BMC Molecular and Cell Biology

Keloids are fibroproliferative skin disorders arising following dermal injury that extend beyond the original wound margins. Their pathogenesis remains poorly understood, and current treatments are associated with high recurrence rates. Identifying transcriptomic biomarkers that distinguish keloids from other skin and scar phenotypes may provide insight into disease mechanisms and facilitate the development of targeted therapeutic approaches. However, previous transcriptomic studies have often been limited by small sample sizes, pairwise comparisons between tissue classes, heterogeneous data-integration strategies, and a reliance on conventional differential gene expression (DGE) analysis. Here, we employed a multi-stage machine learning (ML) workflow for robust keloid biomarker discovery using transcriptomic datasets derived from both bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq). We assembled and harmonized, to the best of our knowledge, the largest curated cross-study keloid transcriptomic cohort currently available, comprising 81 samples from 13 independent studies spanning four clinically relevant tissue classes: normal skin, normotrophic scar, hypertrophic scar, and keloid scar. Through study-aware cross-validation, feature selection, partition-stability analysis, and bootstrap validation across multiple ML classifiers, we identified a panel of eight highly consistent biomarkers capable of distinguishing keloid from non-keloid samples. These biomarkers were associated with dysregulation of extracellular matrix homeostasis, fibrosis-resolution pathways, vascular remodelling, and metabolic reprogramming. Comparison with conventional DGE analysis demonstrated substantial agreement while also highlighting important differences between the two approaches. In particular, FASN was consistently identified by the ML workflow as an upregulated discriminatory biomarker despite exhibiting weak, non-significant differential expression in the DGE analysis. Cell-type-specific analysis further supported this finding, revealing significant FASN upregulation in fibroblast and vascular endothelial populations. These results demonstrate that ML and DGE capture complementary aspects of transcriptomic variation. This study provides a robust strategy for cross-study transcriptomic biomarker discovery and identifies candidate genes and pathways for future mechanistic and therapeutic investigation in keloids. 1 Author SummaryKeloids are abnormal scars that continue to grow beyond the original wound and can be difficult to treat because they frequently recur after therapy. Although many studies have investigated the biology of keloids, the molecular mechanisms that distinguish them from other scar types remain incompletely understood. Identifying biomarkers involved in keloid formation may help inform improved treatment strategies. Previous transcriptomic studies have often been limited by small sample sizes and inconsistent analytical approaches. In this study, we combined gene-expression data from multiple independent studies to create, to the best of our knowledge, the largest cross-study transcriptomic collection available for keloid analysis. We then applied several machine learning approaches to identify genes that consistently distinguished keloids from other skin and scar phenotypes. The identified biomarkers were associated with extracellular matrix remodeling, fibrosis, vascular function, and cellular metabolism. One gene involved in fatty-acid synthesis, FASN, was repeatedly identified by the machine learning analyses despite being overlooked by conventional gene-expression methods. Additional single-cell analyses confirmed elevated FASN expression in specific cell populations within keloid tissue. More broadly, this work provides a strategy for discovering robust biomarkers from heterogeneous biological datasets and identifies molecular targets for future studies of keloid disease.

