Regulation Of Transcription Initiation Research Articles

House of CarDs: Functional insights into the transcriptional regulator CdnL.

Regulation of bacterial transcription is a complex and multi-faceted phenomenon that is critical for growth and adaptation. Proteins in the CarD_CdnL_TRCF family are widespread, often essential, regulators of transcription of genes required for growth and metabolic homeostasis. Research in the last decade has described the mechanistic and structural bases of CarD-CdnL-mediated regulation of transcription initiation. More recently, studies in a range of bacteria have begun to elucidate the physiological roles of CarD-CdnL proteins as well as mechanisms by which these proteins, themselves, are regulated. A theme has emerged wherein regulation of CarD-CdnL proteins is central to bacterial adaptation to stress and/or changing environmental conditions.

MSC-derived mitochondria promote axonal regeneration via Atf3 gene up-regulation by ROS induced DNA double strand breaks at transcription initiation region

BackgroundThe repair of peripheral nerve injury poses a clinical challenge, necessitating further investigation into novel therapeutic approaches. In recent years, bone marrow mesenchymal stromal cell (MSC)-derived mitochondrial transfer has emerged as a promising therapy for cellular injury, with reported applications in central nerve injury. However, its potential therapeutic effect on peripheral nerve injury remains unclear.MethodsWe established a mouse sciatic nerve crush injury model. Mitochondria extracted from MSCs were intraneurally injected into the injured sciatic nerves. Axonal regeneration was observed through whole-mount nerve imaging. The dorsal root ganglions (DRGs) corresponding to the injured nerve were harvested to test the gene expression, reactive oxygen species (ROS) levels, as well as the degree and location of DNA double strand breaks (DSBs).ResultsThe in vivo experiments showed that the mitochondrial injection therapy effectively promoted axon regeneration in injured sciatic nerves. Four days after injection of fluorescently labeled mitochondria into the injured nerves, fluorescently labeled mitochondria were detected in the corresponding DRGs. RNA-seq and qPCR results showed that the mitochondrial injection therapy enhanced the expression of Atf3 and other regeneration-associated genes in DRG neurons. Knocking down of Atf3 in DRGs by siRNA could diminish the therapeutic effect of mitochondrial injection. Subsequent experiments showed that mitochondrial injection therapy could increase the levels of ROS and DSBs in injury-associated DRG neurons, with this increase being correlated with Atf3 expression. ChIP and Co-IP experiments revealed an elevation of DSB levels within the transcription initiation region of the Atf3 gene following mitochondrial injection therapy, while also demonstrating a spatial proximity between mitochondria-induced DSBs and CTCF binding sites.ConclusionThese findings suggest that MSC-derived mitochondria injected into the injured nerves can be retrogradely transferred to DRG neuron somas via axoplasmic transport, and increase the DSBs at the transcription initiation regions of the Atf3 gene through ROS accumulation, which rapidly release the CTCF-mediated topological constraints on chromatin interactions. This process may enhance spatial interactions between the Atf3 promoter and enhancer, ultimately promoting Atf3 expression. The up-regulation of Atf3 induced by mitochondria further promotes the expression of downstream regeneration-associated genes and facilitates axon regeneration.

