Consensus Sites Research Articles

Role of mod(mdg4)-67.2 protein in interactions between su(hw)-dependent complexes and their recruitment to chromatin

Su(Hw) belongs to a class of proteins that organize chromosome architecture, determine promoter activity, and participate in the formation of boundaries/insulators between regulatory domains. This protein contains a cluster of 12 zinc fingers of the C2H2 type, some of which are responsible for binding to the consensus site. The Su(Hw) protein forms a complex with the Mod(mdg4)-67.2 and the CP190 proteins, where the last one binds to all known Drosophila insulators. To further study the functioning of Su(Hw)-dependent complexes, we used the previously described su(Hw)E8 mutation, with inactive seventh zinc finger, which produced the mutant protein losing the ability to bind to the consensus site. The present work shows that the Su(Hw)E8 protein continues to directly interact with the CP190 and Mod(mdg4)-67.2 proteins. Through interaction with Mod(mdg4)-67.2, the Su(Hw)E8 protein can be recruited into Su(Hw)-dependent complexes formed on chromatin and enhance their insulator activity. Our results demonstrate that DNA-unbound Su(Hw)-dependent complexes can be recruited to Su(Hw)-binding sites through specific protein-protein interactions that are stabilized by Mod(mdg4)-67.2.

In Silico Analysis of the Missense Variants of Uncertain Significance of CTNNB1 Gene Reported in GnomAD Database.

CTNNB1 pathogenic variants are related to the improper functioning of the WNT/β-catenin pathway, promoting the development of different types of cancer of somatic origin. Bioinformatics analyses of genetic variation are a great tool to understand the possible consequences of these variants on protein structure and function and their probable implication in pathologies. The objective of this study is to describe the impact of the missense variants of uncertain significance (VUS) of the CTNNB1 gene on structure and function of the β-catenin protein. The CTNNB1 variants were obtained from the GnomAD v2.1.1 database; subsequently, a bioinformatic analysis was performed using the VarSome, UCSC Genome Browser, UniProt, the Kinase Library database, and DynaMut2 platforms to evaluate clinical significance, gene conservation, consensus sites for post-translational modifications, and the dynamics and stability of proteins. The GnomAD v2.1.1 database included 826 variants of the CTNNB1 gene, of which 385 were in exons and exon/intron boundaries. Among these variants, 214 were identified as missense, of which 146 were classified as VUS. Notably, 12 variants were in proximity to consensus sites for post-translational modifications (PTMs). The in silico analysis showed a slight tendency towards probably pathogenic for c.59C>T (p.Ala20Val) and c.983T>C (p.Met328Thr) missense VUS. These findings provide possible functional implications of these variants in some types of cancer.

Mck1-mediated proteolysis of CENP-A prevents mislocalization of CENP-A for chromosomal stability in Saccharomyces cerevisiae.

Centromeric localization of evolutionarily conserved CENP-A (Cse4 in Saccharomyces cerevisiae) is essential for chromosomal stability. Mislocalization of overexpressed CENP-A to noncentromeric regions contributes to chromosomal instability in yeasts, flies, and humans. Overexpression and mislocalization of CENP-A observed in many cancers are associated with poor prognosis. Previous studies have shown that F-box proteins, Cdc4 and Met30 of the Skp, Cullin, F-box ubiquitin ligase cooperatively regulate proteolysis of Cse4 to prevent Cse4 mislocalization and chromosomal instability under normal physiological conditions. Mck1-mediated phosphorylation of Skp, Cullin, F-box-Cdc4 substrates such as Cdc6 and Rcn1 enhances the interaction of the substrates with Cdc4. Here, we report that Mck1 interacts with Cse4, and Mck1-mediated proteolysis of Cse4 prevents Cse4 mislocalization for chromosomal stability. Our results showed that mck1Δ strain overexpressing CSE4 (GAL-CSE4) exhibits lethality, defects in ubiquitin-mediated proteolysis of Cse4, mislocalization of Cse4, and reduced Cse4-Cdc4 interaction. Strain expressing GAL-cse4-3A with mutations in three potential Mck1 phosphorylation consensus sites (S10, S16, and T166) also exhibits growth defects, increased stability with mislocalization of Cse4-3A, chromosomal instability, and reduced interaction with Cdc4. Constitutive expression of histone H3 (Δ16H3) suppresses the chromosomal instability phenotype of GAL-cse4-3A strain, suggesting that the chromosomal instability phenotype is linked to Cse4-3A mislocalization. We conclude that Mck1 and its three potential phosphorylation sites on Cse4 promote Cse4-Cdc4 interaction and this contributes to ubiquitin-mediated proteolysis of Cse4 preventing its mislocalization and chromosomal instability. These studies advance our understanding of pathways that regulate cellular levels of CENP-A to prevent mislocalization of CENP-A in human cancers.

CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment

The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.

Identification and Characterization of a Pepsin- and Chymotrypsin-Resistant Peptide in the α Subunit of the 11S Globulin Legumin from Common Bean (Phaseolus vulgaris L.).

The 11S globulin legumin typically accounts for approximately 3% of the total protein in common beans (Phaseolus vulgaris). It was previously reported that a legumin peptide of approximately 20 kDa is resistant to pepsin digestion. Sequence prediction suggested that the pepsin-resistant peptide is located at the C-terminal end of the α-subunit, within a glutamic acid-rich domain, overlapping with a chymotrypsin-resistant peptide. Using purified legumin, the peptide of approximately 20 kDa was found to be resistant to pepsin digestion in a pH-dependent manner, and its location was determined by two-dimensional gel electrophoresis and LC-MS-MS. The location of the chymotrypsin-resistant peptide was confirmed by immunoblotting with peptide-specific polyclonal antibodies. The presence of a consensus site for proline hydroxylation and arabinosylation, the detection of hydroxyproline residues, purification by lectin affinity chromatography, and a difference in electrophoretic migration between the chymotrypsin- and pepsin-resistant peptides suggest the presence of a large O-glycan within these peptides.

Role of Mod(mdg4)-67.2 Protein in Interactions between Su(Hw)-Dependent Complexes and Their Recruitment to Chromatin.

Su(Hw) belongs to the class of proteins that organize chromosome architecture, determine promoter activity, and participate in formation of the boundaries/insulators between the regulatory domains. This protein contains a cluster of 12 zinc fingers of the C2H2 type, some of which are responsible for binding to the consensus site. The Su(Hw) protein forms complex with the Mod(mdg4)-67.2 and the CP190 proteins, where the last one binds to all known Drosophila insulators. To further study functioning of the Su(Hw)-dependent complexes, we used the previously described su(Hw)E8 mutation with inactive seventh zinc finger, which produces mutant protein that cannot bind to the consensus site. The present work shows that the Su(Hw)E8 protein continues to directly interact with the CP190 and Mod(mdg4)-67.2 proteins. Through interaction with Mod(mdg4)-67.2, the Su(Hw)E8 protein can be recruited into the Su(Hw)-dependent complexes formed on chromatin and enhance their insulator activity. Our results demonstrate that the Su(Hw) dependent complexes without bound DNA can be recruited to the Su(Hw) binding sites through the specific protein-protein interactions that are stabilized by Mod(mdg4)-67.2.