Tropomyosins are coiled-coil dimers that polymerize head-to-tail along actin filaments. They stabilize distinct filament populations and regulate the access of myosins and actin-binding proteins in both muscle and non-muscle contexts. Despite their central regulatory role, how filament length and isoform identity of different tropomyosin homologues might modulate actin affinity is not completely understood, especially across species. Here, we present a stepwise computational docking pipeline combining AlphaFold2-Multimer coiled-coil models, experimentally informed residue-level restraints, and pseudo-energy analysis via PPCheck to build and evaluate actin-tropomyosin co-polymer models for three isoforms: human TPM1 (hTPM1; 284 residues), human TPM4 (hTPM4; 248 residues), and Schizosaccharomyces pombe Cdc8 (SpCdc8; 161 residues). Interface energetics reveal a consistent hierarchy in which the shortest filament, SpCdc8, achieves the most stabilizing and residue-rich actin contacts, consistent with reduced cumulative geometric penalty along the actin helix. Among human isoforms, hTPM1 forms stronger interfaces with actin than hTPM4. The hTPM1-actin model also exhibits higher contact density and additional energetic hotspots, in agreement with the experimentally established slower exchange kinetics of TPM1 isoforms on actin filaments relative to TPM4. Hotspot mapping identifies conserved acidic residues at equivalent positions across all three isoforms, emphasizing the importance of electrostatic anchor points in maintaining interface integrity across diverse evolutionary contexts. Modeling of four temperature-sensitive SpCdc8 mutations (A18T, R21H, E31K and E129K) reveals that these substitutions substantially destabilize the coiled-coil dimer without significantly affecting actin interactions, suggesting that subtle regulatory failure arises from compromised longitudinal cable continuity rather than from direct loss of actin affinity. Taken together, our results support a hierarchical model of tropomyosin dimer stability, actin-tropomyosin recognition in which filament length imposes a geometric baseline on interface stability, onto which isoform-specific sequence evolution superimposes functional tuning. The tropomyosin homologues we studied appear to retain conserved electrostatic hotspots thereby providing a common structural scaffold across tissues and organisms.

Emerin (EMD), an inner nuclear membrane protein essential for nuclear architecture integrity, gene expression, cellular signaling, and chromatin stability, interacts with the LINC complex and participates in cytoskeleton-nucleoskeleton communication by binding to nuclear actin filaments. EMD is implicated in migration, invasion, and metastasis in some tumors, but its role in glioblastoma (GBM) remains unclear. This study evaluated the effects of EMD knockdown and overexpression in GBM cell lines following genotoxic treatment with cisplatin. In both wild-type p53 (U87-MG) and mutant p53 (U138-MG) GBM cells, EMD expression is high, and cisplatin treatment did not affect these protein levels. EMD knockdown in U87-MG cells significantly increased cisplatin IC50, viability, and proliferation. Conversely, stable overexpression of EMD in U87-MG cells led to reduced cisplatin IC50, viability, proliferation, and migration. EMD knockdown or overexpression did not affect any U138-MG phenotypes, with or without cisplatin treatment. Modulation of EMD levels causes morphological changes in stress fiber cytoskeleton, whereas overexpression of EMD in U87-MG cells promotes an increase and a decrease in nuclear and cytoplasmic actin levels, respectively. These biological responses of U87-MG cells overexpressing EMD were coincidentally associated with alterations in the levels of pH2AX(Ser139), p-p53(Ser15), p53, and p21Kip1 proteins after cisplatin exposure. In sum, modulation of EMD levels affects the viability, migration, and proliferation of wild-type p53 GBM cells treated with cisplatin, suggesting unknown roles in the DNA damage response and repair. This work highlights EMD as a potential regulator of GBM chemoresistance and a target for therapeutic intervention.

Significance Missense mutations can lead to pathological effects in human cells. Predictive methods that account for structural context, such as AlphaMissense, can provide pathogenicity scores. The accumulation of pathogenicity hotspots can reveal important structural features within individual proteins of protein families, such as GLUT transporters. Mapping pathogenicity scores onto the structure can thus provide a mechanistic explanation of the protein function necessary for its role in the cell. Abstract Non-synonymous amino acid substitutions (missense mutations) are common in the general population; some are causative of serious disease. Depending on their structural context, they can disrupt protein function, folding, or dynamics. Computational predictive methods developed in recent years, such as AlphaMissense, provide new insights into how missense mutations affect protein structure by predicting and mapping their pathogenicity across each amino acid in the human proteome. In this study, we identify recurring patterns of pathogenicity prediction across the GLUT family membrane transporters encoded by genes slc2a1-14. Within the GLUT transporter family, we observe higher pathogenicity profiles in the transmembrane domains, particularly in pore-lining and binding-site residues. Predicted missense pathogenicity is elevated throughout residues assigned to the central cavity, suggesting sensitivity of the transport pathway. Another finding shows higher pathogenicity in specific transmembrane helices of the protein, with the same pattern across all proteins. On the other hand, we observed lower pathogenicity values in some representatives of the GLUT family. These findings show that the pathogenicity of glucose transport within the GLUT family may be shaped by functional redundancy and physiological essentiality across GLUT groups.

