Effects of topological domain disruption on transcriptional regulation are chromatin context dependent.

Perfluorooctanoic acid disrupts thyroid-specific genes expression and regulation via the TSH-TSHR signaling pathway in thyroid cells

The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin

We report here the identification of four gene functions of principal importance for the tolerance of meropenem stress in Escherichia coli: cell division, cell envelope synthesis and maintenance, ATP metabolism, and transcription regulation. The primary mechanism of β-lactam antibiotics such as meropenem is inhibition of penicillin binding proteins, thus interfering with peptidoglycan crosslinking, weakening the cell envelope, and promoting cell lysis. However, recent systems biology approaches have revealed numerous downstream effects that are triggered by cell envelope damage and involve diverse cell processes. Subpopulations of persister cells can also arise, which can survive elevated concentrations of meropenem despite the absence of a specific resistance factor. We used Transposon-Directed Insertion Sequencing with inducible gene expression to simultaneously assay the effects of upregulation, downregulation, and disruption of every gene in a model E. coli strain on survival of exposure to four concentrations of meropenem. Automated Gene Functional Classification and manual categorization highlighted the importance at all meropenem concentrations of genes involved in peptidoglycan remodeling during cell division, suggesting that cell division is the primary function affected by meropenem. Genes involved in cell envelope synthesis and maintenance, ATP metabolism, and transcriptional regulation were generally important at higher meropenem concentrations, suggesting that these three functions are therefore secondary or downstream targets. Our analysis revealed the importance of multiple two-component signal transduction mechanisms, suggesting an as-yet unexplored coordinated transcriptional response to meropenem stress. The inclusion of an inducible, transposon-encoded promoter allowed sensitive detection of genes involved in proton transport, ATP production and tRNA synthesis, for which modulation of expression affects survival in the presence of meropenem: a finding that would not be possible with other technologies. We were also able to suggest new targets for future antibiotic development or for synergistic effects between gene or protein inhibitors and existing antibiotics. Overall, in a single massively parallel assay we were able to recapitulate many of the findings from decades of research into β-lactam antibiotics, add to the list of genes known to be important for meropenem tolerance, and categorize the four principal gene functions involved.

Coxsackievirus and adenovirus receptor (CAR) is a junction molecule that expresses on Sertoli and germ cells. It mediates Sertoli-germ cell adhesion and facilitates migration of preleptotene/leptotene spermatocytes across the blood-testis barrier, suggesting that CAR-based cell adhesion and migration are crucial for spermatogenesis. Interferon-gamma (IFNG) and tumor necrosis factor alpha (TNF) are two major cytokines that are elevated during testicular inflammation and cause reduced fertility. We investigated the mechanism by which IFNG and TNF exert their disruptive effects on testicular cell adhesion. We have demonstrated that combined treatment with IFNG and TNF (IFNG+TNF) exerts a synergistic effect by downregulating CAR mRNA and protein levels. Immunofluorescence staining revealed that IFNG+TNF treatment effectively removes CAR from the site of cell-cell contact. Using inhibitor and co-immunoprecipitation, we confirmed that IFNG+TNF mediates CAR protein degradation via ubiquitin-proteasome and NFKB pathways. Blockage of ubiquitin-proteasome pathway significantly inhibits CAR degradation, as indicated by the reappearance of CAR at the site of cell-cell contact. Additionally, IFNG+TNF reduces CAR mRNA via transcriptional regulation. Mutational studies have shown that IFNG+TNF-induced CAR repression is achieved by suppression of the basal transcription. Electrophoretic mobility shift assay and chromatin immunoprecipitation assays further confirmed that IFNG+TNF treament not only inhibits binding of the basal transcription factors but also promotes binding of NFKB subunits and Sp1 (negative regulators) to the CAR promoter region. Taken together, IFNG+TNF treatment significantly downregulates CAR expression, which provides an explanation of how cell sloughing in the epithelium mediates, by loss of CAR-based cell adhesion, during testicular inflammation.

Identification of toxic substances considering circadian disruption: an integrated approach combining reduced transcriptomic analysis, behavioral monitoring, and time-course gene expression profiling.

