Biology subjects

Shen, Y.

Publications and source records attributed to Shen, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Identification of novel components of the Ced and Ups systems in Saccharolobus islandicus REY15A

In the cells of Sulfolobales, the Ced (Crenarchaeal system for exchange of DNA) and Ups (UV-inducible pili of Sulfolobus) systems are highly induced by DNA damages and function in chromosomal DNA exchange by mediating DNA import and cell aggregation, respectively. The Ced system is composed of CedA, CedA1, CedA2, and CedB. The Ups is composed of UpsA, UpsB, UpsE and UpsF. However, how the DNA is transported by these systems is far from clear. Here, we report two novel components of the Ced system, CedD (SiRe_1715) and CedE (SiRe_2100), which are paralogs of CedB and CedA, respectively, and one new component of the Ups system, UpsC (SiRe_1957), which is a paralog of UpsA and UpsB, in Saccharolobus islandicus REY15A. DNA exchange assay revealed that cedD, cedE, and upsC are essential for DNA import while cedE and upsC are also important for DNA export. Further microscopy analysis revealed that upsC is involved in cell aggregation like other Ups genes. Besides, we found that cedB and cedD co-occur in the genomes of crenarchaea which lack virB4 and the presence of cedB and cedD, and virB4 is complementary. Both proteins show homology to different parts of the N-terminal domain of VirB4 in a complementary manner and form stable homo-oligomers in vitro. Collectively, our results indicate that CedD and CedE, and UpsC are essential components of the Ced and Ups systems, respectively.

microbiology↗

bioRxiv2024

Super-enhancer profiling reveals ThPOK/ZBTB7B, a CD4+ cell lineage commitment factor, as a master regulator that restricts breast cancer cells to a luminal non-migratory phenotype

Despite efforts to understand breast cancer biology, metastatic disease remains a clinical challenge. Identifying suppressors of breast cancer progression and mechanisms of transition to more invasive phenotypes could provide game changing therapeutic opportunities. Transcriptional deregulation is central to all malignancies, highlighted by the extensive reprogramming of regulatory elements that underlie oncogenic programs. Among these, super-enhancers (SEs) stand out due to their enrichment in genes controlling cancer hallmarks. To reveal novel breast cancer dependencies, we integrated the analysis of the SE landscape with master regulator activity inference for a series of breast cancer cell lines. As a result, we identified T-helper-inducing Poxviruses and Zinc-finger (POZ)/Kruppel-like factor (ThPOK, ZBTB7B), a CD4+ cell lineage commitment factor, as a breast cancer master regulator that is recurrently associated with a SE. ThPOK expression is highest in luminal breast cancer but is significantly reduced in the basal subtype. Manipulation of ThPOK levels in cell lines shows that its repressive function restricts breast cancer cells to an epithelial phenotype by suppressing the expression of genes involved in the epithelial-mesenchymal transition (EMT), WNT/{beta}-catenin target genes, and the pro-metastatic TGF{beta} pathway. Our study reveals ThPOK as a master transcription factor that restricts the acquisition of metastatic features in breast cancer cells.

cancer biology↗

bioRxiv2024

The conversion of forests to agricultural land reduced the content of soil black carbon fractions in a karst rocky desertification area of Southwest China

Understanding the effects of land use on soil black carbon (BC) is critical for correctly interpreting the role of BC in the carbon cycle of karst areas. This study investigated the distribution characteristics of organic carbon (OC), BC, char, and soot and soil physicochemical properties of the soil profiles (0-40 cm) of secondary forest, shrub, farmland, and wasteland in a rocky desertification area of Guangxi Province, a typical karst rocky desertification area in Southwest China. We used a combination of soot/char and {delta}13CBC isotope analysis to identify the source of BC of these soils. The average value of soil BC was the highest in secondary forest, followed by shrub, farmland, and wasteland in the 0-40 cm soil layer. BC had a positive correlation with OC, char, soot,soil nitrogen, phosphorus and potassium, showed a negative correlation with bulk density. In the black carbon component, char occupies a greater proportion than soot, with the heavy fraction OC exhibiting a higher concentration of BC than the light fraction OC. Conclusively, the BC content was mainly due to C3 plant burning, vehicle exhaust emissions, and fossil fuel utilization.Vegetation restoration improved the soil BC content associated with OC sequestration in the typical karst rocky desertification mountainous area of Southwest Guangxi.

