Chromatin-modifying Enzymes Research Articles

Exploring the Frontier of Cyclic Dipeptides: A Bioinformatics Approach to Potential Therapeutic Applications in Schizophrenia.

Cyclic dipeptides (CDPs), known for their diverse biological activities, have potential therapeutic applications in mental and behavioral disorders (MBDs), particularly schizophrenia. This study explores the CDPs' therapeutic potential using bibliometric analysis, network pharmacology, molecular docking, and experimental verification, focusing on the interactions with the SIGMA1 receptor. A literature review over three decades utilizing the Web of Science Core Collection (WOSCC) was conducted to identify the emerging trends in CDPs research. A compound library was constructed from the PubChem database, and target prediction using SwissTargetPrediction revealed 800 potential protein targets. A compound-target network highlighted the key interactions with kinases, G protein-coupled receptors, and chromatin-modifying enzymes. Enrichment analysis revealed significant associations with schizophrenia and other MBDs. Schizophrenia-related targets among the potential protein targets were identified using the GEO database. Molecular docking results showed interactions of MC4R, OPRK1, SIGMA1, and CDK5R1 with various CDPs compounds, with SIGMA1 being especially noteworthy. Most CDPs exhibited lower binding energies than the control compounds NE-100 and duloxetine. Experimental validation demonstrated that CDPs such as Cyclo(Ala-Gln), Cyclo(Ala-His), and Cyclo(Val-Gly) exhibited IC50 values of 13.4, 19.4, and 11.5 μM, respectively, against SIGMA1, indicating biological activity. Our findings underscore their potential as therapeutic agents for schizophrenia, highlighting the need for further modifications to enhance specificity and efficacy. This work paves the way for future investigations into CDPs, contributing to developing targeted treatments for schizophrenia and related mental health disorders.

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On the Cover: lncRNAs mechanisms of action: As a scaffold aids in the assembly of RNA protein complexes, thereby facilitating or inhibiting transcription. (B) As a signal molecule recruits chromatin modification enzymes such as deacetylases, acetylases, and histone methylases in response to varying stimuli to suppress locus genes. (C) LncRNAs sponge miRNAs to repress miRNA‐mediated gene regulation. (D) As a guide from transcription complexes to control the expression of downstream genes. (E) Decoy lncRNAs prevent the binding of regulatory factors to the genome and terminate its regulation. (F) Upon binding to RBPs, and changing their cellular localization which in turn alters the expression of RBPs target genes by Ebrahimnezhad et al.; Article first published: 1 August 2024; https://doi.org/10.1002/iub.2888.image

8569 Defining Cell-Intrinsic Defects In Hepatic Insulin Resistance In Type 2 Diabetes Using A Human iPS Cell-Derived Disease-In-A-Dish Model