Abstract 1702: Loss of KEAP1 promotes R-loop formation independent of NRF2

Abstract This study investigates the mechanism of R-loop formation as a consequence of KEAP1 depletion. R-loops, described as three-stranded nucleic acid structures consisting of a DNA:RNA hybrid and a non-template single-stranded DNA, are assemblies often attributed with pathological consequences like genomic instability and replication stress. However, they have significant physiological roles, inter alia, regulation of transcription initiation, splicing and termination. Loss in R-loop resolution factors (like RNaseH nucleases, senataxin) can result in “unscheduled” or “pathological” R-loops, which can compromise genome stability. R-loops are commonly associated with an active transcription bubble, with nascent RNA trailing the RNA polymerase re-annealing to the template DNA strand. Increased transcriptional stress can lead to accumulation of R-loops. In a 2016 eLife study by Stork et al., estrogen induction resulted in concomitantly increased transcription and R-loop formation in the same subset of genes. Similar to estrogen induction, activation of the NRF2/KEAP1 pathway upon oxidative stress causes NRF2 to be released from KEAP1 and enter the nucleus to turn on transcription of its target genes. Kelch-like ECH associated protein 1, encoded by the KEAP1 gene, is a canonical binding partner of NRF2. Under basal conditions, KEAP1 binds NRF2 and targets it for degradation. Mutations in KEAP1 and epigenetic modifications have been reported in lung and breast cancer phenotypes. In lieu of chemical manipulation, NRF2 can be activated by knocking down KEAP1 via RNAi. We therefore asked whether transcription activation downstream of the NRF2/KEAP1 pathway can lead to accumulation of R-loops.We have observed the consequences of depleting KEAP1 (for NRF2 activation) with RNAi on global transcription using ethynyl uridine (EU) incorporation with click-iT chemistry and flow cytometry, on R-loop levels using S9.6 antibody immunocytochemistry and on transcriptional profile changes with RNA-seq. We observe that loss of KEAP1 leads to an increased accumulation of R-loops. Surprisingly, this is not accompanied by an expected increase in transcription as measured quantitatively with EU flow cytometry. This phenomenon was found to consistently occur in various cell lines across cancer types (breast, lung). Interestingly, depleting NRF2 cannot mitigate the effects of KEAP1 loss, suggesting that KEAP1 loss-associated R-loop formation is independent of NRF2 activation. Analysis of RNA-seq data shows that TOP2 is downregulated in KEAP1 deficient cells. As TOP2 has been previously known to regulate R-loop formation, we predict that KEAP1 loss can sensitize cells to topoisomerase inhibitors.In conclusion, interaction of KEAP1 with other players in its interactome outside of NRF2 may regulate R-loop formation and therefore R-loop-induced genome instability. Citation Format: Pramiti Mukhopadhyay, Nicklas Bassani, Alexander J. Bishop. Loss of KEAP1 promotes R-loop formation independent of NRF2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1702.

Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types.

Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of Escherichia coli K-12. An RI groups the transcription factor, its effect (positive or negative) and the regulated target, a promoter, a gene or transcription unit. We improved the evidence codes so that specific methods are incorporated and classified into independent groups. On this basis we updated the computation of confidence levels, weak, strong, or confirmed, for the collection of RIs. These updates enabled us to map the RI set to the current collection of HT TF-binding datasets from ChIP-seq, ChIP-exo, gSELEX and DAP-seq in RegulonDB, enriching in this way the evidence of close to one-quarter (1329) of RIs from the current total 5446 RIs. Based on the new computational capabilities of our improved annotation of evidence sources, we can now analyze the internal architecture of evidence, their categories (experimental, classical, HT, computational), and confidence levels. This is how we know that the joint contribution of HT and computational methods increase the overall fraction of reliable RIs (the sum of confirmed and strong evidence) from 49% to 71%. Thus, the current collection has 3912 reliable RIs, with 2718 or 70% of them with classical evidence which can be used to benchmark novel HT methods. Users can selectively exclude the method they want to benchmark, or keep for instance only the confirmed interactions. The recovery of regulatory sites in RegulonDB by the different HT methods ranges between 33% by ChIP-exo to 76% by ChIP-seq although as discussed, many potential confounding factors limit their interpretation. The collection of improvements reported here provides a solid foundation to incorporate new methods and data, and to further integrate the diverse sources of knowledge of the different components of the transcriptional regulatory network. There is no other genomic database that offers this comprehensive high-quality architecture of knowledge supporting a corpus of transcriptional regulatory interactions.

Precision run-on sequencing (PRO-seq) for microbiome transcriptomics.

Bacteria respond to environmental stimuli through precise regulation of transcription initiation and elongation. Bulk RNA sequencing primarily characterizes mature transcripts, so to identify actively transcribed loci we need to capture RNA polymerase (RNAP) complexed with nascent RNA. However, such capture methods have only previously been applied to culturable, genetically tractable organisms such as E. coli and B. subtilis. Here we apply precision run-on sequencing (PRO-seq) to profile nascent transcription in cultured E. coli and diverse uncultured bacteria. We demonstrate that PRO-seq can characterize the transcription of small, structured, or post-transcriptionally modified RNAs, which are often absent from bulk RNA-seq libraries. Applying PRO-seq to the human microbiome highlights taxon-specific RNAP pause motifs and pause-site distributions across non-coding RNA loci that reflect structure-coincident pausing. We also uncover concurrent transcription and cleavage of CRISPR guide RNAs and transfer RNAs. We demonstrate the utility of PRO-seq for exploring transcriptional dynamics in diverse microbial communities.