ecology↗

bioRxiv2024

Role of Forkhead box F1 in the Pathobiology of Pulmonary Arterial Hypertension

RationaleApproximately 80% of patients with non-familial pulmonary arterial hypertension (PAH) lack identifiable pathogenic genetic variants. While most genetic studies of PAH have focused on predicted loss-of-function variants, recent approaches have identified ultra-rare missense variants associated with the disease. FOXF1 encodes a highly conserved transcription factor, essential for angiogenesis and vasculogenesis in human and mouse lungs. ObjectivesWe identified a rare FOXF1 missense coding variant in two unrelated probands with PAH. FOXF1 is an evolutionarily conserved transcription factor required for lung vascular development and vascular integrity. Our aims were to determine the frequency of FOXF1 variants in larger PAH cohorts compared to the general population, study FOXF1 expression in explanted lung tissue from PAH patients versus control (failed-donor) lungs, and define potential downstream targets linked to PAH development. MethodsThree independent, international, multicenter cohorts were analyzed to evaluate the frequency of FOXF1 rare variants. Various composite prediction models assessed the deleteriousness of individual variants. Bulk RNA sequencing datasets from human explanted lung tissues were compared to failed-donor controls to determine FOXF1 expression. Bioinformatic tools identified putative FOXF1 binding targets, which were orthogonally validated using mouse ChIP-seq datasets. Measurements and Main ResultsSeven novel or ultra-rare missense coding variants were identified across three patient cohorts in different regions of the FOXF1 gene, including the DNA binding domain. FOXF1 expression was dysregulated in PAH lungs, correlating with disease severity. Histological analysis showed heterogeneous FOXF1 expression, with the lowest levels in phenotypically abnormal endothelial cells within complex vascular lesions in PAH samples. A hybrid bioinformatic approach identified FOXF1 downstream targets potentially involved in PAH pathogenesis, including BMPR2. ConclusionsLarge genomic and transcriptomic datasets suggest that decreased FOXF1 expression or predicted dysfunction is associated with PAH.

genomics↗

bioRxiv2024

RIPK1 is essential for Herpes Simplex Virus-triggered ZBP1-dependent necroptosis in human cells

Necroptosis initiated by the host sensor Z-NA Binding Protein-1 (ZBP1) is essential for host defense against a growing number of viruses, including Herpes Simplex Virus-1 (HSV-1). Studies with HSV-1 and other necroptogenic stimuli in murine settings have suggested that ZBP1 triggers necroptosis by directly complexing with the kinase RIPK3. Whether this is also the case in human cells, or whether additional co-factors are needed for ZBP1-mediated necroptosis, is unclear. Here, we show that ZBP1-induced necroptosis in human cells requires RIPK1. We have found that RIPK1 is essential for forming a stable and functional ZBP1-RIPK3 complex in human cells, but is dispensable for the formation of the equivalent murine complex. The RIP Homology Interaction Motif (RHIM) in RIPK3 is responsible for this difference between the two species, because replacing the RHIM in human RIPK3 with the RHIM from murine RIPK3 is sufficient to overcome the requirement for RIPK1 in human cells. These observations describe a critical mechanistic difference between mice and humans in how ZBP1 engages in necroptosis, with important implications for treating human diseases.

