R plasmid R6-5 retains an active tet protein repressor gene.
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Escherichia coli↗
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Synthesis of an R plasmid protein associated with tetracycline resistance is negatively regulated.
Synthesis of proteins encoded by the R222 plasmid was observed in a DNA-directed cell-free system and the products were compared to those plasmid proteins synthesized in Escherichia coli minicells. A greater number of plasmid-specified proteins was detected in the in vitro system than in the minicell, suggesting the presence of control factors for plasmid gene expression in the minicell. Synthesis of a newly detected plasmid protein (TET protein) is induced by tetracycline in minicells containing tetracycline-resistant plasmids, including R222, and this induced synthesis correlates with induced host resistance to the drug. This TET protein was synthesized in vitro from R222 DNA in the absence of tetracycline, indicating that no positive regulatory role for tetracycline is required for the protein's synthesis. TET proteon synthesis was inhibited in vitro when cell-free extracts prepared from cells containing the R222 plasmid were used.
Bacterial Proteins↗
Regulation of TET function by PROSER1 in development and hematologic malignancies.
Ten eleven translocation (TET) proteins are central regulators of DNA methylation homeostasis and play essential roles in development and disease, including hematopoietic malignancies. Among the three TET family members, mutations in TET2 are frequently observed in hematologic disorders. TET enzymes catalyze the iterative oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives, enabling DNA demethylation. Beyond catalysis, TET proteins also perform important non-enzymatic functions mediated through interactions with diverse protein partners, highlighting the importance of defining their regulatory interactome. Previous studies identified several TET-associated factors, including O-Linked N-acetylglucosamine transferase (OGT), members of the Drosophila behavior/human splicing (DBHS) protein family, and proline and serine-rich protein 1 (PROSER1). However, these interactions were largely considered independently. Recent findings now demonstrate that TET proteins, OGT, PROSER1, and DBHS proteins assemble into a higher-order regulatory unit termed the TOPD (TET-OGT-PROSER1-DBHS) complex. In this review, we discuss how TOPD provides a conceptual framework for understanding multicomponent regulation of TET function, spatial control of DNA demethylation, and maintenance of epigenetic homeostasis, with implications for developmental syndromes and hematopoiesis.
Humans↗
Identification of elements determining KIR gene demethylation at the CD56-bright stage of NK cell development.
The variegated expression of the KIR family of class I MHC receptors generates specialized natural killer (NK) cells capable of allele-specific HLA recognition. Understanding the mechanism of KIR gene activation will lead to improved methods for the generation of fully functional NK cells. A central RUNX-binding site in the KIR proximal promoter is required for gene activation. RUNX proteins recruit ten-eleven translocation (TET) proteins that generate 5-hydroxymethylcytosine (5hmC) and drive DNA demethylation. Assessment of 5-methylcytosine (5mC) and 5hmC residues at four stages of NK cell development reveals deposition of 5hmC primarily in a CREB site next to the RUNX site at the CD56Bright stage but not the subsequent CD56Dim stage representing fully mature NK cells. KIR promoter demethylation is delayed relative to other lineage-associated genes, indicating a high threshold for KIR gene demethylation in developing NK cells, and a window of opportunity for RUNX/TET-dependent KIR gene activation in CD56Bright NK cells.
6-base sequencing↗
A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
5-Methylcytosine↗
Glucose-6-phosphate dehydrogenase variants modify 3D genomic organization to suppress maladaptive gene expression and vascular disease.