Abstract Disclosure: A. Gattu: None. M. Tanzer: None. T. Yaron: None. L. Cantley: None. C.R. Kahn: None. Hepatic insulin resistance is central to type 2 diabetes (T2D). Understanding the cellular drivers underlying insulin resistance in the liver is challenging since, in vivo, this can be due to cell-intrinsic defects in insulin signaling, as well as the effects of multiple circulating factors that can modify insulin signaling. Here, we have utilized inducible pluripotent stem cells (iPS) from 8 control and 8 T2D patients differentiated in vitro into hepatocytes (iHeps) to dissect the cell-intrinsic defects in hepatic insulin resistance. We find that following stimulation with insulin, T2D iHeps displayed “pathway-selective insulin resistance,” in which insulin failed to suppress gene expression of critical gluconeogenic enzymes (PCK1, G6PC) but continued to stimulate expression of the lipogenic enzymes (FASN, ACACA). This was associated with a 1.5-fold higher level of insulin stimulation of C[1]4 acetate into lipids, i.e., de novo lipogenesis. Immunoblotting analysis showed T2D iHeps exhibited a 50% reduction in phosphorylation of the insulin receptor IRY[1][1]35 and ∼ 30% reductions in AKTT308, GSK3αS2[1]/GSK3βS9, and FOXO1T24/FOXO3aT32 in T2D following insulin stimulation for 10 minutes. To define the full spectrum of alterations in signaling in iHeps, we used unbiased LC-MS/MS-based phosphoproteomics. This revealed alterations in 987 insulin-regulated phosphosphorylations that had increased phosphorylation after insulin treatment and alterations in 723 sites for which insulin decreased phosphorylation (with a |fold-change| >1.5 and adj. p < 0.05). These alterations were of two types: 43% of the altered insulin-regulated phosphosites showed reduced or “impaired” insulin regulation, but 57% of the phosphosites displayed new or significantly increased insulin-regulated phosphorylations in T2D, i.e., “emergent” signaling. The impaired signaling in T2D included losses in the insulin receptor signaling cascade, Rho-GTPase pathway, Notch-HLH, and anti-viral mechanisms of IFN-stimulated genes. In contrast, emergent signaling included other components of the Rho-GTPase pathway, metabolism of RNA, membrane trafficking, and chromatin-modifying enzymes. Using an AI-based kinase-substrate association analysis, we found that the deficiencies in signaling represented reduced actions of kinases AKT2, AKT3, PKCθ, CHK2, PHKG2, and/or STK32C kinases, while the emergent changes represented increases in ROCK1, ROCK2, MST4 and/or BCKDK kinase activity. In summary, phosphoproteomic analyses of iHeps revealed a comprehensive insulin signaling network disrupted in insulin resistance in the liver in T2D, which underlies the etiology of insulin resistance. These alterations can be ascribed to changes in the activity of two classes of upstream kinases, representing potential new targets for treating T2D. Presentation: 6/1/2024

The proteasome inhibitor ixazomib targets epigenetic chromatin modification enzymes upregulated by m2c macrophage polarisation in lung cancer

The proteasome inhibitor ixazomib targets epigenetic chromatin modification enzymes upregulated by m2c macrophage polarisation in lung cancer

AChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs.

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Monoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here, we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.

Autoregulatory mechanism of enzyme activity by the nuclear localization signal of lysine-specific demethylase 1

The N-terminal region of the human Lysine Specific Demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple post-translational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N-terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N-terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays reveal that LSD1’s own electropositive NLS amino acids 107-120 inhibit demethylation activity on a model Histone 3 lysine 4 di-methyl (H3K4me2) peptide (Kiapp ∼ 3.3 μM) and H3K4me2 nucleosome substrates (IC50 ∼ 30.4 μM), likely mimicking the histone H3 tail. Further, when the identical, inhibitory NLS region contains phosphomimetic modifications, inhibition is partially relieved. Based upon these results and biophysical data, a regulatory mechanism for the LSD1-catalyzed demethylation reaction is proposed whereby NLS-mediated autoinhibition can occur through electrostatic interactions, and be partially relieved through phosphorylation that occurs proximal to the NLS. Taken together, the results highlight a dynamic and synergistic role for PTMs, IDRs, and structured regions near LSD1 active site and introduces the notion that phosphorylated mediated NLS regions can function to fine-tune chromatin modifying enzyme activity.

High TLX1 Expression Correlates with Poor Prognosis and Immune Infiltrates in Patients with Lung Adenocarcinoma.