cell biology↗

bioRxiv2024

TRPV3 channel activity helps cortical neurons stay active during fever

Fever raises body temperature (Tb) from [~]37 {degrees}C to beyond 38.4 {degrees}C to combat pathogens. While generally well tolerated below 40 {degrees}C, in rare cases fever can abnormally elevate neural activity and induce seizures in neurotypical children aged 2-5 years. This study investigates the mechanisms by which neuronal activity is maintained and stabilized during exposure to fever-range temperatures. Recordings of layer (L)4-evoked spiking in L2/3 pyramidal neurons (PNs) of mouse somatosensory cortex revealed four outcomes as temperature increased from 30{degrees}C to 36 {degrees}C and 39 {degrees}C (fever-range): neurons remained inactive, stayed active, ceased activity, or initiated activity. Roughly equal proportions of neurons ceased or initiated spiking, making the subset of "STAY" PNs, those that remain active across temperatures, crucial for maintaining stable cortical output. STAY PNs were more prevalent at younger postnatal ages. Their firing stability was supported by a distinct ion channel composition, including the thermosensitive channel TRPV3, which enables continued spiking by adjusting depolarization to meet spike threshold. Intracellular blockade of TRPV3, but not TRPV4, significantly reduced the proportion of STAY PNs and suppressed spiking at 39 {degrees}C. Moreover, in Trpv3-/-mice, temperature increases to 39 {degrees}C reduced both spiking and postsynaptic potential amplitude, and these mice exhibited a delayed seizure onset. Together, these findings suggest that TRPV3 contributes to the preservation of cortical activity during fever.

neuroscience↗

bioRxiv2024

An updated AL-Base reveals ranked enrichment of immunoglobulin light chain variable genes in AL amyloidosis

BackgroundEach monoclonal antibody light chain associated with AL amyloidosis has a unique sequence. Defining how these sequences lead to amyloid deposition could facilitate faster diagnosis and lead to new treatments. MethodsLight chain sequences are collected in the Boston University AL-Base repository. Monoclonal sequences from AL amyloidosis, multiple myeloma and the healthy polyclonal immune repertoire were compared to identify differences in precursor gene use, mutation frequency and physicochemical properties. ResultsAL-Base now contains 2,193 monoclonal light chain sequences from plasma cell dyscrasias. Sixteen germline precursor genes were enriched in AL amyloidosis, relative to multiple myeloma and the polyclonal repertoire. Two genes, IGKV1-16 and IGLV1-36, were infrequently observed but highly enriched in AL amyloidosis. The number of mutations varied widely between light chains. AL-associated {kappa} light chains harbored significantly more mutations compared to multiple myeloma and polyclonal sequences, whereas AL-associated {lambda} light chains had fewer mutations. Machine learning tools designed to predict amyloid propensity were less accurate for new sequences than their original training data. ConclusionsRarely-observed light chain variable genes may carry a high risk of AL amyloidosis. New approaches are needed to define sequence-associated risk factors for AL amyloidosis. AL-Base is a foundational resource for such studies.

bioinformatics↗

bioRxiv2024

Osterix Facilitates Osteocytic Communication by Targeting Connexin43

Osteocytes, terminal-differentiated cells in bone, are now considered as more pivotal regulators of mature bone homeostasis than other bone cells, since they constitute 90- 95% of the bone cell population. Given their non-migratory nature within the mineralized matrix, their unique dendrites are crucial for cell-to-cell communication in response to both intracellular and extracellular stimuli, such as bone fracture or mechanical load. Here, we showed that Osterix (Osx), usually recognized as a specific doorkeeper for osteoblast differentiation during new bone formation marked by collagen type I 1 (Col11), was unexpectedly co-expressed with Col11 in osteocytes within the cortical bone of mice. Deleting Osx in Col11-positive osteocytes disrupted cortical bone structure and osteocytic dendrites in mice, thus impairing transcellular fluid flow and intercellular communication. Conversely, overexpression of Osx in osteocytes enhanced these processes. Furthermore, we identified Connexin43, a critical protein of gap junction channel, was a direct transcriptional target of Osx in regulating dendrites of osteocytes. Pharmacological restoration of Connexin43 levels rescued the dysfunction in Osx-deficient osteocytes both in vitro and in vivo. Taken together, this work demonstrated Osxs distinct role in osteocyte function through maintaining intercellular signaling, which broadened the current understanding of its role in Col11-positive bone cells, extending beyond osteoblasts and bone mineralization, offering new insights into bone diseases such as fracture nonunion or disuse osteoporosis.