The 3D genome architecture is a higher-order organization of chromosomes within the nucleus that is critical to the control of epigenomic modifications. However, our knowledge regarding the role of 3D genomic organization in the regulation of vascular gene expression and function is lacking. In the present study, CRISPR-engineered rats modelled after two common polymorphisms (S188F and N126D) in human glucose-6-phosphate dehydrogenase (G6PD) revealed modifications to the 3D genome in aortas from rats expressing a deficient G6PD variant (S188F), but not a non-deficient one (N126D), is associated with: 1] up-regulated expression of TET enzymes that augmented expression of genes encoding antiproliferative proteins, 2] suppressed expression of genes encoding inflammatory/thrombotic/fibrotic proteins, and 3] reduced angiotensin II-induced aortic stiffness and hypertension. G6PD interacted with MATRIN-3, a nuclear matrix/scaffold protein, and a deficient G6PD variant increased the relative abundance of MATR3 and CCCTC-binding factors, potentially modifying 3D-genome structure. Additionally, G6PD deficiency-induced enrichment of H3K27ac likely influences the establishment and maintenance of the 3D genome. Therefore, we propose that the nexus between metabolism and the 3D genome regulates arterial gene expression and vascular disease.
Animals↗
Minimal Perturbation Analysis of mRNA Degradation Rates with Tet-Off and RT-qPCR.
Messenger RNA stability is an important variable in gene expression and its dynamics. High stability ensures a constant level of synthesized protein, whereas mRNA instability can be critical for regulatory processes in which protein production needs to be stopped, such as development, inflammation, or adaptation to stress. Accurate measurements of RNA degradation rates are important for understanding how RNA features and RNA binding proteins affect the posttranscriptional life of an mRNA. As an alternative to global transcriptional inhibition methods, the use of a Tet-off repressible promoter has the advantage that cells are minimally perturbed by the addition of doxycyclin during the assay. We illustrate the use of a reporter mRNA expressed from a plasmid in Saccharomyces cerevisiae cells, but similar methods can be applied to other regulated promoters, on plasmids or by genome editing, and in other organisms. RNA levels are measured by reverse transcription followed by quantitative PCR. An exponential decay law is then used to estimate how well the measurements follow this expected trend for the simplest possible mechanism of RNA degradation, where the decay is proportional to the amount of RNA present at any given time.
RNA Stability↗
Age as a core disease modifier: Distinct clinical, molecular and prognostic landscapes of essential thrombocythaemia in adolescents and young adults.
Essential thrombocythaemia (ET) in adolescents and young adults (AYA, 15-39 years) is a distinct entity with an incompletely defined prognosis. In this multicentre retrospective study, 1728 ET patients from 29 centres across China were stratified into AYA (n = 328) and non-AYA (≥40 years, n = 1400) cohorts. We compared their clinical profiles, genomic landscapes, long-term outcomes and risk factors for progression to post-ET myelofibrosis (MF). AYA patients had fewer cardiovascular risks and lower thrombosis rates, but higher rates of extreme thrombocytosis. Molecularly, AYA patients were enriched for calreticulin (CALR) mutations, whereas Janus kinase 2 (JAK2) predominated in older patients. The burden of non-driver mutations (tet methylcytosine dioxygenase 2 [TET2], DNA methyltransferase 3A [DNMT3A], ASXL transcriptional regulator 1 [ASXL1], SH2‑B adaptor protein 3 [SH2B3]) was lower in AYA patients. Consequently, AYA patients achieved superior long-term outcomes across all key survival endpoints, including overall, myelofibrosis-free and leukaemia-free survival. Analysis of post-ET MF progression risks identified age-specific patterns: CALR mutations are enriched in younger patients and show an age-specific association with MF progression. AYA-ET constitutes a unique clinicomolecular subtype with a favourable prognosis, supporting age-stratified management. The enrichment of CALR mutations and their specific link to MF progression in young patients underscore the urgent need for targeted therapies against CALR-mutant clones.
adolescents and young adults (AYA)↗
Organization of structural and regulatory genes that mediate tetracycline resistance in transposon Tn10.
The location of Tn10 genes encoding tetracycline resistance and its regulation was determined by analyzing the properties of recombinant plasmids carrying partial HpaI digestion products of lambda::Tn10 transducing phage deoxyribonucleic acid. Within a 2,700-base pair region are encoded tetracycline resistance, the structural gene (tet) for a tetracycline-inducible polypeptide, and the regulatory elements for the induction of both the resistance phenotype and the polypeptide. Fusion of different sequences to an HpaI site in the tet gene alters the molecular weight and stability of the polypeptide as well as the tetracycline resistance phenotype of strains producing fusion polypeptides. These results indicate the orientation of the tet gene and support the conclusion that the tet polypeptie is required for tetracycline resistance. A HincII cleavage site immediately upstream from the tet gene is protected by ribonucleic acid polymerase, but only the absence of ribonucleotide triphosphates. The possibility that tet transcription is initiated at this site is discussed.