<h3>Abstract</h3> In <i>Escherichia coli</i>, translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regulation, we develop a spatially resolved supercoiling model of transcription, describing RNAP-supercoiling interactions, topoisomerase activities, stochastic topological domain formation, and supercoiling diffusion in all transcription stages. This model establishes that transcription-induced supercoiling mediates the cooperation of co-transcribing RNAP molecules in highly expressed genes. It reveals that supercoiling transmits RNAP-accessible information through DNA and enables different RNAP molecules to communicate within and between genes. It thus predicts that a topological domain could serve as a transcription regulator, generating substantial transcription bursting and coordinating communications between adjacent genes in the domain. The model provides a quantitative platform for further theoretical and experimental investigations of how genome organization impacts transcription. <h3>Author Summary</h3> DNA mechanics and transcription dynamics are intimately coupled. During transcription, the translocation of RNA polymerase overwinds the DNA ahead and underwinds the DNA behind, rendering the DNA supercoiled. The supercoiled DNA could, in return, influences the behavior of the RNA polymerase, and consequently the amount of mRNA product it makes. Furthermore, supercoils could propagate on the DNA over thousands of base pairs, impacting RNA polymerase molecules at faraway sites. These complicated interplays between supercoiling and RNA polymerase makes supercoiling an important transcription regulator. To quantitatively investigate the role of supercoiling in transcription, we build a spatially resolved model that links transcription with the generation, propagation, and dissipation of supercoiling. Our model reveals that supercoiling mediates transcription at multiple length scales. At a single-gene scale, we show that supercoiling gives rise to the collective motion of co-transcribing RNA polymerase molecules, supporting recent experimental observations. Additionally, large variations in mRNA production of a gene can arise from the constraints of supercoiling diffusion in a topological domain. At a multi-gene scale, we show that supercoiling dynamics allow two adjacent genes influence each other’s transcription kinetics, thus serving as a transcription regulator.

Transforming growth factor (TGF)-β induces various cellular responses principally through Smad-dependent transcriptional regulation. Activated Smad complexes cooperate with transcription factors in regulating a group of target genes. The target genes controlled by the same Smad-cofactor complexes are denoted a synexpression group. We found that an Id-like helix-loop-helix protein, human homologue of Maid (HHM), is a synexpression group-restricted regulator of TGF-β signalling. HHM suppressed TGF-β-induced growth inhibition and cell migration but not epithelial–mesenchymal transition. In addition, HHM inhibited TGF-β-induced expression of plasminogen activator inhibitor-type 1 (PAI-1), PDGF-B, and p21WAF, but not Snail. We identified a basic-helix-loop-helix protein, Olig1, as one of the Smad-binding transcription factors affected by HHM. Olig1 interacted with Smad2/3 in response to TGF-β stimulation, and was involved in transcriptional activation of PAI-1 and PDGF-B. HHM, but not Id proteins, inhibited TGF-β signalling-dependent association of Olig1 with Smad2/3 through physical interaction with Olig1. HHM thus appears to regulate a subset of TGF-β target genes including the Olig1-Smad synexpression group. HHM is the first example of a cellular response-selective regulator of TGF-β signalling with clearly determined mechanisms.