Abstract 845: Population attributable fraction of cancer incidence due to infectious agents in 2020 in the Republic of Korea

Abstract Purpose: Earlier in 2009, National Cancer Center Korea estimated population attributable fraction (PAF) of cancer incidence due to infectious agents as 24.5% in men and 15.4% in women. This study aimed to investigate the proportion of cancer incidence attributable to infectious agents in the Korean population as of 2020. Materials and Methods: We organized the Consensus Committee to establish strategy and methodology of PAF estimation. Based on the consensus, infectious agents and cancer sites for PAF estimation were selected according to the IARC List of classification with sufficient evidence in human. As a result, infectious agents included hepatitis B and C virus (HBV and HCV), Helicobacter pylori (H. pylori), human papilloma virus (HPV), Clonorchis sinensis (C.sinensis), Epstein Barr virus, and human immunodeficiency virus, and cancer sites included hepatocellular carcinoma (HCC), cholangiocarcinoma (CCC), gastric cancer, pancreatic cancer, cervical cancer, and non-Hodgkin lymphoma. The PAF was calculated by using Levin’s formula including exposure prevalence and relative risks (RRs). Exposure prevalence data were collected from literature review of studies in Korean population in 2005 or earlier, assuming at least 15 years of latent period from risk exposure to cancer development. We performed systematic review for cohort studies and case-control studies which investigated RRs or ORs of cancer due to infectious agents in Korean population. Pooled RRs were estimated by meta-analysis of RRs or ORs by using random-effects model. Results: The fractions of all cancer incidence attributable to infectious agents were estimated to be 13.5% and 7.1% in men and women, respectively. The reduction in PAFs of cancer incidence due to infection in 2020 compared to 2009 is considered due to decrease in exposure prevalence. The major findings regarding infectious agents with large PAFs are as the following. We found that the fractions of HCC cases attributable to HBV infection were 47.7% and 38.4% for cancer incidence in men and women, respectively. The estimated PAFs of gastric cancer due to H. pylori were 40.4% in men and 38.2% in women. C. sinensis was related to 9.8% of CCC cases in men and 5.2% in women. A total of 77.7% of cervical cancer incidence was attributed to HPV infection. Conclusion: Although the total PAF due to infection has decreased over the last decade, infection still contributes a substantial fraction to cancer incidence in Korea. These recent estimates of cancer burden due to infection are important for planning and evaluating the national cancer prevention programs. Citation Format: Kyung-Shin Lee, Hwa Jin Lee, Yoon-Jung Choi, Moran Ki, Aesun Shin, Jong-Hun Kim, Sue-Kyung Park, So-Seul Sung, Sung Ji Moon, Hong Gwan Seo, Jin-Kyoung Oh, Jeong-Soo Im. Population attributable fraction of cancer incidence due to infectious agents in 2020 in the Republic of Korea [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 845.

Abstract 1977: ACR-2316: A potentially first-in-class, potent, selective WEE1/PKMYT1 inhibitor rationally designed for superior single agent activity through synergistic disruption of cell cycle checkpoints