Reporting Two Rare Mutations With Associated Clinical Features in Bangladeshi Hb E/B Thalassemia Patients

Thalassemia is one of the most common genetic disorders in Bangladesh. We have performed an investigation among 360 patients with Hb E/β-thalassemia to understand the heterogeneity in thalassemia severity among Bangladeshi patients. The analysis revealed that one of the common mutations CD26 (G>A) is found with two rare mutations HBB: c.-79A>G (-29A>G) and HBB: c.45_46insG (CD14/15 (+G)) in two patients individually which are not prevalent in geographically adjacent populations. Among these two rare mutations, -29A>G is located at the ‘TATA’ box region of the promoter sequence regulating transcription initiation and CD14/15 (+G) leads to a premature stop codon. We performed transcription factor binding site prediction analysis and found that ‘AP-1’, ‘c-Jun’, and ‘kr’ transcription factors bind at the ‘TATA’ box region. From this analysis, we can predict that -29A>G mutation can alter the level of HBB transcription whereas the CD14/15 (+G) mutation causes a truncated (and possibly non-functional) HBB protein. Aligned with such assumption, it was observed from patients’ medical history that, the patient who had CD14/15 (+G) and CD26 (G>A) mutations was severely blood transfusion-dependent whereas the patient carrying -29A>G and CD26 (G>A) mutations was moderately transfusion dependent. The comprehensive analysis of the mutations offers crucial insights and approaches for enhanced management of thalassemia among the Bangladeshi population. Bioresearch Commu. 10(1): 1442-1448, 2024 (January)

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrievaland accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0can be accessed at https://regulondb.ccg.unam.mx.

EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning

BackgroundN6, 2'-O-dimethyladenosine (m6Am) is an abundant RNA methylation modification on vertebrate mRNAs and is present in the transcription initiation region of mRNAs. It has recently been experimentally shown to be associated with several human disorders, including obesity genes, and stomach cancer, among others. As a result, N6,2′-O-dimethyladenosine (m6Am) site will play a crucial part in the regulation of RNA if it can be correctly identified.ResultsThis study proposes a novel deep learning-based m6Am prediction model, EMDL_m6Am, which employs one-hot encoding to expressthe feature map of the RNA sequence and recognizes m6Am sites by integrating different CNN models via stacking. Including DenseNet, Inflated Convolutional Network (DCNN) and Deep Multiscale Residual Network (MSRN), the sensitivity (Sn), specificity (Sp), accuracy (ACC), Mathews correlation coefficient (MCC) and area under the curve (AUC) of our model on the training data set reach 86.62%, 88.94%, 87.78%, 0.7590 and 0.8778, respectively, and the prediction results on the independent test set are as high as 82.25%, 79.72%, 80.98%, 0.6199, and 0.8211.ConclusionsIn conclusion, the experimental results demonstrated that EMDL_m6Am greatly improved the predictive performance of the m6Am sites and could provide a valuable reference for the next part of the study. The source code and experimental data are available at: https://github.com/13133989982/EMDL-m6Am.

Mechanisms and regulation of human mitochondrial transcription.

The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.

Targeted RNAi screen identifies transcriptional mechanisms that prevent premature degeneration of adult photoreceptors.

Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to identify the transcriptional mechanisms that are necessary to maintain photoreceptor viability and function during aging. To do this, we performed a targeted photoreceptor-specific RNAi screen in Drosophila to identify transcriptional regulators whose knockdown results in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of transcription factors, chromatin remodelers, and histone modifiers, we identified 18 high-confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. These 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show similar changes in gene expression to those observed in photoreceptors with advanced age. Together, our data suggest that dysregulation of factors involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate but might also contribute to an increased risk of retinal degeneration.

Structural basis of transcription reduction by a promoter-proximal +1 nucleosome

At active human genes, the+1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiationcomplex (PIC). However, at inactive genes, the+1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal+1 nucleosome can reduce RNA synthesis invivo and invitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the+1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.