Bacterial Proteins↗
Mechanism of transferable resistance to chloramphenicol in Haemophilus parainfluenzae.
A clinical isolate of Haemophilus parainfluenzae resistant to chloramphenicol and tetracycline transferred both cam and tet determinants to Escherichia coli K-12 during mixed cultivation on solid media irrespective of the selection employed. The doubly resistant transconjugant was found to contain levels of the enzyme chloramphenicol acetyltransferase (CAT) comparable to those found in R plasmid-bearing chloramphenicol-resistant enteric bacteria. Purification of CAT from the transconjugant was achieved by affinity chromatography, and the electrophoretically homogeneous protein was compared with previously characterized CAT variants specified by R plasmids. Although the CAT associated with cam from H. parainfluenzae was found to be distinct from the three types described previously, its N-terminal peptide amino acid sequence was identical with that determined for a type II CAT. Attempts to demonstrate covalently closed circular deoxyribonucleic acid in the H. parainfluenzae donor and the E. coli transconjugant were unsuccessful. The cam and tet determinants were nontransmissible from E. coli but could be cotransferred following the introduction of a suitable conjugative plasmid.
Cell-Free System↗
Methylome profiling of SetDB1-deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency.
SetDB1 is best known for catalyzing H3K9me3, but it also influences H3K27me3 deposition, CTCF-binding, and DNA methylation (DNAme). Given the interplay between DNAme and the other epigenetic features, we profiled DNAme following Setdb1 knockout (KO) in ground-state and serum-grown mouse embryonic stem cells (ESCs) to illuminate DNAme-dependent and -independent functions of SetDB1. Time-course whole-genome bisulfite sequencing of serum-grown ESCs shows that nearly half of SetDB1 binding sites are enriched with DNAme and H3K9me3, primarily at retrotransposons. Upon Setdb1 KO, both H3K9me3 and DNAme are reduced, with DNAme rapidly removed at many sites by TET enzymes. Some retrotransposons, primarily IAPs, are TET-resistant and lose DNAme slowly via passive dilution. Notably, SetDB1-mediated regulation of H3K27me3, CTCF-binding, and SMAD3 are uncoupled from the DNAme-H3K9me3 axis, and from each other. AlphaFold modeling and co-immunoprecipitation mass spectrometry suggest this uncoupling involves competitive binding to distinct SetDB1 protein domains, highlighting the complex coordination underlying SetDB1 functions.
AlphaFold modeling↗
[Genomic characteristics of multi-drug resistant of non-O1/non-O139 Vibrio cholerae ST1565 from sepsis cases].
To analyze the genomic characteristics of multi-drug resistant of non-O1/non-O139 Vibrio cholerae ST1565 from sepsis cases. An 88 years old male patient admitted to Huashan Hospital in Shanghai on July 2, 2025, who was retrospectively analyzed. The clinical diagnosis was severe bacterial enteritis and secondary NOVC sepsis. Blood culture confirmed the presence of non-O1/non-O139 group Vibrio cholerae. The strain was a multidrug-resistant isolated of ST1565 as determined by whole-genome sequencing. The ResFinder database predicted 11 resistance genes for 6 classes of antibiotics: qnrVC5, sul2, floR, tet(59), aph(6)-Id, aph(3'')-Ib, dfrA15, dfrA31, almE, almF, and almG. Except for the quinolone qnrVC5, which was not expressed, the other resistance genes were consistent matched the phenotypic results. Additionally, 8 insertion sequences were identified: ISVch1, ISVvu4, ISVch6, ISVvu8, ISVpa3, ISVpa4, ISVsa3, and ISShfr9. Important virulence factors included 3 secreted protein toxin genes: Vibrio cholerae hemolysin, repeat toxin, and Vibrio parahaemolyticus thermostable direct hemolysin. The patient was cured after sequential treatment with meropenem, levofloxacin, and doxycycline. NOVC/ST1565 is a newly identified sequence type in China, which exhibits multidrug-resistant and hypervirulent phenotypes.
