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BMC Plant Biology Oct 2020Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited...
BACKGROUND
Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited genetic information is currently available. Therefore, we combined a PacBio single-molecule real-time (SMRT) transcriptome library and the Illumina RNA-seq data of sodium selenate (NaSeO)-treated C. violifolia to further reveal the molecular mechanism of Se metabolism.
RESULTS
The concentrations of the total, inorganic, and organic Se in C. violifolia seedlings significantly increased as the NaSeO treatment concentration increased. From SMRT full-length transcriptome of C. violifolia, we obtained 26,745 annotated nonredundant transcripts, 14,269 simple sequence repeats, 283 alternative splices, and 3407 transcription factors. Fifty-one genes from 134 transcripts were identified to be involved in Se metabolism, including transporter, assimilatory enzyme, and several specific genes. Analysis of Illumina RNA-Seq data showed that a total of 948 differentially expressed genes (DEGs) were filtered from the four groups with NaSeO treatment, among which 11 DEGs were related to Se metabolism. The enrichment analysis of KEGG pathways of all the DEGs showed that they were significantly enriched in five pathways, such as hormone signal transduction and plant-pathogen interaction pathways. Four genes related to Se metabolism, adenosine triphosphate sulfurase 1, adenosine 5'-phosphosulfate reductase 3, cysteine (Cys) desulfurase 1, and serine acetyltransferase 2, were regulated by lncRNAs. Twenty potential hub genes (e.g., sulfate transporter 1;1, Cys synthase, methionine gamma-lyase, and Se-binding protein 1) were screened and identified to play important roles in Se accumulation and tolerance in C. violifolia as concluded by weighted gene correlation network analysis. Based on combinative analysis of expression profiling and annotation of genes as well as Se speciation and concentration in C. violifolia under the treatments with different NaSeO concentrations, a putative Se metabolism and assimilation pathway in C. violifolia was proposed.
CONCLUSION
Our data provide abundant information on putative gene transcriptions and pathway involved in Se metabolism of C. violifolia. The findings present a genetic resource and provide novel insights into the mechanism of Se hyperaccumulation in C. violifolia.
Topics: Cardamine; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Metabolic Networks and Pathways; Selenium; Sequence Analysis, RNA; Transcriptome
PubMed: 33109081
DOI: 10.1186/s12870-020-02694-9 -
BMC Evolutionary Biology Oct 2016SMRT and NCoR are corepressor paralogs that help mediate transcriptional repression by a variety of transcription factors, including the nuclear hormone receptors. The...
BACKGROUND
SMRT and NCoR are corepressor paralogs that help mediate transcriptional repression by a variety of transcription factors, including the nuclear hormone receptors. The functions of both corepressors are extensively diversified in mice by alternative mRNA splicing, generating a series of protein variants that differ in different tissues and that exert different, even diametrically opposite, biochemical and biological effects from one another.
RESULTS
We report here that the alternative splicing previously reported for SMRT appears to be a relatively recent evolutionary phenomenon, with only one of these previously identified sites utilized in a teleost fish and a limited additional number of the additional known sites utilized in a bird, reptile, and marsupial. In contrast, extensive SMRT alternative splicing at these sites was detected among the placental mammals. The alternative splicing of NCoR previously identified in mice (and shown to regulate lipid and carbohydrate metabolism) is likely to have arisen separately and after that of SMRT, and includes an example of convergent evolution.
CONCLUSIONS
We propose that the functions of both SMRT and NCoR have been diversified by alternative splicing during evolution to allow customization for different purposes in different tissues and different species.
Topics: Alternative Splicing; Animals; Co-Repressor Proteins; Evolution, Molecular; Humans; Liver; Mice; Nuclear Receptor Co-Repressor 1; Nuclear Receptor Co-Repressor 2; Opossums; RNA Splice Sites; RNA, Messenger; Sheep; Species Specificity; Xenopus; Zebrafish
PubMed: 27756201
DOI: 10.1186/s12862-016-0781-2 -
Biochimica Et Biophysica Acta.... Sep 2018At high doses, glucocorticoids (GC) have been associated with enhanced serum bile acids and liver injury. We have evaluated the effect of GC, in the absence of...