cell biology↗

bioRxiv2024

WheresWalker: a pipeline for rapid mutation mapping using whole genome sequencing

Forward genetic screening is a powerful approach to assign functions to genes and can be used to elucidate the many genes whose functions remain unknown. Chemical mutagenesis is an unbiased and efficient method for generating point mutations in the founding generation of animals in a forward genetic screening experiment. Missense and nonsense mutations induced by chemical mutagenesis can lead to the generation of partial function, gain-of-function, or null alleles that underlie compelling phenotypes, but positional cloning of the underlying causative single base pair changes can be laborious and time-consuming, especially in large polymorphic genomes. Current methods use a bioinformatic mapping-by-sequencing approach which often identifies large genomic regions which contain an intractable number of candidate genes for testing. Here, we describe WheresWalker, a modern mapping-by-sequencing algorithm that identifies a mutation-containing interval and then supports positional cloning to refine the interval which drastically reduces the number of potential candidates allowing for extremely rapid mutation identification. We validated this method using mutants from a forward genetic mutagenesis screen in zebrafish for modifiers of ApoB-lipoprotein metabolism. WheresWalker correctly maps and identifies novel zebrafish mutations in mttp, apobb.1, and mia2 genes, as well as a previously published mutation in maize. Further, we use WheresWalker to identify a previously unappreciated ApoB-lipoprotein metabolism-modifying locus, slc3a2a.

genetics↗

bioRxiv2024

Systemic metabolic changes in acute and chronic lymphocytic choriomeningitis virus infection

Viral infection of cells leads to metabolic changes, but how viral infection changes whole-body and tissue metabolism in vivo has not been comprehensively studied. In particular, it is unknown how metabolism might be differentially affected by an acute infection that the immune system can successfully clear, compared to a chronic and persistent infection. Here we used metabolomics and isotope tracing to identify metabolic changes in mice infected with acute or chronic forms of lymphocytic choriomeningitis virus (LCMV) for three or eight days. Both types of infection alter metabolite levels in blood and tissues, including itaconate and thymidine. However, we observed more dramatic metabolite changes in the blood and tissues of mice with chronic LCMV infection compared to those with acute infection. Isotope tracing revealed that the contribution of both glucose and glutamine to the tricarboxylic acid (TCA) cycle increase in the spleen, liver, and kidneys of mice infected with chronic LCMV, while acute LCMV only increases the contribution of glutamine to the TCA cycle in the spleen. We found that whole-body turnover of both glutamine and thymidine increase during acute and chronic infection, whereas whole-body glucose turnover was surprisingly unchanged. Activated T cells in vitro produce thymidine and mice with T cell leukemia display elevated serum thymidine, nominating T lymphocytes as the source of thymidine in LCMV infection. In sum, we provide comprehensive measurements of whole-body and tissue metabolism in acute and chronic viral infection, and identify altered thymidine metabolism as a marker of viral infection.