Cell division cycle 42 (Cdc42) is a member of the Rho family of small GTPases, which plays crucial roles in regulating cytoskeletal remodeling, and membrane trafficking. While previous studies implicated Cdc42 in controlling intestinal epithelial homeostasis, the involvement of this small GTPase in the process of intestinal fibrogenesis remains unexplored. Our study was designed to determine whether Cdc42 regulates the fibrogenic activation of intestinal myofibroblasts in vitro. The study was conducted using a CCD-18Co normal human colonic fibroblast cell line, and primary human intestinal myofibroblasts (HIMF) isolated from Crohns disease (CD) patients. CCD-18Co and HIMF cells were stimulated by transforming growth factor-{beta}1 (TGF-{beta}1). Cdc42 was inhibited either genetically, using siRNA-mediated knockdown, or pharmacologically using specific Cdc42 inhibitors, ML141 and CASIN. Genetic and pharmacologic inhibition of Cdc42 markedly reduced TGF-{beta}1 induced expression of the major contractile cytoskeletal proteins, -smooth muscle actin, calponin 1 and L-caldesmon. Furthermore, Cdc42 inhibition significantly attenuated expression of key extracellular matrix (ECM) proteins, fibronectin and collagen I, in activated CCD-18Co cells and HIMF. Interestingly, decreased expression of contractile and ECM proteins in Cdc42-depleted myofibroblasts was not due to downregulation of the TGF-{beta}1 signaling, decreased mRNA transcription or increased lysosomal or proteasomal degradation of these proteins. Such suppressed pro-fibrotic activation of Cdc42-deficient CCD-18Co cells and HIMF involved a selective inhibition of protein translation due to inactivation of the AKT-mammalian target of rapamycin (mTOR) signaling module. These findings highlight Cdc42 as a key regulator of intestinal fibrosis that controls mTOR activation to enhance ECM production and contractile actomyosin cytoskeleton in intestinal myofibroblasts.

Effective communication between cells is essential for the typical development and behaviour of an organism. In this context, gap junctions represent the most universally preserved components at cellular membranes of multicellular organisms, facilitating metabolic and electrical connections between cells. Disruptions in these junctions have been linked to various developmental abnormalities and pathological conditions in humans. The invertebrate gap junction proteins, referred to as innexins, exhibit conserved cellular and molecular mechanisms of functioning with their vertebrate counterparts, known as connexins. Consequently, they provide valuable means for studying and understanding the functions of gap junctions in development. In the Drosophila embryo, innexin-2 is expressed in the amnioserosa and ectoderm, where it is required for epithelial morphogenesis. Genetic depletion of innexin-2 results in cuticular defects and embryonic lethality. Pannier, a GATA family transcription factor, is a key regulator of dorsal tissue development in Drosophila and is expressed in the amnioserosa, dorsal ectoderm and the dorsal vessel during embryogenesis. Pannier mutants exhibit defects in dorsal closure, cuticle formation, and cardiac specification. Although substantial evidence from vertebrate systems indicate that connexin expression is regulated by transcription factors such as GATA4, Nkx2.5, Tbx2, Tbx3, and Tbx5, whether a similar regulatory relationship exists between these transcription factors and gap junction proteins in Drosophila remains unknown. In this study, we investigate how innexin mediated intercellular communication impacts pannier dependent morphogenetic processes during Drosophila embryogenesis.