The development of normal pregnancy at early stages is conditioned by epigenetic programs and is impossible without proper formation of the placenta and embryo. In the first trimester, epigenetic mechanisms are involved in these processes, one of which is DNA methylation. DNA methylation is involved in the regulation of various biological processes, such as cell differentiation and development, regulation of gene expression (as a rule, genes with reduced methylation levels in promoters are expressed), X-chromosome inactivation, genome imprinting, maintenance of chromosome stability, and others. Disruption of this process can lead to the formation of pathologic phenotypes such as spontaneous abortion (SA), pre-eclampsia (PE), and gestational diabetes mellitus (GDM). Currently, researchers have found many methylation abnormalities in these pathologies: for example, 54 differentially methylated regions (DMRs) associated with blood pressure, 1703 differentially methylated sites (DMSs) in early-onset pre-eclampsia, more than 200 DMRs in gestational diabetes mellitus, and 4 differentially expressed genes associated with spontaneous abortion have been identified in the trophoblast of chorionic villi. The emerging findings in such studies indicate that some epigenetic abnormalities and gene expression disorders may be involved in the development of gestational pathologies, affecting the cause of their formation -abnormal placentation. The methylation abnormalities observed in the considered pathologies of pregnancy may be particular cases of more general placental methylome disorders, the severity of phenotypic manifestation of which may vary from embryo death at early stages of development to term delivery. Given this and current theories of the pathogenesis of these diseases based on disorders of trophoblast development, it can be assumed that these pathologies may share common DNA methylation alterations. On the other hand, differences in the severity of clinical manifestations suggest the presence of unique methylation patterns, particularly in spontaneous abortion as an extreme manifestation of the phenotype. Detection of such abnormalities will have important diagnostic value for prognosis and preservation of pregnancy. In this study, we comparatively analysed differential DNA methylation data in chorionic villi from PE, GDM and SA. Methylation data in PE and GSD were obtained from the publicly available Genome Expression Omnibus (GEO) data repository - GSE200659, GSE100197, and GSE98224 datasets. Data for SA were obtained using reduced representation bisulfite sequencing (RRBS) on spontaneous abortus material with normal karyotype (n = 7) compared to medical abortus (n = 7). Methylation data were analysed in R 4.3.0., using function packages in R (dplyr,data.table,tibble,tidyr,stringr, tibble) and function packages in UNIX (bedtools) and BMIQ and NOOB normalisation methods (function packages in R - ChAMP, minifi). Thus, 7 differentially methylated genes (DMGs) common to SA, PE and GDM were obtained: 3 hypomethylated genes - WDR5, TMC4, MIR4533; 3 hypermethylated genes - ADARB2, INPPP5E, TUBB4A; and 1 gene with different methylation differences in different parts of gene - PRDMl 6. There were 114 DMGs unique to SA: 32 hypomethylated and 81 hypermethylated genes. Enrichment analyses were performed using the DAVID v2024q2 database (https://da-vid.ncifcrf.gov/home.jsp). Common DMGs were found to be involved in pathways related to transmembrane transport processes, regulation of transcription and differentiation, RNA processing, cell adhesion, lipid metabolism and mitotic cycle regulation. DMGs unique to SA have been implicated in processes related to the regulation of transcription, translation, mitotic cycle, histogenesis, migration, cell proliferation and differentiation. Some of the unique DMGs, according to the mammalian phenotype database (https://www.informatics.jax.org/batch), were found to be associated with the em-bryolethality phenotype - LRRC8A, HDLBP, HIC1 and ST14, while others were involved in the process of placenta development - BOK, BOK-AS1. The analysis showed that the pathologies under consideration have common and unique patterns of differential DNA methylation. We identified 7 common (3 hypo-methylated, 3 hypermethylated and 1 with different methylation patterns) and 114 differentially methylated genes unique to SA (33 hypomethylated and 81 hypermethylated). However, the effects of methylation disruption of the identified genes remain unclear, and further studies at the transcriptional level in larger samples are needed. The article contains 15 References. The Authors declare no conflict of interest.

Transcription Dynamics

In Escherichia coli, translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regulation, we developed a spatially resolved supercoiling model of transcription. The integrated model describes how RNAP activity feeds back with the local DNA supercoiling and how this mechanochemical feedback controls transcription, subject to topoisomerase activities and stochastic topological domain formation. This model establishes that transcription-induced supercoiling mediates the cooperation of co-transcribing RNAP molecules in highly expressed genes, and this cooperation is achieved under moderate supercoiling diffusion and high topoisomerase unbinding rates. It predicts that a topological domain could serve as a transcription regulator, generating substantial transcriptional noise. It also shows the relative orientation of two closely arranged genes plays an important role in regulating their transcription. The model provides a quantitative platform for investigating how genome organization impacts transcription.

In Escherichia coli, translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regulation, we developed a spatially resolved supercoiling model of transcription. The integrated model describes how RNAP activity feeds back with the local DNA supercoiling and how this mechanochemical feedback controls transcription, subject to topoisomerase activities and stochastic topological domain formation. This model establishes that transcription-induced supercoiling mediates the cooperation of co-transcribing RNAP molecules in highly expressed genes, and this cooperation is achieved under moderate supercoiling diffusion and high topoisomerase unbinding rates. It predicts that a topological domain could serve as a transcription regulator, generating substantial transcriptional noise. It also shows the relative orientation of two closely arranged genes plays an important role in regulating their transcription. The model provides a quantitative platform for investigating how genome organization impacts transcription.

Self-compatibility in Arabidopsis thaliana represents the relatively recent disruption of ancestral obligate cross pollination, recognized as one of the prevalent evolutionary pathways in flowering plants, as noted by Darwin. Our previous study found that inversion of the male specificity gene (SP11/SCR) disrupted self-incompatibility, which was restored by overexpressing the SCR with the reversed inversion. However, SCR in A. thaliana has other mutations aside from the pivotal inversion, in both promoter and coding regions, with probable effects on transcriptional regulation. To examine the functional consequences of these mutations, we conducted reciprocal introductions of native promoters and downstream sequences from orthologous loci of self-compatible A. thaliana and self-incompatible A. halleri. Use of this inter-species pair enabled us to expand the scope of the analysis to transcriptional regulation and deletion in the intron, in addition to inversion in the native genomic background. Initial analysis revealed that A. thaliana has a significantly lower basal expression level of SCR transcripts in the critical reproductive stage compared to that of A. halleri, suggesting that the promoter was attenuated in inducing transcription in A. thaliana. However, in reciprocal transgenic experiments, this A. thaliana promoter was able to restore partial function if coupled with the functional A. halleri coding sequence, despite extensive alterations due to the self-compatible mode of reproduction in A. thaliana. This represents a synergistic effect of the promoter and the inversion resulting in fixation of self-compatibility, primarily enforced by disruption of SCR. Our findings elucidate the functional and evolutionary context of the historical transition in A. thaliana thus contributing to the understanding of the molecular events leading to development of self-compatibility.