Drug Resistance, Multiple, Bacterial↗
[Genome structure of influenza virus].
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Animals↗
Triethyltin sulfate-induced neuropathy in rats. Electrophysiologic, morphologic, and biochemical studies.
Adult rats given high orally administered doses of triethyltin (TET) sulfate lost weight, developed hind limb wasting, and became paraplegic or quadriplegic within three weeks of intoxication. A 33% reduction in the motor nerve conduction velocity (MNCV) of the sciatic nerve in the absence of significant demyelination was observed. There was observed, however, intramyelinic edema formation and an increased number of axonal neurofilaments and neurotubules; changes that paralleled the decrease in MNCV during the period of intoxication. Although the animals became asymptomatic and the MNCV normalized within two to three weeks of discontinuing the TET intoxication, the intramyelinic vacuoles and the increased numbers of neurofilaments and neurotubules persisted.
Animals↗
Preparation of competent single-cell suspensions of Mycoplasma hominis tets and Mycoplasma salivarium tets for genetic transformation to tetracycline resistance by DNA extracted from Mycoplamsa hominis tetr.
DNA extracted from Mycomplasma hominis (Sprott strain), resistant to 100 micrograms of tetracycline/ml transformed M. hominis strain H29 and Mycoplasma salivarium strain S9, which are sensitive to 2.5 and 5.0 micrograms of tetracycline/ml, respectively, to resistance. The transformants were selected on agar medium containing 10 micrograms of tetracycline/ml. Some transformants were resistant also to 20 micrograms of tetracycline/ml, a finding confirming that transformation occurred between homologous and heterologous species and that resistance is stepwise and controlled by several genetic loci. Medium containing 10 micrograms of tetracycline/ml was bacteriostatic. Prototype experiments employing mixtures of strains that were tetr and tets (tetracycline-resistant and tetracycline-sensitive, respectively) demonstrated that tetr mutants and transformants formed typical fried-egg colonies when mixtures containing not more than 10(9) mycoplasmas were spread on tetracycline agar plates. No mutants to tetracycline resistance were detected. Both M. hominis and M. salivarium were competent after treatment with MgCl2 and CaCl2, while Mycoplasma orale type 2 was inactivated. During DNA extraction different quantities of DNA formed insoluble precipitates with protein, thus preventing quantitative experiments.
Calcium Chloride↗
Specificity of the bacteriophage lambda N gene product (pN): nut sequences are necessary and sufficient for antitermination by pN.
We have cloned the nutR site together with the tR1 site of bacteriophage lambda in the E. coli galactose operon to examine whether the lambda promoter sequences PR and PL are involved in the recognition specificity of the lambda N gene product (pN). We first constructed a derivative of plasmid pBR322 in which the expression of the tetracycline genes (tet) is controlled by the gal promoter (Pgal). This new plasmid contains a unique Hind III site between Pgal and tet into which the nutR and tR1 sites were introduced. The order of the relevant genetic markers in this second plasmid is Pgal-nutR-tR1-tet. Cells transformed with this plasmid express tet only if pN is provided and if the plasmid contains an intact gal promoter. Our data suggest that transcription which originates at Pgal is modified by pN at nutR, enabling it to pass through tR1 into tet. We conclude that promoters do not play a specific role in pN recognition and that nut sequences are both necessary and sufficient for pN action.
Bacteriophage lambda↗
Integrating advanced analytical methods to assess epigenetic marks affecting response to hypomethylating agents in higher risk myelodysplastic syndrome.