The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial proteins. Approximately 99 % of mitochondrial proteins are synthesized as precursor proteins (preproteins) in the cytosol and subsequently translocated into mitochondria through the TOM complex. The TOM complex exists in a dynamic equilibrium among multiple assembly states through spatial rearrangements of its subunits. The recent cryo-electron microscopy (cryo-EM) studies revealed near-atomic structures of the TOM core dimer, whereas previous biochemical studies indicated the TOM complex functions as a trimer in intact mitochondria. However, the relationship between the core dimer and the functional trimer remains unclear. In the present study, we analyzed the dynamics of the TOM complex using high-speed atomic force microscopy (HS-AFM) to investigate the assembly states and conformation transitions of the TOM complexes. We demonstrated that purified yeast TOM complexes predominantly adopt a trimeric organization but dynamically dissociate into dimeric and monomeric states during HS-AFM observation. The trimeric particles observed by HS-AFM exhibited spherical molecular shapes consistent with a trimeric structural model proposed from previous crosslinking analyses. In contrast, the dissociated dimeric particles closely resembled the dimensions of the TOM core-dimer structures determined by cryo-EM. Furthermore, HS-AFM analyses provided insight into the spatial arrangement of the Tom20 receptor, consistent with previous models of the trimeric TOM complex. These observations enabled characterization of the trimeric TOM complex in vitro and provide a foundation for future structural and functional analyses of TOM complex assembly.

Sutures are the primary sites of cranial bone growth, allowing the skull to accommodate the growing brain. External mechanical stimulus has been shown to delay suture fusion and induce tissue remodelling. Recent studies suggest that in vivo cyclic bone loading increased proliferation of mesenchymal stem cells (MSC) in the coronal suture. The overall aim of this study was to understand how many loading sessions (exposure-response) and how long after loading (time-course) did MSC proliferation increase in the coronal suture. In the exposure-response analysis, mice underwent 1, 3, or 5 loading sessions between Postnatal day 7 (P7) and P11, and in the time-course analysis, treated mice underwent 10 loading sessions between P7 and P21. Loading sessions were 10 minutes at a frequency of 1 Hz and a force of 10 g (0.1 N). The loading tip was positioned on the posterior aspect of the left frontal bone, dorsal to the coronal suture. The EdU marker shows a statistically significant increase in proliferation after one loading session and a decrease after three loading sessions. The PCNA marker shows a statistically significant increase after three and five loading sessions. The exposure-response analysis showed that when the results of both markers are combined, levels of proliferation cannot be interpreted until at least five loading sessions have been completed, after which a clear increase in proliferation was observed. In the time-course analysis, proliferation was highest immediately after the final treatment session and 24 hours after the final loading session the effects of mechanical bone loading gradually returned to baseline.

Humans and other vertebrates contain two estrogen receptors (ERs), ER-alpha and ER-beta, which mediate the physiological actions of three estrogens: estrone (E1), estradiol (E2) and estriol (E3). Of these three estrogens, in vivo, E2 is the strongest transcriptional activator of ER-alpha and ER-beta, E1 is next most active, followed by E3. We studied transcriptional activation of human ER-alpha and ER-beta by E2, E1 and E3 in African green monkey kidney (COS-7) cells, which we compared with studies of estrogen stimulation of ER transcription in human em-bryonic kidney (HEK-293) cells. To our surprise, in COS-7 cells, E3 had the lowest half-maximal response (EC50) for human ER-alpha and ER-beta than either E2, which was second most active estrogen, or E1. In contrast, for human ER-alpha and ER-beta transfected into HEK-293 cells, E2 was the most active estrogen, followed by E1 and E3. Similar results were found in COS-7 cells and HEK-293 cells transfected with elephant shark ER-alpha and ER-beta. Thus, under some conditions, E3 is a more active estrogen than either E2 or E1. This suggests that E3 may be a novel physiological ligand for the ER in some mammalian cells.