At high doses, glucocorticoids (GC) have been associated with enhanced serum bile acids and liver injury. We have evaluated the effect of GC, in the absence of hepatotoxicity, on FXR/FGF91(Fgf15)/FGF21-mediated ileum-liver crosstalk. Rats and mice (wild type and Fxr, Fgf15 and int-Gr strains; the latter with GC receptor (Gr) knockout selective for intestinal epithelial cells), were treated (i.p.) with dexamethasone, prednisolone or budesonide. In both species, high doses of GC caused hepatotoxicity. At a non-hepatotoxic dose, GC induced ileal Fgf15 down-regulation and liver Fgf21 up-regulation, without affecting Fxr expression. Fgf21 mRNA levels correlated with those of several genes involved in glucose and bile acid metabolism. Surprisingly, liver Cyp7a1 was not up-regulated. The expression of factors involved in transcriptional modulation by Fxr and Gr (p300, Drip205, CBP and Smrt) was not affected. Pxr target genes Cyp3a11 and Mrp2 were not up-regulated in liver or intestine. In contrast, the expression of some Pparα target genes in liver (Fgf21, Cyp4a14 and Vanin-1) and intestine (Vanin-1 and Cyp3a11) was altered. In mice with experimental colitis, liver Fgf21 was up-regulated (4.4-fold). HepG2 cells transfection with FGF21 inhibited CYP7A1 promoter (prCYP7A1-Luc2). This was mimicked by pure human FGF21 protein or culture in medium previously conditioned by cells over-expressing FGF21. This response was not abolished by deletion of a putative response element for phosphorylated FGF21 effectors present in prCYP7A1. In conclusion, GC interfere with FXR/FGF19-mediated intestinal control of CYP7A1 expression by the liver and stimulate hepatic secretion of FGF21, which inhibits CYP7A1 promoter through an autocrine mechanism.
Topics: Animals; Autocrine Communication; Bile Acids and Salts; Cholesterol; Cholesterol 7-alpha-Hydroxylase; Colitis; Disease Models, Animal; Female; Fibroblast Growth Factors; Glucocorticoids; Hep G2 Cells; Humans; Ileum; Liver; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Rats; Rats, Wistar; Receptors, Cytoplasmic and Nuclear; Signal Transduction; Up-Regulation
PubMed: 29883717
DOI: 10.1016/j.bbadis.2018.06.003 -
Frontiers in Genetics 2020The tea aphid, , has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the...
The tea aphid, , has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of . It will assist the future functional study of genes involved in its development and reproduction.
PubMed: 33304379
DOI: 10.3389/fgene.2020.558394 -
Molecular Cell Mar 2021While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the...
While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the involvement of corepressors is not. Using inflammatory macrophage activation as a model, we investigate here a corepressor complex containing GPS2 and SMRT both genome-wide and at the Ccl2 locus, encoding the chemokine CCL2 (MCP-1). We report that corepressors co-occupy candidate enhancers along with the coactivators CBP (H3K27 acetylase) and MED1 (mediator) but act antagonistically by repressing eRNA transcription-coupled H3K27 acetylation. Genome editing, transcriptional interference, and cistrome analysis reveals that apparently related enhancer and silencer elements control Ccl2 transcription in opposite ways. 4C-seq indicates that corepressor depletion or inflammatory signaling functions mechanistically similarly to trigger enhancer activation. In ob/ob mice, adipose tissue macrophage-selective depletion of the Ccl2 enhancer-transcribed eRNA reduces metaflammation. Thus, the identified corepressor-eRNA-chemokine pathway operates in vivo and suggests therapeutic opportunities by targeting eRNAs in immuno-metabolic diseases.
Topics: Adipose Tissue; Animals; CRISPR-Cas Systems; Chemokine CCL2; Co-Repressor Proteins; Enhancer Elements, Genetic; Gene Editing; Gene Expression Regulation; HEK293 Cells; Histone Acetyltransferases; Histones; Humans; Intracellular Signaling Peptides and Proteins; Lipopolysaccharides; Macrophage Activation; Male; Mediator Complex Subunit 1; Mice; Mice, Obese; Nuclear Receptor Co-Repressor 2; Obesity; RAW 264.7 Cells; RNA, Untranslated; Signal Transduction; Silencer Elements, Transcriptional
PubMed: 33503407
DOI: 10.1016/j.molcel.2020.12.040 -
Current Opinion in Genetics &... Oct 2008Histone deacetylases (HDACs) are essential catalytic components of the transcription silencing machinery and they play important roles in the programming of... (Review)
Review
Histone deacetylases (HDACs) are essential catalytic components of the transcription silencing machinery and they play important roles in the programming of multicellular development. HDACs are present within multisubunit protein complexes, other components of which govern HDAC target gene specificity by controlling interactions with sequence-specific DNA-binding proteins. Here, I review the different developmental roles of the Sin3, NuRD, CoREST and NCoR/SMRT Class I HDAC complexes. With their distinct subunit composition, these versatile molecular devices function in many different settings, to promote axis specification and tissue patterning, to maintain stem cell pluripotency, facilitate self-renewal, guide lineage commitment and drive cell differentiation.