Abstract WEE1 and PKMYT1 kinases play essential roles in cell cycle checkpoints and DNA damage response. Genetic interaction has been documented between WEE1 and PKMYT1, and clinical trials have reported clinical activity with inhibitors of WEE1 (adavosertib, azenosertib) and PKMYT1 (lunresertib). Here, we report the discovery and characterization of ACR-2316, a dual inhibitor of WEE1 and PKMYT1 specifically designed for optimal selectivity through co-crystallography and superior single agent activity uniquely enabled by Acrivon Predictive Precision Proteomics (AP3). Mass spectrometry-based AP3 profiling was conducted across several novel WEE1 and PKMYT1 inhibitor leads generated through co-crystallography-based rational drug design. Selective leads originating from one series were further optimized using AP3 for biological structure-activity relationship analysis. AP3 profiling revealed WEE1 inhibitor-upregulated phosphorylation sites across a subset of phosphoproteins that were oppositely regulated (quenched) by PKMYT1 inhibitors. Consensus sites for these included CDK1 T14, a direct PKMYT1 phosphorylation site, as well as CHK1 S296. A particular lead compound, ACR-2316, demonstrated a desirable potent, balanced ratio of cellular WEE1 (IC50 = 2 nM, IC90 = 10 nM) and PKMYT1 (IC20 = 44 nM) inhibition resulting in superior activation of the mitotic kinases CDK1, CDK2, and PLK1 compared to adavosertib and lunresertib, based on annotated kinase substrate relationships. ACR-2316 is more selective than adavosertib, azenosertib, and lunresertib based on >200 kinases profiled by AP3 and 468 kinases assessed by KINOMEscan. Cell cycle analyses demonstrated a drastic ACR-2316-induced S-G2/M accumulation qualitatively distinct from adavosertib or lunresertib. In a 19-cancer cell line proliferation assay (CellTiter-Glo), ACR-2316 demonstrated greater potency in all cell lines tested compared to adavosertib and lunresertib (mean IC50 = 70, 252 and 364 nM, respectively). Superior anti-cancer activity of ACR-2316 was observed in 12 ovarian cancer patient-derived xenograft models tested ex vivo (CellTiter-Glo 3D) compared to azenosertib and lunresertib (mean IC50 = 9, 248 and 1620 nM, respectively). Across human tumor xenograft mouse models, oral administration of ACR-2316 demonstrated superior, durable, dose-dependent efficacy compared to azenosertib and lunresertib and was well tolerated at all doses. Complete responses observed with ACR-2316 were associated with strong WEE1 and intermediate PKMYT1 inhibition in tumors. In conclusion, ACR-2316 is a potent, selective dual WEE1/PKMYT1 inhibitor with superior single-agent activity compared to clinical WEE1 or PKMYT1 inhibitors. ACR-2316 is progressing through IND-enabling studies in preparation for clinical monotherapy development. Citation Format: Caroline Wigerup, Helén Nilsson, Lei Shi, Joon Jung, Joelle Baddour-Sousounis, Ruban Cornelius, Nina Lipjankic, Uthira Muralitharan, Valentina Siino, Ignacio Arribas Diez, Zachary Best, Martina Pasetto, William Dahlberg, Shahrzad Rafiei, Portia Lombardo, Magnus E. Jakobsson, Reina Improgo, Christina Scherer, John van Duzer, David A. Proia, Kristina Masson, Peter Blume-Jensen. ACR-2316: A potentially first-in-class, potent, selective WEE1/PKMYT1 inhibitor rationally designed for superior single agent activity through synergistic disruption of cell cycle checkpoints [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 1977.

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.

The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment-lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein-ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.

SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model.

SUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to fully expand and/or recognize the SUMOylated proteome. Herein, we present a novel, deep learning-based approach called SumoPred-PLM for human SUMOylation prediction with sensitivity, specificity, Matthew's correlation coefficient, and accuracy of 74.64%, 73.36%, 0.48% and 74.00%, respectively, on the CPLM 4.0 independent test dataset. In addition, this novel platform uses contextualized embeddings obtained from a pre-trained protein language model, ProtT5-XL-UniRef50 to identify SUMO2/3-specific conjugation sites. The results demonstrate that SumoPred-PLM is a powerful and unique computational tool to predict SUMOylation sites in proteins and accelerate discovery.

Subcellular localization of core beta(1,2)-xylosylated N-glycoproteins in the green microalgae Chlamydomonas reinhardtii

The green microalgae Chlamydomonas reinhardtii synthesizes a N-glycan precursor within the endoplasmic reticulum (ER) that is then transferred to specific asparagine residues of the protein N-glycosylation consensus sites. Maturation of this precursor in the ER and then in the Golgi apparatus results in N-glycans composed of a non-canonical linear Man5GlcNAc2 that is partially O-methylated and carries out one or two xylose residues. One xylose residue was demonstrated to be a core beta(1,2)-xylose. Recently, two xylosyltransferases, named A (XTA) and B (XTB) respectively, were demonstrated to be responsible for the addition of this core beta(1,2)-xylose. Nowadays, even if information is available regarding the protein N-glycosylation pathway and especially the core beta(1,2)-xylosylation in C. reinhardtii, no data regarding the subcellular localization of this subset of glycosylated proteins is available. Therefore, in this work, subcellular immunolocalization of N-glycoproteins bearing the core beta(1,2)-xylose epitope was carried out using an optimized protocol of transmission electron microscopy of CC-5325 and CC-5155 reference strains (wild types) compared to the MXTAxIMXTB double insertional mutant strain in which the core beta(1,2)-xylosylation is fully-lacking. Such a study gives a first cartography of specific glycoepitopes in microalgae and new insights on the distribution of core beta(1,2)-xylosylated glycoproteins in C. reinhardtii organelles.