Extensive experiments document that SPARCL1, a secreted protein that is produced primarily by astrocytes in brain and endothelia throughout the body and that is also known as Hevin, enhances synapse formation. However, the mode of action of SPARCL1 at synapses remains unclear owing to divergent results in the literature. Here, we use cultured neurons from newborn male and female mouse embryos to show that the C-terminal follistatin-like and Ca2+-binding domains of SPARCL1, which account for only 35% of the total SPARCL1 sequence, are sufficient to potently enhance synapse numbers. SPARCL1 acts at nanomolar concentrations at which SPARCL1 does not robustly bind to neurexins, neuroligins or neurexin/neuroligin complexes but avidly interacts with all teneurins. Strikingly, the follistatin-like domain of SPARCL1 on its own strongly binds to teneurins but is unable to stimulate synapse formation. Only when combined with the SPARCL1 Ca2+- binding domain does the follistatin-like domain induce synapses, suggesting that SPARCL1 enhances synapse numbers by binding to teneurins via its C-terminal follistatin-like domain and by activating synapse formation via its Ca2+-binding domain. SIGNIFICANCE STATEMENTSPARCL1 (also known as Hevin) is a synaptogenic factor that is produced primarily by astrocytes in brain, and that enhances synapse formation. How SPARCL1 acts at synapses, however, remains unclear because divergent results describe its binding partners at synapses and the sequences involved in its synaptogenic activity remain unclear. In the present study, we show that SPARCL1 avidly binds to the presynaptic teneurins adhesion molecules, that this binding is mediated by its small follistatin-like domain, and that its synaptogenic activity requires both its follistatin-like and its Ca2+-binding EC domains. Thus, our results suggest that SPARCL1 is recruited to developing synapses by binding of its follistatin-like domain to teneurins and then induces synapse assembly via its Ca2+-binding domain.

Delta-like protein 1 (DLK1) is a transmembrane protein involved in the regulation of cellular differentiation and stem cell maintenance in several tissues, including the pituitary gland. Although DLK1 expression has been reported in the adult pituitary, its spatiotemporal distribution during mouse pituitary development remains incompletely characterized. The aim of this study was to analyse the distribution of DLK1 during embryonic and postnatal development of the mouse pituitary gland and to characterize its relationship with hormone-producing cell populations. Immunohistochemistry was performed in Swiss albino mice from embryonic day 9.5 (e9.5) to postnatal day 15 (p15). Double immunofluorescence was used at e18.5 and p15 to examine the association of DLK1 immunoreactivity with ACTH-, TSH-, GH-, FSH- and PRL-producing cells. DLK1 immunoreactivity was detected from the earliest stages of pituitary development in Rathkes pouch and the ventral diencephalon. During embryonic development, DLK1-ir cells were widely distributed throughout adenohypophyseal and neurohypophyseal primordia and subsequently became progressively regionalized within the anterior, intermediate and tuberal lobes, as well as in the median eminence and posterior lobe. Cells displaying overlapping immunoreactivity for DLK1 and all hormone-producing cell populations analysed were observed at late embryonic and postnatal stages. Semiquantitative analysis at p15 indicated that approximately 32% of adenohypophyseal cells were DLK1-immunoreactive. These findings provide a detailed description of the spatiotemporal distribution of DLK1 during mouse pituitary ontogeny and reveal its association with differentiating endocrine cell populations throughout pituitary development.

CCCTC-binding factor (CTCF) is frequently mutated in endometrial cancer, resulting in genetic haploinsufficiency that contributes to tumour progression. We previously showed that depletion of CTCF disrupted cell polarity in KLE endometrial cancer spheroids; however, the implications for gene dysregulation and endometrial cancer pathophysiology remains poorly understood. ZNF185, an actin-associated and LIM domain-containing protein involved in cytoskeletal remodelling, was identified as a dysregulated target following CTCF haploinsufficiency. In this study, shRNA-mediated knockdown of CTCF was used to model haploinsufficiency in endometrial cancer cells, leading to the identification of a previously unrecognised isoform of ZNF185, named ZNF185B. Unlike the full-length protein, ZNF185B lacked co-localisation with F-actin and exhibited a diffuse cytoplasmic distribution, and ZNF185B was significantly upregulated in CTCF-depleted endometrial cancer cells and in an auxin-inducible degron model in a dose-dependent manner. Functional studies demonstrated that depletion of ZNF185 expression reduced endometrial cancer cell proliferation and clonogenic potential. Together, these findings identify ZNF185B as a novel isoform negatively regulated by CTCF protein dosage and establish ZNF185 as a requirement for endometrial cancer cell proliferation. Our results suggest that dysregulated ZNF185 expression is a crucial downstream consequence of CTCF haploinsufficiency and may contribute to tumour progression in endometrial cancer.