To develop optimal personalized therapy for lung adenocarcinoma (LUAD), potential biomarkers associated with the prognosis are urgently needed. It is unclear what role T Cell Leukemia Homeobox 1 (TLX1) plays in LUAD. In this study, TLX1's relationship with LUAD was investigated using TCGA database analysis, bioinformatics analysis, and experimental validation. We examined the expression of TLX1 in pan cancer and LUAD, the relationship between TLX1 expression and clinical features, immune infiltration, its diagnostic and prognostic value, as well as TLX1 related pathways. The analysis included various statistical methods, including the Kaplan-Meier method, Cox regression analysis, GSEA, and immune infiltration analysis. TLX1 expression in LUAD cell lines was validated using qRT-PCR. In LUAD patients, high expression of TLX1 was associated with T stage (P<0.001). High TLX1 expression was associated with worse overall survival (OS) (HR: 1.57; 95% CI: 1.18-2.1; P=0.002). And TLX1 HR: 1.619; 95% CI: 1.012-2.590; P=0.044) was independently correlated with OS in LUAD patients. TLX1 expression was associated with the pathways, including Rho GTPase effectors, DNA repair, TCF dependent signaling in response to WNT, signaling by Nuclear Receptors, signaling by Notch, chromatin-modifying enzymes, ESR-mediated signaling, cellular senescence, and transcriptional regulation by Runx1. TLX1 expression was correlated with aDC, Tcm, and TReg cells. The expression of TLX1 was significantly increased in LUAD cells compared to BEAS-2B cells. An association between high TLX1 expression and poor survival and immune infiltration was found in LUAD patients. There may be a potential role for TLX1 in diagnosis, prognosis, and immunotherapy for LUAD.

Abstract IA001: Cellular and molecular underpinnings of field cancerization and progression to invasive carcinoma in bladder cancer

Abstract Two major concerns in clinical management of bladder cancer are: (i) the high frequency of recurrence; and (ii) the morbidity and mortality associated with progression to invasive disease (invasive urothelial carcinoma, IUC). To gain a better understanding of these issues we have used the murine BBN (N-butyl-N-(4-hydroxylbutyl) nitrosamine) experimental model of bladder cancer, as well as tissue samples from normal human bladders and from bladders of patients at various stages of bladder cancer formation and progression. We have documented in the BBN model a CIS-like stage, prior to invasion, in which clonal expansion from a single cell occupies a significant fraction of the urothelium. With this experimental murine model alongside observations from patient samples and data from The Cancer Genome Atlas (TCGA), we have ascertained that a key event in progression of pre-invasive to invasive carcinoma is the silencing of the Sonic hedgehog (Shh) member of the Hedgehog gene family. Silencing-associated invasion appears due to the loss of SHH-induced differentiation signals, which when present slow growth and block invasion. Despite the consistent loss of SHH expression in invasive murine and human bladder cancers, however, TCGA data show few if any mutations in the SHH gene of IUC cells. Instead, our studies of patient samples and cancer-derived cell lines reveal that the loss of SHH expression is due to tighter chromosomal packaging and reduced accessibility of a bladder-specific enhancer located ~200 kb upstream of the SHH transcription start site. We have found that inhibitors of certain chromatin-modifying enzymes, including an FDA-approved drug, are capable of re-activating SHH expression, and are testing the possibility that these drugs may block or reverse invasion of urothelial carcinoma. The high frequency of bladder cancer recurrence is thought to result from field cancerization, that is, an increased probability of new cancer formation in apparent normal urothelium, even after successful resection of the primary tumor. To understand the basis for this field effect, we compared apparent normal urothelium from cancer patients to truly normal urothelium from bladders never affected by malignancy. We found that apparent normal samples display a dramatically increased basal character in transcriptomic assays, using as a metric of basalization an index constructed from single cell RNA-seq analysis of normal urothelium. We and others have demonstrated previously by lineage tracing and cell ablation studies in the BBN model that IUC arises from basal stem cells of the urothelium. The basalization of urothelium distant from the primary tumor that we observe thus may account for the increased probability of cancer formation in the apparent normal urothelium of bladder cancer patients. We have found that several FDA-approved antagonists of EGF signaling can reverse this basalization in the mouse BBN model as well as in organoid culture, and that these drugs dramatically reduce the formation of tumors following BBN exposure. Citation Format: Philip A. Beachy, Kris B. Prado, Aaron M. Kershner, Karim Mrouj, Bernard M. Kiss, Hua Dong, Ozgu Aydogdu, Ye Tian, Joseph C. Liao. Cellular and molecular underpinnings of field cancerization and progression to invasive carcinoma in bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr IA001.