immunology↗

bioRxiv2024

CGPA: multi-context insights from the cancer gene prognosis atlas

Cancer transcriptomic data are used extensively to interrogate the prognostic value of targeted genes, yet basic scientists and clinicians have predominantly relied on univariable survival analysis for this purpose. This method often fails to capture the full prognostic potential and contextual relevance of the genes under study, inadvertently omitting a group of genes we term univariable missed-opportunity prognostic (UMOP) genes. Recognizing the complexity of revealing multifaceted prognostic implications, especially when extending the analysis to include various covariates and thresholds, we present the Cancer Gene Prognosis Atlas (CGPA). This platform greatly enhances gene-centric biomarker research across cancer types by offering an interactive and user-friendly interface for highly customized, in-depth prognostic analysis. CGPA notably supports data-driven exploration of gene pairs and gene-hallmark relationships, elucidating key composite biological mechanisms like synthetic lethality and immunosuppression. It further expands its capabilities to assess multi-gene panels using both public and user-provided data, facilitating a seamless mechanism-to-machine analysis. Additionally, CGPA features a designated portal for discovering prognostic gene modules using curated cancer immunotherapy data. Ultimately, CGPAs comprehensive, accessible tools allow cancer researchers, including those without statistical expertise, to precisely investigate the prognostic landscape of genes, customizing the model to fit specific research hypotheses and enhancing biomarker discovery and validation through a synergy of mechanistic and data-driven strategies. SignificanceCGPA is a streamlined, interactive platform for multi-context gene-centric prognostic analysis, simplifying biomarker discovery and validation in oncology for clinicians and basic scientists, and bridging a critical gap in translational cancer research.

bioinformatics↗

bioRxiv2024

Synapse protein signatures in cerebrospinal fluid and plasma predict cognitive maintenance versus decline in Alzheimers disease

Rates of cognitive decline in Alzheimers disease (AD) are extremely heterogeneous, with ages of symptom onset ranging from age 40-100 years and conversion from mild cognitive impairment to AD dementia taking 2-20 years. Development of biomarkers for amyloid-beta (A{beta}) and tau protein aggregates, the hallmark pathologies of AD, have improved patient monitoring/stratification and drug development, but they still only explain 20-40% of the variance in cognitive impairment (CI) in AD. To discover additional molecular drivers and biomarkers of AD dementia, we perform cerebrospinal fluid (CSF) proteomics on 3,416 individuals from six deeply phenotyped prospective AD case-control cohorts. We identify synapse proteins as the strongest correlates of CI, independent of A{beta} and tau. Using machine learning we derive the CSF YWHAG:NPTX2 synapse protein ratio, a robust correlate of CI, which explains 27% of the variance in CI beyond CSF PTau181:A{beta}42, 10% beyond tau PET, and 50% beyond CSF NfL in A{beta} positive individuals. We find YWHAG:NPTX2 also increases with normal aging as early as age 20 and increases at a faster rate in APOE4 carriers and autosomal dominant-AD mutation carriers. Most notably, YWHAG:NPTX2+ individuals (top 25th percentile) are 15-times (HR=15.4 [10.6-22.2]) more likely to experience cognitive decline over 15 years compared to YWHAG:NPTX2- individuals (bottom 25th percentile), and this rises to 19-times (HR=18.9 [10.83-32.9]) with additional stratification by A{beta} and phosphorylated tau status. Lastly, we perform plasma proteomics on 4,245 individuals to develop a plasma-based signature of CI which partly recapitulates CSF YWHAG:NPTX2. Overall, our findings underscore CSF YWHAG:NPTX2 and the corresponding plasma signature as robust prognostic biomarkers for AD onset and progression beyond gold-standard biomarkers of A{beta}, tau, and neurodegeneration and implicate synapse dysfunction as a core driver of AD dementia.

neuroscience↗

bioRxiv2024

PA2gamma promotes the malignant progression of tumor by elevating mitochondrial function via C1QBP

Proteasome activator 28{gamma} (PA28{gamma}) plays a critical role in malignant progression of various tumors, however, its role and regulation are not well understood. Here, using oral squamous cell carcinoma (OSCC) as main research model, we discovered that PA28{gamma} interacted with complement 1q binding protein (C1QBP), which is dependent on the N-terminus of C1QBP rather than the known functional domain (amino acids 168-213). Notably, we found that PA28{gamma} enhances C1QBP protein stability in OSCC. Functionally, PA28{gamma} contributes to the malignant progression of OSCC by affecting mitochondrial morphology and oxidative phosphorylation (OXPHOS) through C1QBP in vitro and vivo. Mechanically, PA28{gamma} upregulates the expression of optic atrophy 1 (OPA1), mitofusin 1 (MFN1), mitofusin 2 (MFN2), and the mitochondrial respiratory complex via C1QBP. Moreover, in a clinical cohort of OSCC patients, PA28{gamma} was positively correlated with C1QBP expression and negatively correlated with prognosis. Therefore, C1QBP represents a potential therapeutic target for cancer treatment and prognosis.