Microtubules are cytoskeletal polymers that play essential roles in eukaryotic cells, including structural support, cell division, and intracellular transport. During intracellular transport, kinesin motor proteins move cargo along microtubule tracks via their processive stepping. Recent studies have shown that the kinesin-1 KIF5C can damage the microtubule lattice while stepping. Microtubule damage can be repaired through incorporation of new tubulin subunits, however, excessive lattice damage results in microtubule breakage and disassembly. To identify cellular factors involved in microtubule repair, we performed an siRNA screen targeting microtubule-associated proteins (MAPs) known to regulate microtubule dynamics and stability. Based on the results, we investigated whether the end binding protein EB1 and cytoplasmic linker-associated protein 2 (CLASP2) contribute to repair of microtubule damage. To test this, we used a microtubule destruction assay in which damage was induced in microtubules gliding over surfaces coated with wild-type or mutant KIF5C proteins. Our findings suggest that CLASP2 directly facilitates microtubule repair, whereas EB1 does not. We further examined CLASP function using a microtubule repair assay and found that CLASP2 promotes repair by enhancing tubulin incorporation and reducing microtubule breakage. Together, these findings demonstrate that CLASP proteins play an important role in repairing and protecting against lattice damage caused by kinesin-1 motor activity. Our results further suggest that MAPs can directly regulate microtubule lattice integrity under mechanical stress generated by motor protein-driven intracellular transport.

Photoreceptor outer segments are sensory cilia whose maintenance depends on a balance between basal disc renewal and tip shedding, controlled by intraflagellar transport and axonemal microtubule organization. Microtubule plus-end proteins regulate microtubule dynamics and are strong candidates for roles in this process. In this study, mCherry-tagged EB1, EB3, and DCX were overexpressed in zebrafish (Danio rerio) cone photoreceptors under a cone-specific promoter. Eyes were examined at 5 and 10 dpf, and eyecup depth, diameter, and cone photoreceptor area were quantified relative to uninjected controls. At 5 dpf, all three constructs produced eyes indistinguishable from those of controls. By 10 dpf, all three constructs significantly increased eye cup depth and cone photoreceptor area. EB1 and DCX also significantly increased eye cup diameter. EB1 and, more severely, EB3 also caused retinal holes, mainly in the retinal pigment epithelium and at the outer nuclear/outer plexiform layer, along with misshapen cells near the inner plexiform layer. DXC did not cause retinal holes, but, like EB1 and EB3, produced enlarged, bulbous cone outer segments. The results show that overexpression of any of the three +TIPs results in a similar eye and photoreceptor overgrowth phenotype, while also producing construct-specific defects: EB1 and EB3 disrupt the broader retinal architecture, whereas DCX produces enlarged eyes. The shared outer segment hypertrophy suggests an imbalance between cargo delivery at the basal end and shedding of the distal tips. The organomegaly may reflect altered progenitor signaling in the ciliary marginal zone.