O06 Naïve human keratinocytes initiate a chromatin-protective mechanism in response to ultraviolet radiation through the upregulation of histone deacetylase 5

Abstract Introduction and aims During normal development and throughout life, epigenetic changes arise in response to an individuals’ behaviour and environmental exposures. Histone deacetylases (HDACs) are chromatin-modifying enzymes that regulate gene expression and their activity and expression in primary human keratinocytes alters with increasing age. Solar ultraviolet radiation (UVR) is a major causative factor of skin ageing, but how this factor affects HDAC expression and activity is largely unknown. We aimed to determine how UVR exposure affects HDAC expression and activity in primary human keratinocytes. Methods Normal human epidermal keratinocytes (NHEKs) from juvenile (aged 1–6 years; n = 3), middle-aged (56–61 years; n = 3) and aged (83–85 years; n = 3) donors were exposed to solar-simulated radiation (SSR) and HDAC abundance and activity were assayed. Results Exposure to SSR significantly increased HDAC activity in primary NHEKs irrespective of donor age (P &amp;lt; 0.05). However, Western blotting for HDAC abundance revealed that there was a differential response to SSR exposure across age groups; juvenile NHEKs expressed significantly more HDAC5 in response to SSR (P &amp;lt; 0.05) than cells from middle-aged or aged donors. Furthermore, following SSR exposure of juvenile NHEKs, the cellular localization of HDAC5 was redistributed to the nucleus from the cytoplasm. Dual immunofluorescence staining revealed that those NHEKs with nuclear HDAC5 expression were also positive for p16INK4a, a robust marker of cellular senescence (P &amp;lt; 0.01). Conclusions Our Results suggest that naïve human keratinocytes are responsive to UVR exposure and appear to initiate a chromatin-protective mechanism through the upregulation of HDAC5 to prevent gene expression of damaged DNA.

Novel protein-truncating variants of a chromatin-modifying gene MSL2 in syndromic neurodevelopmental disorders

Numerous large scale genomic studies have uncovered rare but recurrent pathogenetic variants in a significant number of genes encoding epigenetic machinery in cases with neurodevelopmental disorders (NDD) especially autism spectrum disorder (ASD). These findings provide strong support for the functional importance of epigenetic regulators in neurodevelopment. After the clinical genomics evaluation of the patients using exome sequencing, we have identified, three novel protein-truncating variants (PTVs) in the MSL2 gene (OMIM: 614802) which encodes a chromatin modifying enzyme. MSL2 modifies chromatin through both mono-ubiquitination of histone 2B on lysine 34 (K34) and acetylation of histone H4 on lysine 16 (K16). We reported first time the detailed clinical features associated with 3 MSL2 PTVs. There are 15 PTVs (13 de novo) reported from the large genomics studies (12 cases) or ClinVar (3 cases) of NDD, ASD, and developmental disorders (DD) but the specific clinical features for these cases are not described. Taken together, our descriptions of dysmorphic face and other features support the causal role of MSL2 in a likely syndromic neurodevelopmental disorder and add MSL2 to a growing list of epigenetic genes implicated in ASD.

Abstract PO4-24-06: The function of GATA3-PARP1 complex in breast cancer during GATA3-mediated cellular reprogramming