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei.

Paternal genomes are compacted during spermiogenesis and decompacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in Xenopus egg extracts. In pronuclei, chromatin compartmentalization increases, but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, and cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.

A splice donor variant of GAS8 induces structural disorganization of the axoneme in sperm flagella and leads to nonsyndromic male infertility.

Motile cilia and flagella are closely related organelles structured around a highly conserved axoneme whose formation and maintenance involve proteins from hundreds of genes. Defects in many of these genes have been described to induce primary ciliary dyskinesia (PCD) mainly characterized by chronic respiratory infections, situs inversus and/or infertility. In men, cilia/flagella-related infertility is usually caused by asthenozoospermia due to multiple morphological abnormalities of the sperm flagella (MMAF). Here, we investigated a cohort of 196 infertile men displaying a typical MMAF phenotype without any other PCD symptoms. Analysis of WES data identified a single case carrying a deleterious homozygous GAS8 variant altering a splice donor consensus site. This gene, also known as DRC4, encodes a subunit of the Nexin-Dynein Regulatory Complex (N-DRC), and has been already associated to male infertility and mild PCD. Confirming the deleterious effect of the candidate variant, GAS8 staining by immunofluorescence did not evidence any signal from the patient's spermatozoa whereas a strong signal was present along the whole flagella length in control cells. Concordant with its role in the N-DRC, transmission electron microscopy evidenced peripheral microtubule doublets misalignments. We confirm here the importance of GAS8 in the N-DRC and observed that its absence induces a typical MMAF phenotype not necessarily accompanied by other PCD symptoms.

Abstract 19018: Unraveling the Regulatory Landscape of NKX2-5 in Human Left Atrial Tissue: Implications for Atrial Fibrillation

Cardiac transcription factors are emerging as crucial modulators of atrial fibrillation (AF), with rare and common variation implicated in AF. Mutations in NKX2-5 and more recently, NFATC1 were reported in families with autosomal dominant young-onset AF. Here, we explore the landscape of NKX2-5 and NFATC1 in human left atrium, using Chromatin Immunoprecipitation Sequencing (ChIP-seq), DAVID functional annotation and HOMER motif analyses. Post-mortem human left atrial tissue samples (n=5) were obtained from the National Disease Research Interchange (NDRI) within a recovery interval of < 4 hours. Preserved microstructural integrity and normal staining patters for TNNT2 and vimentin were verified using confocal microscopy. ChIP-seq analysis revealed an average of 2.62k NKX2-5 binding peaks, with 118 genes bound in all samples. Functional analysis identified significant enrichment in gene ontology categories and pathways (Table 1), including adrenergic and PPAR signaling pathways known to participate in AF susceptibility. Using HOMER, we mapped 55 NFATC1 consensus binding sites to the NKX2-5 ChIP peaks. Two NFATC1 consensus sites localized to an NKX2-5 binding peak located upstream from MEF2A (Figure 1). Published HI-C data from human right atrium indicates the NFATC1 binding sites are adjacent to the promoter of MEF2A in 3D space, suggesting that NKX2-5 and NFATC1 co-regulate MEF2A. In murine atria, mef2A regulates genes involved in fibrosis and adhesion, processes that are crucial in the pathogenesis of atrial fibrillation. Our data, together with published literature, provide a framework for understanding transcriptional networks that may predispose to human AF.