Many products of secondary metabolism are activated by quorum sensing (QS), yet even at cell densities sufficient for QS, their production may be repressed under suboptimal growth conditions via mechanisms that still require elucidation. For many beneficial plant-associated bacteria, secondary metabolites such as phenazines are important for their competitive survival and plant-protective activities. Previous work established that phenazine biosynthesis in Pseudomonas chlororaphis 30-84 is regulated by the PhzR/PhzI QS system, which in turn is regulated by transcriptional regulator Pip, two-component system RpeA/RpeB and stationary phase/stress sigma factor RpoS. Disruption of MiaA, a tRNA modification enzyme, altered primary metabolism and growth leading to widespread effects on secondary metabolism, including reduced phenazine production and oxidative stress tolerance. Thus, the miaA mutant provided the opportunity to examine the regulation of phenazine production in response to altered metabolism and growth or stress tolerance. Despite the importance of MiaA for translation efficiency, the most significant effect of miaA disruption on phenazine production was the reduction in the transcription of phzR, phzI and pip, whereas neither the transcription nor translation of RpeB, a transcriptional regulator of pip, was affected. Constitutive expression of rpeB or pip in the miaA mutant completely restored phenazine production, but it resulted in further growth impairment. Constitutive expression of RpoS alleviated sensitivity to oxidative stress resulting from RpoS translation inefficiency in the miaA mutant, but it did not restore phenazine production. Our results support the model that cells curtail phenazine biosynthesis under suboptimal growth conditions via RpeB/Pip-mediated regulation of QS.

The X-linked neurological disorder Rett syndrome (RTT) presents with autistic features and is caused primarily by mutations in a transcriptional regulator, methyl CpG-binding protein 2 (MECP2). Current treatment options for RTT are limited to alleviating some neurological symptoms; hence, more effective therapeutic strategies are needed. We identified the protein tyrosine phosphatase PTP1B as a therapeutic candidate for treatment of RTT. We demonstrated that the PTPN1 gene, which encodes PTP1B, was a target of MECP2 and that disruption of MECP2 function was associated with increased levels of PTP1B in RTT models. Pharmacological inhibition of PTP1B ameliorated the effects of MECP2 disruption in mouse models of RTT, including improved survival in young male (Mecp2-/y) mice and improved behavior in female heterozygous (Mecp2-/+) mice. We demonstrated that PTP1B was a negative regulator of tyrosine phosphorylation of the tyrosine kinase TRKB, the receptor for brain-derived neurotrophic factor (BDNF). Therefore, the elevated PTP1B that accompanies disruption of MECP2 function in RTT represents a barrier to BDNF signaling. Inhibition of PTP1B led to increased tyrosine phosphorylation of TRKB in the brain, which would augment BDNF signaling. This study presents PTP1B as a mechanism-based therapeutic target for RTT, validating a unique strategy for treating the disease by modifying signal transduction pathways with small-molecule drugs.

Heme, an essential prosthetic group involved in mitochondrial respiration and transcriptional regulation, is synthesized via the rate-limiting enzyme 5-aminolevulinic acid synthase (ALAS). Utilizing heterozygous mouse models for ALAS1 and ALAS2, our studies have revealed diverse systemic consequences of chronic heme deficiency. ALAS1-heterozygous (ALAS1+/-) mice develop metabolic dysfunction characterized by insulin resistance, glucose intolerance, and abnormal glycogen accumulation, linked mechanistically to reduced AMP-activated protein kinase (AMPK) signaling. These mice also exhibit pronounced mitochondrial dysfunction, impaired autophagy, and accelerated aging phenotypes, including sarcopenia and metabolic decline, highlighting heme's role as a critical metabolic regulator. Additionally, ALAS2 heterozygosity (ALAS2+/-) leads to impaired erythropoiesis, resulting in anemia and ineffective iron utilization. Importantly, supplementation with the heme precursor 5-aminolevulinic acid (5-ALA) significantly mitigates ALAS1+/- phenotypes, restoring metabolic function, mitochondrial health, autophagy, and immune competence. This review encapsulates key findings from our group's research together with advances made by multiple research groups over the past decade, collectively establishing heme homeostasis as a central regulator of systemic physiology and highlighting the therapeutic potential of 5-ALA in treating heme-deficient pathologies.