Abstract In eukaryotic cells, genomic DNA is packaged into chromatin, a complex of DNA, histones, and other proteins. Chromatin acts as a physical barrier for many transcription factors, preventing them from efficiently binding to their recognition sequences within the nucleosome. Pioneer factors are a class of transcription factors that bind to nucleosomes and activate silent chromatin. Pioneer factors are frequently involved in various immune cell pathways, tissue development, and homeostasis, thereby, underscoring their important roles in development and disease. Previous research found that pioneer factors have at least three fundamental properties: However, the molecular mechanisms of pioneer factor-mediated cellular reprogramming (mesenchymal-to-epithelial transition (MET)) are largely unknown. For this study, I will use GATA3-mediated MET to study the pioneer factor-mediated cellular reprogramming. GATA3 is a transcription factor that plays a pivotal role in mammary gland development, luminal epithelial differentiation, and cellular reprogramming. Additionally, it has been implicated in various cellular processes such as proliferation, migration, and invasion and is a critical regulator in breast cancer, including triple-negative breast cancer (TNBC). In TNBC, GATA3 expression is often downregulated, correlating with poor prognosis. Our lab and others have shown that GATA3 functions as a pioneer factor that actively changes the chromatin state from closed to open. In luminal breast cancer cells, ER-alpha and FOXA1 are well-known GATA3 co-factors. In mesenchymal breast cancer cells, GATA3 can suppress tumor metastasis by inducing MET in the absence of well-known GATA3 co-factors FOXA1 and ER-alpha1. These findings suggest that GATA3 works with additional, unknown co-factors during MET. We have been studying how GATA3 activates silent chromatin. More than 7 million GATA3 motifs exist in the human genome, yet the experimental data from GATA3 ChIP-seq analysis indicates less than 1% of the motifs are occupied by the pioneer factor, GATA3. In addition to binding selectivity, we have shown that the pioneer factor action is site-specific (context-dependent) and only induces chromatin opening and enhancer formation at a subset of binding sites. To identify a novel co-factor that is involved in GATA3-mediated MET, we performed a rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) assay, which identified the chromatin-modification enzyme, Poly ADP-ribose polymerase 1 (PARP1), as a potential GATA3 co-factor. PARP1 is essential for gene expression regulation and initiating DNA repair. Previous studies have shown PARP1 as a co-factor to the pioneer factor, SOX2. Our genomics data strongly suggest that PARP1 is involved in such context-dependent action of GATA3. Our overall goal is to investigate GATA3-PARP1 interaction during MET to understand the role of pioneer factors in cellular reprogramming. To do so, we are dissecting the GATA2-PARP1 function in two distinct steps: Citation Format: Mikhala Cooper, Motoki Takaku. The function of GATA3-PARP1 complex in breast cancer during GATA3-mediated cellular reprogramming [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-06.

Abstract 112: Endothelial Mixed Lineage Leukemia 1 (kmt2a/MLL1) As A Central Mediator Of Immunothrombosis During SARS-CoV-2 Infection

Background: Endotheliitis in severe SARS-CoV-2 (CoV2) results in increased cellular adhesion molecules (CAMs) and procoagulant molecules (PCMs). Cell surface CAMs increase endothelial cell (EC) interactions with circulating immune cells (IC). Increased EC-IC interactions and a procoagulant EC phenotype augment immunothrombotic risk during CoV2 infection. Prophylactic anticoagulants during CoV2 infection are associated with unacceptably high bleeding risk. New targets to treat endotheliitis are required. Hypothesis: We hypothesize chromatin modifying enzymes (CME)s associated with inflammatory NF-kB signaling drive transcriptional changes in endothelial cells (ECs) leading to a prothrombotic and procoagulant phenotype. Aims: Identify potential CMEs that drive CoV-2 endotheliitis. Methods: Public human single cell RNA sequencing data evaluated the pulmonary endothelial epigenetic transcriptome (PMID34876692). Murine venous ECs (mVECs), EOMA cells, and human venous ECs (HUVECs) were treated with murine beta-coronavirus (MHV-A59) or CoV2 spike protein (S1), respectively. Pharmacologic and siRNA inhibition were used to accomplish MLL1 silencing. Results: Humans with fatal CoV2 infection demonstrated marked increase in the KMT2/MLL class of histone methyltransferases in pulmonary ECs. mVEC infection significantly increased transcription of CME kmt2a, CAM esel, and PCMs plau and f3. Significant enrichment of H3K4 methylation and MLL1 are seen on promotors of identified genes. Inhibition of MLL1 reduced CAM and PCM transcripts. Functional EC-IC adhesion testing revealed significant decreases in monocyte adhesion with MLL1 inhibition. Conclusion: Kmt2a/MLL1 positively regulates CoV-2 induction of CAMs and PCMs, endothelial inflammation via positive regulation of CAM gene transcription, and resultant EC-IC interactions. MLL1 may represent a novel therapeutic target to ameliorate immunothrombotic risk during CoV-2 infection.