Topics: Body Patterning; Cell Differentiation; DNA-Binding Proteins; Gene Silencing; Histone Deacetylases; Mi-2 Nucleosome Remodeling and Deacetylase Complex; Models, Genetic; Nuclear Receptor Co-Repressor 2; Protein Subunits; Repressor Proteins; Signal Transduction; Sin3 Histone Deacetylase and Corepressor Complex; Substrate Specificity
PubMed: 18929655
DOI: 10.1016/j.gde.2008.10.001 -
PloS One 2022Silencing Mediator of Retinoid and Thyroid hormone receptors (SMRT; NCoR2) is a transcriptional corepressor (CoR) which has been recognized as an important player in the...
BACKGROUND
Silencing Mediator of Retinoid and Thyroid hormone receptors (SMRT; NCoR2) is a transcriptional corepressor (CoR) which has been recognized as an important player in the regulation of hepatic lipogenesis and in somatic development in mouse embryo. SMRT protein is also widely expressed in mouse connective tissues, for example adipocytes and muscle. We recently reported that mice with global deletion of SMRT develop significant obesity and muscle wasting which are independent from thyroid hormone (TH) signaling and thermogenesis. However, the tissue specific role of SMRT in skeletal muscle is still not clear.
METHODS
To clarify role of SMRT in muscle differentiation, we made myogenic C2C12 clones which lack SMRT protein (C2C12-SKO) by using CRISPR-Cas9. Wild-type C2C12 (C2C12-WT) and C2C12-SKO cells were cultured in differentiation medium, and the resulting gene and protein profiles were compared between the two cell lines both before and after differentiation. We also analyzed muscle tissues which were dissected from whole body SMRT knockout (KO) mice and their controls.
RESULTS
We found significant up-regulation of muscle specific β-oxidation markers; Peroxisome proliferator-activated receptor δ (PPARδ) and PPARγ coactivator-1α (PGC-1α) in the C2C12-SKO cells, suggesting that the cells had a similar gene profile to what is found in exercised rodent skeletal muscle. On the other hand, confocal microscopic analysis showed the significant loss of myotubes in C2C12-SKO cells similar to the morphology found in immature myoblasts. Proteomics analysis also confirmed that the C2C12-SKO cells had higher expression of markers of fibrosis (ex. Collagen1A1; COL1A1 and Fibroblast growth factor-2; FGF-2), indicating the up-regulation of Transforming growth factor-β (TGF-β) receptor signaling. Consistent with this, treatment with a specific TGF-β receptor inhibitor ameliorated both the defects in myotube differentiation and fibrosis.
CONCLUSION
Taken together, we demonstrate that SMRT functions as a pivotal transcriptional mediator for both β-oxidation and the prevention for the fibrosis via TGF-β receptor signaling in the differentiation of C2C12 myoblasts. In contrast to the results from C2C12 cells, SMRT does not appear to play a role in adult skeletal muscle of whole body SMRT KO mice. Thus, SMRT plays a significant role in the differentiation of myoblasts.
Topics: Animals; Mice; Cell Differentiation; Fibroblast Growth Factor 2; Fibrosis; Muscle Fibers, Skeletal; Muscle, Skeletal; PPAR delta; Nuclear Receptor Co-Repressor 2
PubMed: 36454860
DOI: 10.1371/journal.pone.0277830 -
Frontiers in Microbiology 2022Silage fermentation is a dynamic process involving the succession of microbial communities and changes in metabolites. Fresh branched and leaves of paper mulberry were...