MYC oncoprotein binding at promoters and enhancers influences RNA polymerase II (RNAPII)-driven gene expression. Numerous genes also bind MYC near their transcriptional end sites (TESs). This often allows direct promoter-TES contact via looping and further regulates total and 'read-through' transcription that extends beyond standard termination sites. We aimed here to better clarify the rules governing TES associated MYC and/or RNAPII binding cross-talk in human and murine cells. Using ChIPseq and RNAseq datasets from the ENCODE portal and elsewhere, MYC and RNAPII binding profiles were found to differ around TESs and transcriptional start sites (TSSs). Variations in E box flanking sequences likely accounted for the somewhat lower affinities of MYC for TES-associated sites. Motifs for numerous other transcription factors were also observed to cluster non-randomly and in close proximity to MYC and RNAPII binding site peak summits. On average, genes with TES-proximal MYC or RNAPII sites were more highly expressed than those without, although co-binding tended to be suppressive. Both normal and neoplastic proliferative stimuli altered the MYC and RNAPII binding patterns of many genes, indicating that 'category switching' was common, subject to disparate external signals and often reversible. Functionally related gene sets with high levels of read-through transcription were uniformly marked by significant amounts of TES-associated MYC and/or RNAPII binding. These findings indicate that, both independently and together, MYC and RNAPII binding near TESs dynamically impact total and read-through transcription while also coordinating the expression of many common purpose gene sets.

The heterotrimeric G-protein transducin (Gt) is among the key proteins mediating phototransduction in rod and cone cells of the vertebrate retina. Even though this protein has been extensively characterized in mammals, little is known about its expression patterns in migratory songbirds. Here we characterised Gt expression in the European robin, a night-migratory songbird known for its light-dependent magnetoreception. The mechanism underlying magnetoreception is not fully understood, but one well-supported hypothesis involves a radical-pair formation in the blue light receptor cryptochrome type 4a. The - and {gamma}-subunits of cone specific transducin have been identified as possible interaction partners of cryptochrome 4a. Therefore, we analysed the expression patterns of various G-protein subunits in bird photoreceptors. Specifically, we combined single cell RNA sequencing and immunohistochemistry, and tested for protein interaction by pulldown, co-immunoprecipitation, and NanoBiT luminescence assays. We show that genes for G-protein subunits GNB1 and GNB3 (coding for Gt{beta}1 and Gt{beta}3, respectively) are predominantly expressed in rods and cones. Among {gamma}-subunits, GNGT2 (coding for Gt{gamma}T2) was the principal isoform in cones, whereas GNG11 (coding for Gt{gamma}11) was associated with rods. In contrast, we did not detect GNG10 (coding for Gt{gamma}10) expression in either photoreceptor type. Interaction assays demonstrated that all three {beta}{gamma} combinations; {beta}{gamma}T2, {beta}{gamma}10, and {beta}{gamma}11, can associate in vitro. These findings indicate that {beta}{gamma} dimer formation in vivo is likely constrained by the photoreceptor-specific expression of the respective subunits. Furthermore, the absence of GNG10 expression in rods and cones does not support a role of this {gamma}-subunit in photoreceptor-based magnetoreception.

Gene model for the ortholog of raptor in the D. grimshawi May 2011 (Agencourt dgri_caf1/DgriCAF1) Genome Assembly (GenBank Accession: GCA_000005155.1) of Drosophila grimshawi. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

The IFN-I (type I interferon) signaling pathway is the first line of defence against foreign pathogens. Stringent control of signalling pathways is necessary to maintain host immune responses and homeostasis. However, the underlying mechanism for its tight regulation is yet completely understood. In this study, we demonstrated that the TRIM family protein tripartite motif-containing 52 (TRIM52) is a novel negative regulator of IFN-{beta} production. Ectopically expressed TRIM52 markedly inhibited the activation of the IFN-{beta} promoter by ectopic expression of cGAS/STING, RIG-IN, or TRIF, MAVS, STING, and TBK1 but not by IRF3/5D, indicating that TRIM52 targets TBK1. TRIM52 also significantly inhibited the IFN-{beta}, ISG54, and ISG56 production, the dimerization of IRF3 and the nuclear localization of IRF3-YFP induced by ectopic expression of TBK1. Co-immunoprecipitation experiment revealed that TRIM52 specifically interacted with TBK1. Furthermore, the TBK1 protein, but not its mRNA, decreased considerably with increasing expression of TRIM52, and TRIM52 did not decrease the expression of the cGAS, STING, or IRF3 proteins. In addition, proteasome inhibitor MG-132 blocked the reduced TBK1 induced by TRIM52, indicating that TRIM52 caused TBK1 degradation via the proteasome pathway. Co-IP and ubiquitination assays demonstrated that TRIM52 promotion of K48-linked ubiquitination of TBK1, which depends on its E3 ubiquitin ligase. Collectively, our findings identify a previously unrecognized role of TRIM52 in regulating the IFN-I signalling pathway through targeting TBK1 for polyubiquitination and degradation.