Chromatin Profiles Are Prognostic of Clinical Response to Bortezomib-Containing Chemotherapy in Pediatric Acute Myeloid Leukemia: Results from the COG AAML1031 Trial.

The addition of the proteasome inhibitor bortezomib to standard chemotherapy did not improve survival in pediatric acute myeloid leukemia (AML) when all patients were analyzed as a group in the Children's Oncology Group phase 3 trial AAML1031 (NCT01371981). Proteasome inhibition influences the chromatin landscape and proteostasis, and we hypothesized that baseline proteomic analysis of histone- and chromatin-modifying enzymes (HMEs) would identify AML subgroups that benefitted from bortezomib addition. A proteomic profile of 483 patients treated with AAML1031 chemotherapy was generated using a reverse-phase protein array. A relatively high expression of 16 HME was associated with lower EFS and higher 3-year relapse risk after AML standard treatment compared to low expressions (52% vs. 29%, p = 0.005). The high-HME profile correlated with more transposase-accessible chromatin, as demonstrated via ATAC-sequencing, and the bortezomib addition improved the 3-year overall survival compared with standard therapy (62% vs. 75%, p = 0.033). These data suggest that there are pediatric AML populations that respond well to bortezomib-containing chemotherapy.

Epigenetic regulation of heart failure.

The studies on chromatin-modifying enzymes and how they respond to different stimuli within the cell have revolutionized our understanding of epigenetics. In this review, we provide an overview of the recent studies on epigenetic mechanisms implicated in heart failure. We focus on the major mechanisms and the conceptual advances in epigenetics as evidenced by studies in humans and mouse models of heart failure. The significance of epigenetic modifications and the enzymes that catalyze them is also discussed. New findings from the studies of histone lysine demethylases demonstrate their significance in regulating fetal gene expression, as well as their aberrant expression in adult hearts during HF. Similarly, the relevance of histone deacetylases inhibition in heart failure and the role of HDAC6 in cardio-protection are discussed. Finally, the role of LMNA (lamin A/C), a nuclear membrane protein that interacts with chromatin to form hundreds of large chromatin domains known as lamin-associated domains (LADs), and 3D genome structure in epigenetic regulation of gene expression and heart failure is discussed. Epigenetic modifications provide a mechanism for responding to stress and environmental variation, enabling reactions to both external and internal stimuli, and their dysregulation can be pathological as in heart failure. To gain a thorough understanding of the pathological mechanisms and to aid in the development of targeted treatments for heart failure, future research on studying the combined effects of numerous epigenetic changes and the structure of chromatin is warranted.

Strain background of Candida albicans interacts with SIR2 to alter phenotypic switching.

The genetic background between strains of a single species and within a single strain lineage can significantly impact the expression of biological traits. This genetic variation may also reshape epigenetic mechanisms of cell identity and environmental responses that are controlled by interconnected transcriptional networks and chromatin-modifying enzymes. Histone deacetylases, including sirtuins, are critical regulators of chromatin state and have been directly implicated in governing the phenotypic transition between the 'sterile' white state and the mating-competent opaque state in Candida albicans, a common fungal commensal and pathogen of humans. Here, we found that a previously ambiguous role for the sirtuin SIR2 in C. albicans phenotypic switching is likely linked to the genetic background of mutant strains produced in the RM lineage of SC5314. SIR2 mutants in a specific lineage of BWP17 displayed increased frequencies of switching to the opaque state compared to the wild-type. Loss of SIR2 in other SC5314-derived backgrounds, including newly constructed BWP17 sir2Δ/Δ mutants, failed to recapitulate the increased white-opaque switching frequencies observed in the original BWP17 sir2Δ/Δ mutant background. Whole-genome sequencing revealed the presence of multiple imbalanced chromosomes and large loss of heterozygosity tracts that likely interact with SIR2 to increase phenotypic switching in this BWP17 sir2Δ/Δ mutant lineage. These genomic changes are not found in other SC5314-derived sir2Δ/Δ mutants that do not display increased opaque cell formation. Thus, complex karyotypes can emerge during strain construction that modify mutant phenotypes and highlight the importance of validating strain background when interpreting phenotypes.