Silage fermentation is a dynamic process involving the succession of microbial communities and changes in metabolites. Fresh branched and leaves of paper mulberry were used to prepared silage. Crop by-products including corn bran, rice bran, and wheat bran were used as exogenous additives. Pacific Biosciences single-molecule real-time (SMRT) sequencing technology and metabolomics are used to explore the interaction mechanism of microbial structure and metabolites during woody silage fermentation and to verify the principle that exogenous additives can modulate silage fermentation. Under the dual stress of anaerobic and acidic environment of silage fermentation, the microbial community changed from Gram-negative to Gram-positive bacteria, and a large amount of lactic acid and volatile fatty acid were produced, which lowered the pH value and caused the rapid death of aerobic bacteria with thin cell walls. The exogenous additives of corn bran and wheat bran accelerated the dynamic succession of lactic acid bacteria as the dominant microbial community in silage fermentation, increased the metabolic pathways of lactic acid, unsaturated fatty acids, citric acid, L-malic acid and other flavoring agents, and inhibited the growth of and , thereby improving the flavor and quality of the silage. However, because rice bran contained butyric acid spore bacteria, it can multiply in an anaerobic environment, led to butyric acid fermentation, and promoted protein degradation and ammonia nitrogen production, thereby reduced the fermentation quality of woody silage. The results showed that during the silage fermentation process, the microbial community and the metabolome can interact, and exogenous additives can affect the fermentation quality of silage. SMRT sequencing technology and untargeted metabolomics revealed the microbiota-metabolome interaction during silage fermentation. Changes in the structure of the microbial community can affect the metabolic pathways, and the final metabolites can inhibit the growth of microorganisms that are not conducive to silage fermentation. Exogenous carbohydrate additives can change the fermentation substrate and affect microbial community structure, thus modulate the silage fermentation.
PubMed: 35794909
DOI: 10.3389/fmicb.2022.857431 -
Genes Apr 2022Pall. is one of the pioneer tree species in saline-alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further...
BACKGROUND
Pall. is one of the pioneer tree species in saline-alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further exploration of the molecular mechanisms in under salt stress.
METHODS
In this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of .
RESULTS
Our results suggested that a total of 234,508 circular consensus sequences (CCSs) with a mean read length of 2121 bp were obtained from the 19.26 Gb raw data. Furthermore, based on transcript cluster analysis, 93,713 consensus isoforms were obtained, including 92,116 high-quality isoforms. After removing redundant sequences, 49,240 non-redundant transcripts were obtained from high-quality isoforms. A total of 37,261 SSRs, 1816 LncRNAs and 47,314 CDSs, of which 40,160 carried complete ORFs, were obtained. Based on our transcriptome data, we also analyzed the coding genes of H-PPase, and the results of both bioinformatics and functional analyses indicated that the gene prediction via full-length transcripts obtained by SMRT technology is reliable and effective. In summary, our research data obtained by SMRT technology provides more reliable and accurate information for the further analysis of the regulatory network and molecular mechanism of under salt stress.
Topics: Gene Expression Profiling; Magnoliopsida; Protein Isoforms; Salt Tolerance; Salt-Tolerant Plants
PubMed: 35456467
DOI: 10.3390/genes13040661 -
The Journal of Biological Chemistry Aug 2013Cytokine modulation of the endothelium is considered an important contributor to the inflammation response. TNFα is an early response gene during the initiation of...
β-Transducin repeat-containing protein 1 (β-TrCP1)-mediated silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) protein degradation promotes tumor necrosis factor α (TNFα)-induced inflammatory gene expression.
Cytokine modulation of the endothelium is considered an important contributor to the inflammation response. TNFα is an early response gene during the initiation of inflammation. However, the detailed mechanism by which TNFα induces proinflammatory gene expression is not completely understood. In this report, we demonstrate that silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) represses the expression of a subset of TNFα target genes in human umbilical vein endothelial cells. Upon TNFα stimulation, we observed an increase in the E3 ubiquitin ligase β-TrCP1 and a decrease in SMRT protein levels. We show that β-TrCP1 interacts with SMRT in a phosphorylation-independent manner and cooperates with the E2 ubiquitin-conjugating enzyme E2D2 to promote ubiquitination-dependent SMRT degradation. Knockdown of β-TrCP1 increases SMRT protein accumulation, increases SMRT association with its targeted promoters, and decreases SMRT target gene expression. Taken together, our results support a model in which TNFα-induced β-TrCP1 accumulation promotes SMRT degradation and the subsequent induction of proinflammatory gene expression.
Topics: Gene Expression Regulation; HEK293 Cells; HeLa Cells; Human Umbilical Vein Endothelial Cells; Humans; Models, Biological; Nuclear Receptor Co-Repressor 2; Phosphorylation; Proteolysis; Tumor Necrosis Factor-alpha; Ubiquitin; beta-Transducin Repeat-Containing Proteins
PubMed: 23861398
DOI: 10.1074/jbc.M113.473124