cancer biology↗

bioRxiv2024

A pan-cancer gamma delta T cell repertoire

This report presents the largest collection of gamma-delta T cell receptor ({gamma}{delta} TCR) reads in human cancer to date, analyzing about 11,000 patient tumor samples across 33 cancer types using the TRUST4 algorithm. Despite {gamma}{delta} T cells being a small fraction of the T cell population, they play a key role in both innate and adaptive immunity. Our comprehensive analysis reveals their significant presence across all cancer types, specifically highlighting the diverse spectrum and clonality patterns of their {gamma}{delta} receptors. This research highlights the complex roles of {gamma}{delta} T cells in tumor tissues and their potential as prognostic biomarkers. We also demonstrate the utility of T cell receptor gamma (TRG) and delta (TRD) gene expression values from standard RNA-seq data. Ultimately, our work establishes a fundamental resource for future tumor-infiltrating {gamma}{delta} T cell research and may facilitate the development of novel {gamma}{delta}-T-cell-based therapeutic strategies. Together, we demonstrate the strong diversity and prognostic potential of {gamma}{delta} T cells in multiple cancer types. HighlightsComprehensive analysis of {gamma}{delta} TCRs from 11,473 tumor samples Significant variability and overall consistency in {gamma}{delta} gene expression and clonotype {gamma}{delta}TCR expression and diversity as prognostic biomarkers across multiple cancers Centralized {gamma}{delta} TCR repertoire database for future therapeutic discovery

genomics↗

bioRxiv2024

MAGE-A4-Responsive Plasma Cells Promote Non-Small Cell Lung Cancer

Adaptive immunity is critical to eliminate malignant cells, while multiple tumor-intrinsic factors can alter this protective function. Melanoma antigen-A4 (MAGE-A4), a cancer-testis antigen, is expressed in several solid tumors and correlates with poor survival in non-small cell lung cancer (NSCLC), but its role in altering antitumor immunity remains unclear. We found that expression of MAGE-A4 was highly associated with the loss of PTEN, a tumor suppressor, in human NSCLC. Here we show that constitutive expression of human MAGE-A4 combined with the loss of Pten in mouse airway epithelial cells results in metastatic adenocarcinoma enriched in CD138+ CXCR4+ plasma cells, predominantly expressing IgA. Consistently, human NSCLC expressing MAGE-A4 showed increased CD138+ IgA+ plasma cell density surrounding tumors. The abrogation of MAGE-A4-responsive plasma cells (MARPs) decreased tumor burden, increased T cell infiltration and activation, and reduced CD163+CD206+ macrophages in mouse lungs. These findings suggest MAGE-A4 promotes NSCLC tumorigenesis, in part, through the recruitment and retention of IgA+ MARPs in the lungs.

immunology↗

bioRxiv2024

Strawberry COP9 signalosome FvCSN5 regulates plant development and fruit ripening by facilitating polyamine oxidase FvPAO5 degradation to control polyamine and H2O2 homeostasis