Circ‐myh8 Promotes Pulmonary Hypertension by Recruiting KAT7 to Govern Hypoxia‐Inducible Factor‐1α Expression

Background Aberrant expression of circular RNAs (circRNAs) contributes to the initiation and progression of pulmonary hypertension (PH). Hypoxia-inducible factor (HIF) is a well-known modulator of hypoxia-induced PH. The role and underlying mechanism of circRNAs in the regulation of HIF expression remains elusive. Methods and Results We profiled pulmonary artery transcriptomes using RNA sequencing and screened circRNAs associated with hypoxia treatment. The expression of a novel circRNA, circ_chr11_67292179-67294612 (circ-myh8), was increased by hypoxia in a time-dependent manner. We evaluated the effects of circ-myh8 overexpression by adeno-associated virusor inhibition by short hairpin RNA on proliferation and cell cycling in mice and pulmonary artery smooth muscle cells. Overexpression of circ-myh8 promotes PH under normoxia, and disruption of circ-myh8 by short hairpin RNA mitigates PH in chronic hypoxic mice. Biologically, circ-myh8 induces the proliferation and cell-cycle progression of pulmonary artery smooth muscle cells in vivo and in vitro. Mechanistically, RNA pull-down and RNA immunoprecipitation assays were used to examine the interaction of circRNAs with the binding protein KAT7 (lysine acetyltransferase 7). The acetylation level of lysine 5 of histone H4 in the transcriptional initiation region of HIF1α was determined by chromatin immunoprecipitation assay followed by reverse transcription-quantitativepolymerase chain reaction. Circ-myh8 acts as a modular scaffold to recruit histone acetyltransferase KAT7 to the promoters of HIF1α, which elicits acetylation of lysine 5 of histone H4 in their promoters. Conclusions Our findings not only reveal the pivotal roles of circ-myh8 in governing histone modification in anti-PH treatment but also advocate triggering the circ-myh8/KAT7/HIF1α pathway to combat PH.

Effective Quality Breeding Directions-Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds.

The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.

Core promoter in TNBC is highly mutated with rich ethnic signature.

The core promoter plays an essential role in regulating transcription initiation by controlling the interaction between transcriptional factors and sequence motifs in the core promoter. Although mutation in core promoter sequences is expected to cause abnormal gene expression leading to pathogenic consequences, limited supporting evidence showed the involvement of core promoter mutation in diseases. Our previous study showed that the core promoter is highly polymorphic in worldwide human ethnic populations in reflecting human history and adaptation. Our recent characterization of the core promoter in triple-negative breast cancer (TNBC), a subtype of breast cancer, in a Chinese TNBC cohort revealed the wide presence of core promoter mutation in TNBC. In the current study, we analyzed the core promoter in a Thai TNBC cohort. We also observed rich core promoter mutation in the Thai TNBC patients. We compared the core promoter mutations between Chinese and Thai TNBC cohorts. We observed substantial differences of core promoter mutation in TNBC between the two cohorts, as reflected by the mutation spectrum, mutation-effected gene and functional category, and altered gene expression. Our study confirmed that the core promoter in TNBC is highly mutable, and is highly ethnic-specific.

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes.

PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T-regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

Structures of +1 nucleosome-bound PIC-Mediator complex.

RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation.

The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex.

Transcription must be properly regulated to ensure dynamic gene expression underlying growth, development, and response to environmental cues. Regulation is imposed throughout the transcription cycle, and while many efforts have detailed the regulation of transcription initiation and early elongation, the termination phase of transcription also plays critical roles in regulating gene expression. Transcription termination can be driven by only a few proteins in each domain of life. Detailing the mechanism(s) employed provides insight into the vulnerabilities of transcription elongation complexes (TECs) that permit regulated termination to control expression of many genes and operons. Here, we describe the biochemical activities and crystal structure of the superfamily 2 helicase Eta, one of two known factors capable of disrupting archaeal transcription elongation complexes. Eta retains a twin-translocase core domain common to all superfamily 2 helicases and a well-conserved C terminus wherein individual amino acid substitutions can critically abrogate termination activities. Eta variants that perturb ATPase, helicase, single-stranded DNA and double-stranded DNA translocase and termination activities identify key regions of the C terminus of Eta that, when combined with modeling Eta-TEC interactions, provide a structural model of Eta-mediated termination guided in part by structures of Mfd and the bacterial TEC. The susceptibility of TECs to disruption by termination factors that target the upstream surface of RNA polymerase and potentially drive termination through forward translocation and allosteric mechanisms that favor opening of the clamp to release the encapsulated nucleic acids emerges as a common feature of transcription termination mechanisms.

