The myometrium, the muscular layer of the uterus, undergoes crucial transitions during pregnancy, maintaining quiescence throughout gestation, and generating coordinated contractions during labor. Dysregulation of this transition can lead to premature labor with serious complications for the infant. Despite extensive gene expression data available for varying myometrial states, the molecular mechanisms governing the increase in contraction-associated gene expression at labor onset remain unclear. Transcription factors, such as JUND and progesterone receptor (PR), play essential roles in regulating transcription of select myometrial contraction-associated genes, however, a broader understanding of their involvement in transcriptional regulation at a genome-wide scale is lacking. This study examines changes in transcription and JUND binding within human myometrial tissue during the transition from quiescence (term-not-in labor/TNIL) to contractility (term labor/TL). Total RNA-sequencing reveals a global increase in primary transcript levels at TL, with AP-1/JUND binding motifs overrepresented in the promoters of upregulated transcripts. Interestingly, ChIP-seq analysis demonstrates higher JUND enrichment in TNIL compared to TL tissues, suggesting its role in preparing the myometrium for labor onset. Integration of JUND and PR ChIP-seq data identifies over 10,000 gene promoters bound by both factors at TNIL and TL, including genes involved in labor-driving processes. Additionally, the study uncovers elevated levels of enhancer RNAs (eRNAs) at intergenic JUND peaks in laboring myometrial tissues, and implicates additional transcription factors, such as NFKB and ETS, in the regulatory switch from quiescence to contractility. In summary, this research enhances our understanding of the myometrial molecular regulatory network during pregnancy and labor, shedding light on the roles of JUND and PR in gene expression regulation genome-wide. These findings open avenues for further exploration, potentially leading to improved interventions for preventing premature labor and the associated complications.

Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate-limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology.

The decline in adult stem cell performance is closely linked to tissue malfunction and the rising incidence of age-related diseases. To investigate the molecular basis of these impairments, our screening strategy identified reduced activity in the pantothenate/coenzyme A (CoA) pathway within aged ISCs. Furthermore, exogenous CoA supplementation restructured ISC metabolic pathways, reversing age-induced hyperproliferation and intestinal dysfunction, and thus extending Drosophila lifespan by curbing excessive iron accumulation in ISCs. These findings uncover a new mechanism of stem cell aging and propose that pantothenate and CoA could be potential therapeutic targets for treating age-related diseases and enhancing healthy aging in humans.

Genome instability is a hallmark of cancer that can be caused by DNA replication stress. Copy number variation (CNV) is a type of genomic instability that has been associated with both tumorigenesis and drug resistance, but how these structural variants form in response to replication stress is not fully understood. Here, we established a direct repeat genetic reporter in Saccharomyces cerevisiae to detect recombination events that result in either a duplication or a deletion. Using this system, we measured recombination resulting from site-specific replication fork stalling initiated by Tus binding to an array of Ter sites. We found that a Tus/Ter fork block downstream of direct repeats induced CNV by a mechanism involving the Mph1 translocase, Exo1-catalyzed end resection and Rad51-dependent strand invasion. While the Slx4 scaffold protein and its nuclease-binding partner, Rad1-Rad10, were shown to be required for duplications, we found that they suppress deletion formation in this context. These opposing functions suggest that both recombination products arise through a large loop heteroduplex intermediate that is cleaved by Rad1-Rad10 in a manner that promotes duplications and eliminates deletions. Taken together, these studies give insight into the mechanisms governing CNV in the context of replication fork stalling, which may ultimately provide a better understanding of how replication stress contributes to cancer and other diseases characterized by genome instability.

LINE-1 is the only active autonomous mobile element in the human, and its mobilization is tightly restricted by the host to maintain genetic stability. We recently reported that human MOV10 recruits DCP2 to decap LINE-1 RNA by liquid-liquid phase separation (LLPS), resulting in the inhibition of LINE-1 retrotransposition, while the detailed mechanism still awaits further exploration. In this report, we found that the extended motif II (563-675aa) and the C-terminal domain (907-1003aa) of MOV10 cooperated to achieve maximal inhibition on LINE-1 retrotransposition. The extended motif II involves the interaction between MOV10 and LINE-1, and the C-terminal domain is required for MOV10's association with G3BP1 and thereby the formation of granules. The association with LINE-1 through the extended motif II is dominantly attributed to MOV10-mediated anti-LINE-1 activity. On this basis, promoting large granules formation by the C-terminal domain warrants maximal inhibition of LINE-1 replication by MOV10. These data together shed light on the detailed mechanism underlying MOV10-mediated inhibition of LINE-1 retrotransposition, and provide further evidence supporting the important role of MOV10-driven granules in the anti-LINE-1 action.