Developmental processes depend on carefully coordinated gene expression. Expression is modulated by the binding of transcription factors (TFs) to cis-regulatory elements (CREs), like enhancers and promoters. Many computational and experimental approaches have been developed to find CREs, particularly enhancers, in the genome, each with strengths and caveats. Given the increasing availability of ATAC-seq data and methods to find TF binding therein, we hypothesized that we could use TF footprinting tools to find clusters of TF binding events within accessible chromatin that may act as CREs. Using Drosophila anterior-posterior patterning network as a test bed, we used a digital genomic footprinting tool (DGT), TOBIAS, on previously published early embryo ATAC-seq data to characterize the TF footprint landscape of 16 TFs essential for embryonic patterning. Even in this system, with its extensive enhancer annotation, most footprinted TF binding sites lie outside of known enhancers, with intergenic and intronic regions hosting the highest TF footprint count, albeit at low density. To find potential novel enhancers, we identified high-density TF footprint clusters that are highly conserved and overlap with active enhancer histone mark signals. Five high confidence candidates were selected for reporter assay validation and all five were found to drive spatially patterned expression in the embryo. This study shows that even in a highly characterized system, the analysis of footprinted TF binding sites in ATAC-seq data can uncover new regulatory regions and suggests this approach may be helpful in using existing ATAC-seq data to find novel CREs. ARTICLE SUMMARYGiven the increasing availability of ATAC-seq datasets, workflows to exploit the data to uncover new cis-regulatory elements (CREs), including enhancers, are valuable. Using early anterior-posterior patterning in the Drosophila embryo as a test case, we find that previously published transcription factor footprinting tools and ATAC-seq data can be analyzed to yield new candidate CREs. Experimental validation confirms the activity of selected candidate CREs, suggesting that existing data can be analyzed to find novel regulatory elements.

The NAD+-dependent histone deacetylase Sirt6 regulates transcription of multiple classes of genes, including those involved in metabolism, immune response, oxidative stress response, and development. Defining the Sirt6-regulated transcriptome is relevant to understanding the various important physiological roles of Sirt6, such as extending lifespan, maintaining metabolic health, and tumor suppression. Numerous studies have identified Sirt6 target genes, using both targeted and genome-wide approaches; however, consensus is limited and there has yet to be a systematic analysis of gene expression changes induced by altering Sirt6 levels. In the present study, we conducted a meta-analysis of 19 mammalian RNA-seq datasets in which Sirt6 levels were perturbed (knockout, knockdown, or overexpression). Our analyses included Gene Set Enrichment Analysis, pathway analysis of differentially expressed genes, and identification of individual differentially expressed genes. Our analysis identified consistent gene expression changes associated with lowering Sirt6 levels, including increased expression of immune response and ribosomal protein genes and reduced expression of lipid oxidation and oxidative phosphorylation genes. Extracellular Matrix and E2F target genes also had consistently increased expression upon Sirt6 reduction, highlighting novel regulation by Sirt6. To determine the conservation of gene regulation by Sirt6, we performed additional RNA-Seq meta-analysis on tissues from Drosophila melanogaster with Sirt6 deletion and overexpression. The fly datasets produced similar results to the mammal results, except for lipid oxidation genes, which were found to increase in Sirt6-low conditions. These results provide consensus about conserved and novel pathways transcriptionally regulated by Sirt6.