Structural insights into the binding mechanism of Clr4 methyltransferase to H3K9 methylated nucleosome

The establishment and maintenance of heterochromatin, a specific chromatin structure essential for genomic stability and regulation, rely on intricate interactions between chromatin-modifying enzymes and nucleosomal histone proteins. However, the precise trigger for these modifications remains unclear, thus highlighting the need for a deeper understanding of how methyltransferases facilitate histone methylation among others. Here, we investigate the molecular mechanisms underlying heterochromatin assembly by studying the interaction between the H3K9 methyltransferase Clr4 and H3K9-methylated nucleosomes. Using a combination of liquid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy, we elucidate the structural basis of Clr4 binding to H3K9-methylated nucleosomes. Our results reveal that Clr4 engages with nucleosomes through its chromodomain and disordered regions to promote de novo methylation. This study provides crucial insights into the molecular mechanisms governing heterochromatin formation by highlighting the significance of chromatin-modifying enzymes in genome regulation and disease pathology.

Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies.

Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)-Not Programmed, without protein-energy supplementation; PP-Partially Programmed, protein-energy supplementation in the final third of pregnancy; and CP-Complete Programming, protein-energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had Longissimus thoracis muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (p > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics.

LncRNA PCAT6 is a predictor of poor prognosis of colorectal cancer.

The long non-coding RNA (lncRNA) prostate cancer-associated transcript 6 (PCAT6) has been studied in many cancers, yet its relationship with colorectal cancer (CRC) remains poorly defined. Here, we conducted an analysis of The Cancer Genome Atlas (TCGA) database to better clarify the role of PCAT6 in this cancer type. Wilcoxon rank-sum tests were utilized to assess relative levels of PCAT6 in CRC tumors and normal tissues, while logistic regression analyses were utilized to compare the relationships between PCAT6 levels and clinicopathological findings. Kaplan-Meier curves and Cox regression analyses were used to gauge correlations between PCAT6 and patient survival outcomes, while the biological roles of this lncRNA were investigated via a gene set enrichment analysis (GSEA) approach. The expression level of PCAT6 in CRC cell lines was detected by quantitative reverse transcription polymerase chain reaction (qRT-PCR). PCAT6 levels were significantly correlated with CRC patient lymph node metastasis (N) stage [odds ratio (OR) =1.8 for N1 & N2 vs. N0], lymphatic invasion [OR =1.9 for yes vs. no), distant metastasis (M stage) (OR =2.1 for M1 vs. M0), carcinoembryonic antigen (CEA) level (OR =1.9 for >5 vs. ≤5), perineural invasion (OR =1.9 for yes vs. no), pathologic stage (OR =1.9 for stage III/IV vs. stage I/II), and neoplasm type (OR =2.1 for rectal adenocarcinoma vs. colon adenocarcinoma) (all P<0.05). CRC patients expressing higher PCAT6 levels exhibited poorer survival outcomes than those expressing low levels of this lncRNA (P=0.017), and in univariate analyses, higher PCAT6 levels were linked to worse overall survival [hazard ratio (HR) =1.540; 95% confidence interval (CI): 1.079-2.199; P=0.017], with this relationship also being preserved in a multivariate analysis (HR =6.892; 95% CI: 1.713-27.727, P=0.007). GSEA revealed high PCAT6 expression to be linked to differential DNA methylation enrichment, with high PCAT6 levels being associated with changes in base excision repair, cellular senescence, G2/M DNA damage checkpoint, chromatin-modifying enzyme, and gene silencing by RNA activity. The high expression of lncRNA PCAT6 in CRC cell lines was demonstrated by PCR experiments. PCAT6 represents a promising prognostic biomarker of poor CRC patient survival outcomes, with DNA methylation and RNA-mediated gene silencing being potentially promising mechanistic pathways whereby this lncRNA may shape patient outcomes.

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations.

There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.