Chronic kidney disease (CKD) is a multifactorial condition driven by diverse etiologies that lead to a gradual loss of kidney function. Although genome-wide association studies (GWAS) have identified numerous genetic loci linked to CKD, a large portion of its genetic basis remains unexplained. This knowledge gap may partly arise from the reliance on single biomarkers, such as estimated glomerular filtration rate (eGFR), to assess kidney function. To address this limitation, we developed and applied a novel multi-phenotype approach, combinatorial Principal Component Analysis (cPCA), to better understand the complex genetic architecture of CKD. Using UK Biobank dataset (n = 337,112), we analyzed 21 CKD-related phenotypes, generating over 2 million composite phenotypes (CPs) through cPCA. Nearly 50,000 of these CPs demonstrated significantly higher classification power for clinical CKD compared to individual biomarkers. The top-ranked CP—a combination of albumin, cystatin C, eGFR, gamma-glutamyltransferase, HbA1c, low-density lipoprotein, and microalbuminuria, achieved an AUC of 0.878 (95% CI: 0.873–0.882), significantly outperforming eGFR alone (AUC: 0.830, 95% CI: 0.825–0.835). Genetic association analysis of the ~ 50,000 high-performing CPs identified all major eGFR-associated loci, except for the SH2B3 locus rs3184504, a loss-of-function variant, which was uniquely identified in CPs (p = 3.110-56) but not in eGFR within the same sample size. In addition, SH2B3 locus showed strong evidence of colocalization with eGFR, supporting its role in kidney function. These results highlight the power of the multi-phenotype cPCA approach in understanding the genetic basis of CKD, with potential applications to other complex diseases.

Gram-negative bacterial cell envelope consists of a surface-exposed lipid bilayer (outer membrane or OM) that serves as a permeability barrier to maintain the cellular integrity. Beneath the OM is the periplasmic space that harbours peptidoglycan (PG), a highly cross-linked mesh-like glycan polymer closely encasing the inner membrane (IM). During growth of a bacterium balanced synthesis of the envelope components is required to maintain the cellular integrity, of which little is known. In this study, we identify sanA, an ORF of unknown function encoding a predicted IM-anchored protein as a factor contributing to balanced synthesis of PG in E. coli. Absence of SanA increased the rate of nascent PG strand incorporation, and restored growth and viability to several mutants defective in either cell division or cell elongation. Detailed mutant analysis of sanA showed that it is defective in the envelope barrier properties. Interestingly, overexpression of the periplasmic endopeptidases that cleave the cross-links of the PG mesh was able to alleviate the phenotypes of sanA mutant implying the envelope defects are due to alterations in the PG sacculus. Additionally, a SanA variant (SSDsbA-SanA) targeted to the periplasm, complemented the SanA− phenotypes suggesting it functions in the periplasmic phase of the PG synthesis. Further, we find that SanA functions independently of its paralog, ElyC, known to regulate the synthesis of enterobacterial common antigen (ECA), a surface polysaccharide found in the cell envelopes of most enteric bacteria. Overall, our results suggest a role for SanA in the maintenance of optimal PG synthesis, providing evidence for the existence of an additional layer of regulation in Gram-negative cell envelope biogenesis.

Paralogs often exhibit functional redundancy, allowing them to effectively compensate for each other's loss. However, this buffering mechanism is frequently disrupted in cancer, exposing unique paralog-specific vulnerabilities. Here, we identify a selective dependency on the splicing factor TRA2A. We find that TRA2A and its paralog TRA2B are synthetic lethal partners that function as widespread and largely redundant activators of both alternative and constitutive splicing. While loss of TRA2A alone is typically neutral due to compensation by TRA2B, we discover that a subset of cancer cell lines are highly TRA2A-dependent. Upon TRA2A depletion, these cell lines exhibit a lack of paralog buffering specifically on shared splicing targets, leading to defects in mitosis and cell death. Notably, TRA2B overexpression rescues both the aberrant splicing and lethality associated with TRA2A loss, indicating that paralog compensation is dosage-sensitive. Together, these findings reveal a complex dosage-dependent relationship between paralogous splicing factors, and highlight how dysfunctional paralog buffering can create a selective dependency in cancer.

Nonhost resistance (NHR) serves as a fundamental defense response in plants against non-adapted pathogens, yet its underlying molecular mechanisms remain poorly understood. This study investigates the rice-Pst (Puccinia striiformis f. sp. tritici) interaction using integrated transcriptomic and metabolomic analyses to unravel the temporal dynamics of gene expression and metabolite changes associated with NHR. Our findings reveal a temporally coordinated activation of defense responses, with early induction of receptor-like kinases (RLKs) and hypersensitive response proteins, followed by later activation of jasmonic acid and systemic acquired resistance pathways, along with the accumulation of amino acids and other phenolic compounds. Notably, metabolic pathways related to cell wall reinforcement were significantly upregulated during Pst infection, highlighted by enhanced lignin biosynthesis (phenylpropanoid pathway), nucleotide sugar metabolism, and tryptophan pathways. Rice mutants deficient in genes involved in lignin biosynthesis (OsPAL3, Os4CL3, Os4CL5, and OsCCoAOMT) displayed reduced lignin deposition at infection sites and compromised resistance to Pst, underscoring a critical role of lignin-based physical barriers in NHR. This study provides novel insights into the molecular framework of rice NHR, emphasizing the pivotal role of structural defenses in plant immunity.

Maintaining protein homeostasis is essential for cellular health. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response, activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPRER), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPRER is inhibited, introducing a previously unknown regulatory component of MCSR. Moreover, proteostasis is enhanced through the upregulation of the PERK-eIF2α signaling pathway, increasing phosphorylation of eIF2α and improving the ER's ability to handle proteostasis. MERSR activation in both polyglutamine and amyloid-beta peptide-expressing C. elegans disease models also led to improvement in both aggregate burden and overall disease outcome. These findings shed light on the coordination between the mitochondria and the ER in maintaining cellular proteostasis and provide further evidence for the importance of intercompartmental signaling.