella. The phylogenetic relationships among members of the “CysB family” in the γ and β subphyla are presented
Different statins produce highly divergent changes in gene expression profiles of human hepatoma cells: a pilot study
Statins are inhibitors of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the key enzyme of the sterol biosynthesis pathway. Statin therapy is commonly regarded as well tolerated. However, serious adverse effects have also been reported, especially during high-dose statin therapy. The aim of our study was to investigate the effect of statins on gene expression profiles in human hepatoma HepG2 cells using Affymetrix Human Genome U133 Plus 2.0 arrays. Expression of 102, 857 and 1091 genes was changed substantially in HepG2 cells treated with simvastatin, fluvastatin and atorvastatin, respectively. Pathway and gene ontology analysis showed that many of the genes with changed expression levels were involved in a broad range of metabolic processes. The presented data clearly indicate substantial differences between the tested statins