Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner and function in various aspects of cell biology, often as key regulators of gene expression. In this study, we ...established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. Of particular interest are lncRNAs upstream of the master chondrocyte transcription factor SOX9 locus. SOX9 is an HMG-box transcription factor that plays an essential role in chondrocyte development by directing the expression of chondrocyte-specific genes. Two of these lncRNAs are upregulated during chondrogenic differentiation of mesenchymal stem cells (MSCs). Depletion of one of these lncRNAs,
, which we termed
(regulator of chondrogenesis RNA), by RNA interference disrupted MSC chondrogenesis, concomitant with reduced cartilage-specific gene expression and incomplete matrix component production, indicating an important role in chondrocyte biology. Specifically, SOX9 induction was significantly ablated in the absence of
, and overexpression of SOX9 rescued the differentiation of MSCs into chondrocytes. Our work sheds further light on chondrocyte-specific SOX9 expression and highlights a novel method of chondrocyte gene regulation involving a lncRNA.
Acute myeloid leukemia (AML) is a hematological malignancy with an undefined heritable risk. Here we perform a meta-analysis of three genome-wide association studies, with replication in a fourth ...study, incorporating a total of 4018 AML cases and 10488 controls. We identify a genome-wide significant risk locus for AML at 11q13.2 (rs4930561; P = 2.15 × 10
; KMT5B). We also identify a genome-wide significant risk locus for the cytogenetically normal AML sub-group (N = 1287) at 6p21.32 (rs3916765; P = 1.51 × 10
; HLA). Our results inform on AML etiology and identify putative functional genes operating in histone methylation (KMT5B) and immune function (HLA).
Plastic pollution is a common concern of global environmental pollution. Polystyrene (PS) and polyethylene (PE) account for almost one-third of global plastic production. However, so far, there have ...been few reports on microbial strains capable of simultaneously degrading PS and PE. In this study, Microbacterium esteraromaticum SW3, a non-pathogenic microorganism that can use PS or PE as the only carbon source in the mineral salt medium (MM), was isolated from plastics-contaminated soil and identified. The optimal growth conditions for SW3 in MM were 2% (w/v) PS or 2% (w/v) PE, 35°C and pH 6.3. A large number of bacteria and obvious damaged areas were observed on the surface of PS and PE products after inoculated with SW3 for 21 d. The degradation rates of PS and PE by SW3 (21d) were 13.17% and 5.39%, respectively. Manganese peroxidase and lipase were involved in PS and PE degradation by SW3. Through Fourier infrared spectroscopy detection, different functional groups such as carbonyl, hydroxyl and amidogen groups were produced during the degradation of PS and PE by SW3. Moreover, PS and PE were degraded into alkanes, ketones, carboxylic acids, esters and so on detected by GC-MS. Collectively, we have isolated and identified SW3, which can use PS or PE as the only carbon source in MM as well as degrade PS and PE products. This study not only provides a competitive candidate strain with broad biodegradability for the biodegradation of PS and/or PE pollution, but also provides new insights for the study of plastic biodegradation pathways.
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•Microbacterium esteraromaticum SW3 can simultaneously degrade PS and PE.•2% PS or 2% PE, 35°C and pH 6.3 were the optimal growth conditions for SW3.•Manganese peroxidase and lipase were involved in PS and PE degradation by SW3.•Carbonyl and hydroxyl groups were produced in PS and PE degradation by SW3.
Neurexins (NRXNs) are presynaptic terminal proteins and candidate neurodevelopmental disorder susceptibility genes; mutations presumably upset synaptic stabilization and function. However, analysis ...of human cortical tissue samples by RNAseq and quantitative real-time PCR at 8-12 postconceptional weeks, prior to extensive synapse formation, showed expression of all three NRXNs as well as several potential binding partners. However, the levels of expression were not identical; NRXN1 increased with age and NRXN2 levels were consistently higher than for NRXN3. Immunohistochemistry for each NRXN also revealed different expression patterns at this stage of development. NRXN1 and NRXN3 immunoreactivity was generally strongest in the cortical plate and increased in the ventricular zone with age, but was weak in the synaptogenic presubplate (pSP) and marginal zone. On the other hand, NRXN2 colocalized with synaptophysin in neurites of the pSP, but especially with GAP43 and CASK in growing axons of the intermediate zone. Alternative splicing modifies the role of NRXNs and we found evidence by RNAseq for exon skipping at splice site 4 and concomitant expression of KHDBRS proteins which control this splicing. NRXN2 may play a part in early cortical synaptogenesis, but NRXNs could have diverse roles in development including axon guidance, and intercellular communication between proliferating cells and/or migrating neurons.