CDK signaling via nonconventional CDK phosphorylation sites.

Since the discovery of cyclin-dependent kinases (CDKs), it has been perceived as a dogma that CDK signaling in the cell cycle is mediated via targeting the CDK consensus sites: the optimal and the minimal motifs S/T-P-x-K/R and S/T-P, respectively. However, more recent evidence suggests that often the CDK phosphorylation events of regulatory importance are mediated via nonconventional CDK sites that lack the required +1Pro of the consensus site motif. In these cases, the loss of specificity seems to be compensated via distant docking interactions facilitated by 1) phosphorylated priming sites binding to phospho-adaptor Cks1 and/or 2) cyclin-specific docking interactions via Short Linear Motifs (SLiMs) in substrates. This Perspective discusses the possible reasons why nonconventional CDK sites are used for CDK signaling. First, the nonconventional CDK sites can act as specificity filters to recognize and distinguish the CDK signal from many other proline-directed kinases in cells. Second, the nonconventional CDK sites in combination with the docking mechanisms provide a much wider range of phosphorylation rates, and thus, also a wider range of CDK thresholds during the accumulation and decline of CDK activity during the cell cycle. As a large number of Cks1-dependent nonconventional CDK sites have been discovered recently, past studies focusing on mutating only the consensus sites should likely be critically reexamined. It is also very likely that phosphorylation of nonconventional sites is crucial in many other kinase-signaling networks.

Distinct Mitotic Functions of Nucleolar and Spindle-Associated Protein 1 (NuSAP1) Are Controlled by Two Consensus SUMOylation Sites.

Nucleolar and Spindle-Associated Protein 1 (NuSAP1) is an important mitotic regulator, implicated in control of mitotic microtubule stability and chromosome segregation. NuSAP1 regulates these processes by interacting with several protein partners. Its abundance, activity and interactions are therefore tightly regulated during mitosis. Protein conjugation with SUMO (Small Ubiquitin-like MOdifier peptide) is a reversible post-translational modification that modulates rapid changes in the structure, interaction(s) and localization of proteins. NuSAP1 was previously found to interact with RANBP2, a nucleoporin with SUMO ligase and SUMO-stabilizing activity, but how this interaction affects NuSAP1 activity has remained elusive. Here, we show that NuSAP1 interacts with RANBP2 and forms proximity ligation products with SUMO2/3 peptides in a RANBP2-dependent manner at key mitotic sites. A bioinformatic search identified two putative SUMO consensus sites in NuSAP1, within the DNA-binding and the microtubule-binding domains, respectively. Site-specific mutagenesis, and mitotic phenotyping in cell lines expressing each NuSAP1 mutant version, revealed selective roles of each individual site in control of NuSAP1 localization and in generation of specific mitotic defects and distinct fates in daughter cells. These results identify therefore two new regulatory sites for NuSAP1 functions and implicate RANBP2 in control of NuSAP1 activity.

Region-specific reversal of epidermal planar polarity in the rosette fancy mouse.

The planar cell polarity (PCP) pathway collectively orients cells with respect to a body axis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment across the skin. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that rosette hair follicles emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6, which alters a consensus site for N-linked glycosylation, inhibiting its membrane localization. Unexpectedly, the Fzd6 trafficking defect does not block asymmetric localization of the other PCP proteins. Rather, the normally uniform axis of PCP asymmetry rotates where the PCP-directed cell movements that orient follicles are reversed, suggesting the PCP axis rotates 180°. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce posterior whorls in the rosette fancy mouse.

A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation.