IFN-γ and LPS Induce Synergistic Expression of CCL2 in Monocytic Cells via H3K27 Acetylation.

BackgroundOverexpression of CCL2 (MCP-1) has been implicated in pathogenesis of metabolic conditions, such as obesity and T2D. However, the mechanisms leading to increased CCL2 expression in obesity are not fully understood. Since both IFN-γ and LPS levels are found to be elevated in obesity and shown to be involved in the regulation of metabolic inflammation and insulin resistance, we investigated whether these two agents could synergistically trigger the expression of CCL2 in obesity.MethodsMonocytes (Human monocytic THP-1 cells) were stimulated with IFN-γ and LPS. CCL2 gene expression was determined by real-time RT-PCR. CCL2 protein was determined by ELISA. Signaling pathways were identified by using epigenetic inhibitors and STAT1 siRNA. Acetylation of H3K27 was analyzed by Western blotting. The acetylation level of histone H3K27 in the transcriptional initiation region of CCL2 gene was determined by ChIP-qPCR.ResultsOur results show that the co-incubation of THP-1 monocytes with IFN-γ and LPS significantly enhanced the expression of CCL2, compared to treatment with IFN-γ or LPS alone. Similar results were obtained using primary monocytes and macrophages. Interestingly, IFN-γ priming was found to be more effective than LPS priming in inducing synergistic expression of CCL2. Moreover, STAT1 deficiency significantly suppressed this synergy for CCL2 expression. Mechanistically, we showed that IFN-γ priming induced acetylation of lysine 27 on histone 3 (H3K27ac) in THP-1 cells. Chromatin immunoprecipitation (ChIP) assay followed by qRT-PCR revealed increased H3K27ac at the CCL2 promoter proximal region, resulting in stabilized gene expression. Furthermore, inhibition of histone acetylation with anacardic acid suppressed this synergistic response, whereas trichostatin A (TSA) could substitute IFN-γ in this synergy.ConclusionOur findings suggest that IFN-γ, in combination with LPS, has the potential to augment inflammation via the H3K27ac-mediated induction of CCL2 in monocytic cells in the setting of obesity.

The frequency of rare ALK fusions and their clinical significance in NSCLC.

e21012 Background: ALK fusion is one of the key driver mechanisms in non-small cell lung cancer. In some case reports, some rare mutant forms have also been found to be active and drug-susceptible. There are few reports on the detection and verification methods of rare ALK fusions. Here, we counted the rare fusions of ALK detected by NGS and verified them by other methods. Methods: We analyzed 184 patients with NSCLC harboring ALK-rearrangement detected by NGS from January 2020 to January 2022. We counted the rare ALK fusion forms, and selected two of them for verification by RNA sequencing or immunohistochemistry. Results: Of the 184 patients with ALK fusion that we included, 105 were female and 79 were male (medium age 53). Most female were non-smokers except one while nearly 50% male were smokers. EML4-ALK fusion accounted for the highest proportion (170, 92.4%), 5 were ALK fusions with other 5’ partners ( C2orf44, KCNG3, KIF5B, KDM5A, DCTN1), 6 were intergenic region- ALK rearrangements, 2 were fusions without transcription initiation region, and 1 was LOC399815 -ALK and ALK-EML4 double fusion. Rare fusion forms accounted for less than 10%. We further verified two of these rare fusion mutations by RNA sequencing or immunohistochemistry. Interestingly, one of the patients with a KCNG3-exon1- ALK-exon20 fusion detected by DNA sequencing was confirmed to be an EML4-ALK fusion by RNA sequencing, and another patient with an intergenic region- ALK fusion was confirmed positive by immunohistochemistry. Conclusions: The vast majority of ALK fusions are EML4-ALK fusions, but there are a small number of other forms of fusions. DNA sequencing, RNA sequencing and ICH may give different conclusions for ALK fusions, which may be limited by the detection method. For some rare fusion forms, a variety of methods can be used to detect whether it is an active ALK fusion form.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.

Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.