ABSTRACT
Osteoarthritis is a degenerative joint disease characterized by a progressive and irreversible loss of the articular cartilage, due in main part to the cleavage of type II collagen within ...the matrix by the enzyme matrix metalloproteinase (MMP)13. Here, we examined the methylation status of MMP13 promoter and report the demethylation of specific CpG dinucleotides within its promoter in osteoarthritic compared to normal cartilage, which correlates with increased MMP13 expression. Of the promoter CpG sites examined, the –104 CpG was consistently demethylated following treatment of human articular chondrocytes with 10μM DNA‐methyltransferase inhibitor 5‐aza‐2'deoxycytidine, again correlating with increased MMP13 expression. Methylation of the –104 CpG site resulted in reduced promoter activity in the chondrosarcoma cell line SW1353 as shown by CpG‐free luciferase reporter. Using electrophoretic mobility shift assays, we identified CREB as the regulating factor able to only bind to the MMP13 promoter when the –104 CpG is demethylated, and confirmed this binding by chromatin immunoprecipitation. Finally, we demonstrated that CREB induces MMP13 expression only following treatment of SW1353 with 0.5 μM Ca2+ ionophore A23187. In summary, the –104 CpG is demethylated in osteoarthritic cartilage, correlating with the elevated MMP13 expression and cartilage destruction, providing a highly novel link between epigenetic status and arthritic disease.—Bui, C., Barter, M. J., Scott, J. L., Xu, Y., Galler, M., Reynard, L. N., Rowan, A. D., Young, D. A. cAMP response element‐binding (CREB) recruitment following a specific CpG demethylation leads to the elevated expression of the matrix metalloproteinase 13 in human articular chondrocytes and osteoarthritis. FASEB J. 26, 3000–3011 (2012). www.fasebj.org
During the course of search for novel and bioactive molecules of microbial origin for drug development,
Stachybotrys
and
Memnoniella
fungi generally have been found to be a rich source of novel and ...bioactive secondary metabolites of great importance. Results of phylogenetic analyses were in agreement that the
Memnoniella
is paraphyletic to
Stachybotrys
. Interestingly, most
Memnoniella
spp. were found to produce the similar chemical substances. Up until now, almost 200 secondary metabolites belonging to diverse structural types of trichothecene, triprenyl phenol, diterpenoid, isochroman, polyketide, cochlioquinone and cyclic peptide have been discovered. Most of these fungal metabolites were reported to possess several interesting biological activities, such as disruption of the complement system, inhibition of TNF-
α
release, endothelin receptor antagonism, anti-influenza A virus, antimalarial, inhibition of avian myeloblastosis virus protease, cholesterol esterase, tyrosine kinase, farnesyl-protein transferase, squalene synthase and human heart chymase as well as stimulation of plasminogen, fibrinolysis, thrombolysis. This review summarizes the research on the isolation, structure elucidation, structural diversity, and bioactivities of the
Stachybotrys
and
Memnoniella
fungal secondary metabolites reported up to the year of 2014, and then highlights some bioactive compounds as well as their mechanisms of action and structure–activity relationships.
The demonstration of impaired C regulation in the thrombotic microangiopathy (TMA) atypical hemolytic uremic syndrome (aHUS) resulted in the successful introduction of the C inhibitor eculizumab into ...clinical practice. C abnormalities account for approximately 50% of aHUS cases; however, mutations in the non-C gene diacylglycerol kinase-
have been described recently in individuals not responsive to eculizumab. We report here a family in which the proposita presented with aHUS but did not respond to eculizumab. Her mother had previously presented with a post-renal transplant TMA. Both the proposita and her mother also had Charcot-Marie-Tooth disease. Using whole-exome sequencing, we identified a mutation in the inverted formin 2 gene (
) in the mutational hotspot for FSGS. Subsequent analysis of the Newcastle aHUS cohort identified another family with a functionally-significant mutation in
In this family, renal transplantation was associated with post-transplant TMA. All individuals with
mutations presenting with a TMA also had aHUS risk haplotypes, potentially accounting for the genetic pleiotropy. Identifying individuals with TMAs who may not respond to eculizumab will avoid prolonged exposure of such individuals to the infectious complications of terminal pathway C blockade.
Nigericin is a polyether antibiotic with potent antibacterial, antifungal, antimalarial and anticancer activity. NigR, the only regulator in the nigericin biosynthetic gene cluster in Streptomyces ...malaysiensis F913, was identified as a SARP family regulator. Disruption of nigR abolished nigericin biosynthesis, while complementation of nigR restored nigericin production, suggesting that NigR is an essential positive regulator for nigericin biosynthesis. Overexpression of nigR in Streptomyces malaysiensis led to significant increase in nigericin production compared to the wild-type strain. Nigericin production in the overexpression strain was found to reach 0.56 g/L, which may be the highest nigericin titer reported to date. Transcriptional analysis suggested that nigR is required for the transcription of structural genes in the nig gene cluster; quantitative RT-PCR analysis revealed that the expression of structural genes was upregulated in the nigR overexpression strain. Our study suggested that NigR acts in a positive manner to modulate nigericin production by activating transcription of structural genes and provides an effective strategy for scaling up nigericin production.
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