Epigenetic mechanisms are essential to establish and safeguard cellular identities in mammals. They dynamically regulate the expression of genes, transposable elementsand higher-order chromatin structures. Consequently, these chromatin marks are indispensable for mammalian development and alterations often lead to disease, such as cancer. Bivalent promoters are especially important during differentiation and development. Here we used a genetic screen to identify new regulators of a bivalent repressed gene. We identify BEND3 as a regulator of hundreds of bivalent promoters, some of which it represses, and some of which it activates. We show that BEND3 is recruited to a CpG-containg consensus site that is present in multiple copies in many bivalent promoters. Besides having direct effect on the promoters it binds, the loss of BEND3 leads to genome-wide gains of DNA methylation, which are especially marked at regions normally protected by the TET enzymes. DNA hydroxymethylation is reduced in Bend3 mutant cells, possibly as consequence of altered gene expression leading to diminished alpha-ketoglutarate production, thus lowering TET activity. Our results clarify the direct and indirect roles of an important chromatin regulator, BEND3, and, more broadly, they shed light on the regulation of bivalent promoters.

Nimbolide Targets Multiple Signalling Pathways to Reduce Neuroinflammation in BV-2 Microglia

Nimbolide, a limonoid compound found in the neem plant, was investigated for effects on neuroinflammation in BV-2 microglia activated with lipopolysaccharide (LPS). Cultured BV-2 cells were treated with nimbolide (125, 250 and 500 nM) followed by stimulation with LPS (100 ng/ml). Results showed that nimbolide caused a significant reduction in the levels of TNFα, IL-6, IFNγ, NO/iNOS and PGE2/COX-2 in LPS-activated BV-2 cells. Further experiments revealed that LPS-induced increased expression of phospho-p65 and phospho-IκBα proteins were reduced in the presence of nimbolide. Also, LPS-induced NF-κB acetylation, increased binding to consensus sites and transactivation, as well as phosphorylation of p38 and JNK MAPKs were reduced by nimbolide. Reduction of cellular ROS generation by nimbolide was accompanied by a reduction in gp91phox protein levels, while antioxidant effects were also observed through elevation in protein levels of HO-1 and NQO-1. It was observed that treatment of BV-2 microglia with nimbolide resulted in reduced levels of cytoplasmic Nrf2, which was accompanied by increased levels in the nucleus. Furthermore, treatment with this compound resulted in increased binding of Nrf2 to antioxidant responsive element (ARE) consensus sites accompanied by enhanced ARE luciferase activity. Knockdown experiments revealed a loss of anti-inflammatory activity by nimbolide in cells transfected with Nrf2 siRNA. Treatment with nimbolide resulted in nuclear accumulation of SIRT-1, while siRNA knockdown of SIRT-1 resulted in the reversal of anti-inflammatory activity of nimbolide. It is proposed that nimbolide reduces neuroinflammation in BV-2 microglia through mechanisms resulting in dual inhibition of NF-κB and MAPK pathways. It is also proposed that activation of Nrf2 antioxidant mechanisms may be contributing to its anti-inflammatory activity.Graphical

Cdc14 phosphatase counteracts Cdk-dependent Dna2 phosphorylation to inhibit resection during recombinational DNA repair

Cyclin-dependent kinase (Cdk) stimulates resection of DNA double-strand breaks ends to generate single-stranded DNA (ssDNA) needed for recombinational DNA repair. Here we show in Saccharomyces cerevisiae that lack of the Cdk-counteracting phosphatase Cdc14 produces abnormally extended resected tracts at the DNA break ends, involving the phosphatase in the inhibition of resection. Over-resection in the absence of Cdc14 activity is bypassed when the exonuclease Dna2 is inactivated or when its Cdk consensus sites are mutated, indicating that the phosphatase restrains resection by acting through this nuclease. Accordingly, mitotically activated Cdc14 promotes Dna2 dephosphorylation to exclude it from the DNA lesion. Cdc14-dependent resection inhibition is essential to sustain DNA re-synthesis, thus ensuring the appropriate length, frequency, and distribution of the gene conversion tracts. These results establish a role for Cdc14 in controlling the extent of resection through Dna2 regulation and demonstrate that the accumulation of excessively long ssDNA affects the accurate repair of the broken DNA by homologous recombination.