BACKGROUND: Patients with higher-risk (HR) myelodysplastic syndrome (MDS), ineligible for allogeneic hematopoietic stem cell transplantation (alloHSCT), require prompt therapeutic interventions, such as treatment with hypomethylating agents (HMAs) to restore normal DNA methylation patterns, mainly of oncosuppressor genes, and consequently to delay disease progression and increase overall survival (OS). However, response assessment to HMA treatment relies on conventional methods with limited capacity to uncover a wide spectrum of underlying molecular events. METHODS: We implemented liquid chromatography-tandem mass spectrometry (LC-MS/MS) to assess 5' methyl-2' deoxycytidine (5mdC), 5' hydroxy-methyl-2'-deoxycytidine (5hmdC) levels and global adenosine/thymidine ([dA]/[T]) ratio in bone marrow aspirates from twenty-one HR MDS patients, pre- and post-HMA treatment. Additionally, targeted methylation analysis was performed by interpretation of NGS-methylation (MeD-seq) data obtained from the same patient cohort. RESULTS: LC/MS-MS analysis revealed a significant hypomethylation status in responders (Rs), already established at baseline and a trend for further DNA methylation reduction post-HMA treatment. Non-responders (NRs) reached statistical significance for DNA hypomethylation only post-HMA treatment. The 5hmdC epigenetic mark was approximately detected at 37.5-40% among NRs and Rs, implying the impairment of the natural active demethylation pathway, mediated by the ten-eleven (TET) 5mdC dioxygenases. R and NR subgroups displayed a [dA]/[T] ratio < 1 (0.727 - 0.633), supporting high frequences of 5mdC transition to thymidine. Response to treatment, according to whole genome MeD-seq data analysis, was associated with specific, scattered hypomethylated DMRs, rather than presenting a global effect across genome. MeD-seq analysis identified divergent epigenetic effects along chromosomes 7, 9, 12, 16, 18, 21, 22, X and Y. Within statistically significant selected chromosomal bins, genes encoding for proteins and non-coding RNAs with reversed methylation profiles between Rs and NRs, were highlighted. CONCLUSIONS: Implementation of powerful analytical tools to identify the dynamic DNA methylation changes in HR MDS patients undergoing HMA therapy demonstrated that LC-MS/MS exerts high efficiency as a broad-based but rapid and cost-effective methodology (compared to MeD-seq) to decode different perspectives of the epigenetic background of HR MDS patients and possess discriminative efficacy of the response phenotype to HMA treatment.
Humans↗
Biomolecular Condensates Integrate Transcriptional and Epigenetic Responses to Hypoxia.
Hypoxia is a defining feature of physiological stress and the core of solid tumors, where aberrant vascularization limits oxygen delivery; cells respond through mechanisms that extend beyond the canonical stabilization of hypoxia-inducible factors (HIFs). Recent studies suggest that hypoxia can promote the formation of specific biomolecular conden-sates, membraneless compartments generated through liquid-liquid phase separation in which regulatory proteins and RNAs become locally enriched at genomic regions, while chromatin mainly serves as an organizational scaffold. Transcription factors, the coacti-vators p300/CBP, Mediator, and BRD4, chromatin-modifying enzymes, and architectural RNAs such as NEAT1 and MALAT1 partition into these compartments, and their con-densation can help reorganize local chromatin structure and enhancer-promoter interac-tions. Because molecular oxygen is a shared co-substrate for the Jumonji-C histone demethylases and the ten-eleven translocation (TET) DNA dioxygenases, hypoxia reshapes histone methylation and DNA methylation in parallel, and readers that bridge these marks, including UHRF1, may participate in condensate-associated chromatin regulation. Hypoxia-driven condensation of ZHX2 rewires enhancer-promoter contacts and higher-order genome architecture, influencing cell identity, stemness, and metastatic potential, and Polycomb condensates represent another candidate epigenetic compartment that may be influenced by hypoxic signaling. These processes may be particularly important in cancer, where chronic hypoxia provides a sustained stimulus for condensate formation and epigenetic remodeling. Together, these findings support a model in which phase separation and epigenetic reprogramming are not separate layers but one integrated response to low oxygen, offering opportunities to target maladaptive condensates in disease.
Epigenesis, Genetic↗