Polyamines (PAs), mainly including putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 signalosome subunit 5A (FvCSN5A)-mediated degradation of the PA oxidase FvPAO5, which catalyzes the conversion of spermidine/spermine to produce H2O2. FvCSN5A is localized in the cytoplasm and nucleus, ubiquitously expressed in strawberry plants, and rapidly increases during fruit ripening. FvCSN5A RNA interference (RNAi) transgenic strawberries exhibit pleiotropic effects on plant development, fertility, and fruit ripening by regulating PA and H2O2 homeostasis, similar to FvPAO5 overexpression transgenic lines. FvCSN5A interacts with FvPAO5 in vitro and in vivo. The ubiquitination and degradation of FvPAO5 are impaired in FvCSN5A RNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry fruits showed that inhibiting FaPAO5 expression could partially rescue the ripening phenotype of FaCSN5A RNAi fruits. Collectively, the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2 homeostasis is crucial to strawberry vegetative and reproductive growth and, final to fruit ripening. Our findings may open a promising avenue for improving crop yield and quality by manipulating the CSN5-PAO5 pair.

plant biology↗

bioRxiv2024

Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis

A long-standing observation is that in fast-growing cells, respiration rate declines with increasing growth rate and is compensated by an increase in fermentation, despite respiration being more efficient than fermentation. This apparent preference for fermentation even in the presence of oxygen is known as aerobic glycolysis, and occurs in bacteria, yeast, and cancer cells. Considerable work has focused on understanding the potential benefits that might justify this seemingly wasteful metabolic strategy, but its mechanistic basis remains unclear. Here we show that aerobic glycolysis results from the saturation of mitochondrial respiration and the decoupling of mitochondrial biogenesis from the production of other cellular components. Respiration rate is insensitive to acute perturbations of cellular energetic demands or nutrient supplies, and is explained simply by the amount of mitochondria per cell. Mitochondria accumulate at a nearly constant rate across different growth conditions, resulting in mitochondrial amount being largely determined by cell division time. In contrast, glucose uptake rate is not saturated, and is accurately predicted by the abundances and affinities of glucose transporters. Combining these models of glucose uptake and respiration provides a quantitative, mechanistic explanation for aerobic glycolysis. The robustness of specific respiration rate and mitochondrial biogenesis, paired with the flexibility of other bioenergetic and biosynthetic fluxes, may play a broad role in shaping eukaryotic cell metabolism.

systems biology↗

bioRxiv2024

Cooperativity among clustered κB sites within promoters and enhancers dictates transcriptional specificity of NF-κB RelA along with specific cofactors

Non-consensus binding sites of transcription factors are often observed within the regulatory elements of genes; however, their effect on transcriptional strength is unclear. Within the promoters and enhancers of NF-{kappa}B-responsive genes, we identified clusters of non-consensus {kappa}B DNA sites, many exhibiting low affinity for NF-{kappa}B in vitro. Deletion of these sites demonstrated their collective critical role in transcription. We explored how these "weak" {kappa}B sites exert their influence, especially given the typically low nuclear concentrations of NF-{kappa}B. Using proteomics approaches, we identified additional nuclear factors, including other DNA-binding TFs, that could interact with {kappa}B site-bound NF-{kappa}B RelA. ChIP-seq and RNA-seq analyses suggest that these accessory TFs, referred to as the TF-cofactors of NF-{kappa}B, facilitate dynamic recruitment of NF-{kappa}B to the clustered weak {kappa}B sites. Overall, the occupancy of NF-{kappa}B at promoters and enhancers appears to be defined by a collective contribution from all {kappa}B sites, both weak and strong, in association with specific cofactors. This congregation of multiple factors within dynamic transcriptional complexes is likely a common feature of transcriptional programs. SIGNIFICANCEThe NF-{kappa}B RelA dimers undergo rapid activation by cytokines and pathogens, driving expeditious expression of target genes upon binding to DNA elements known as {kappa}B sites, located in the regulatory regions. We find that promoter and enhancer regions of RelA target genes harbor multiple {kappa}B sites, most being non-consensus with minimal affinity to NF-{kappa}B in vitro. Recruitment of RelA dimer in vivo depend on these {kappa}B sites, weak and strong, and appears to be regulated by various accessory factors, including other DNA-binding transcription factors. Overall, this study points to a coordinated network of factors communicating with both weak and strong {kappa}B sites to recruit RelA dimers, enabling rapid gene activation.

biochemistry↗