Richard Paul Harvey

Micrococcal nuclease (MNase) digestion is widely used to profile chromatin accessibility and nucleosome footprinting. However, its application is often limited by sensitivity to reaction conditions, high cell input requirements, and the lack of standardized protocols across cell types. Here we developed a robust MNase workflow encompassing buffer composition, DNA purification chemistry, fixation and decrosslinking parameters, cell input scalability, and an in-house yeast spike-in for quantitative normalization. We validated this unified framework across human induced pluripotent stem cells (hiPSCs), hiPSC-derived cardiomyocytes at multiple differentiation stages, primary murine embryonic cardiac cells, and adult mouse cardiomyocytes, and demonstrated comparable digestion efficiencies and kinetics despite marked differences in cellular architecture and chromatin organization. Genome-wide MNase-seq in hiPSCs, combined with the nucMACC bioinformatic pipeline, resolved concentration-dependent nucleosomal occupancy and precise nucleosome positioning at pluripotency-related regulatory elements. This modular, end-to-end, and scalable workflow provides a standardized platform for reproducible MNase-based chromatin profiling across diverse in vitro and in vivo models.

Highlights: • Systematic MNase optimization across buffer, DNA purification, and cell input variables • Unified workflow validated in hiPSCs, hiPSC-CMs, embryonic, and adult mouse cardiomyocytes, and 6 mammalian cell lines • Fixed-cell protocol enables weeks of storage without loss of DNA quality • Cost-effective yeast spike-in ensures quantitative normalization for MNase-seq • Genome-wide analyses in hiPSCs confirm robust and precise nucleosome positioning at regulatory elements

Genetic studies have linked PHACTR1 to a range of vascular diseases, underscoring its pivotal role in vascular biology. However, the full spectrum of PHACTR1-mediated signaling pathways remains largely unexplored. To bridge this gap, we employ a multi-omics pipeline combining pairwise differential expression analysis, multi-omics pathway integration, and feature-level correlation analyses across four distinct omics datasets to map the global signaling networks driven by PHACTR1. By integrating transcriptomic, proteomic, metabolic, and lipidomic profiles from human HT1080 cells with PHACTR1 overexpression or knockdown, and then validating key findings in primary human endothelial cells, here we show that PHACTR1 exerts broad control over fundamental cellular processes beyond cytoskeletal regulation. We demonstrate that PHACTR1 governs cell cycle progression, validating that increased expression alters key regulatory proteins. We also uncover a distinct function in iron metabolism, showing PHACTR1 regulates essential cellular iron-storage proteins and identify the PHACTR1 protein within the mitochondria where it directs morphology and bioenergetics through a signaling axis involving AKAP1 and Drp1. These mitochondrial changes align with observed shifts in lipid metabolism and correlations in human arterial tissue. These findings provide a systems-level blueprint of PHACTR1 function, revealing how this gene influences vascular health and offering potential targets for therapeutic intervention.

SUMMARY: Zebrafish and medaka are powerful cardiovascular models, yet cellular and molecular investigations of adult heart cells have been constrained by suboptimal dissociation and characterization methods. To overcome these barriers, we developed a physiological-temperature workflow that generates high-yield, viable single-cell suspensions for FACS, imaging, and low-input molecular profiling. Using transgenic fluorescent reporters, we consistently isolate ∼6,000 cardiomyocytes per adult zebrafish ventricle and ∼12,000 from medaka, preserving cellular, structural, and molecular integrity. Single-cell morphometrics revealed cardiomyocyte heterogeneity and demonstrated that swimming exercise induces both hypertrophy and hyperplasia, while ventricular injury triggers expansion of regenerative gata4 ⁺ cardiomyocytes. We integrated proteomics and RNA-seq from FACS-purified cells to construct cell-type-specific proteo-transcriptomic atlases. Functional enrichment, transcription factor, and network analyses identified protein hubs and regulatory circuits defining cardiomyocyte and endothelial cell identity. Our platform delivers cell-type-resolved molecular datasets of adult teleost cardiac cells, establishing a systems-level resource for heart regeneration research, cardiovascular disease modeling, and drug discovery. Teaser: A robust workflow for isolation, FACS, imaging, and multi-omics profiling of cardiomyocytes and cardiac endothelial cells in fish. HIGHLIGHTS: Temperature-optimized dissociation and standardized FACS enable high-yield isolation of viable cardiac cells. Single-cell imaging uncovers morphological heterogeneity in adult ventricular cardiomyocytes. Sustained exercise induces both hypertrophy and hyperplasia of zebrafish cardiomyocytes. Proteo-transcriptomics defines core molecular programs and interaction networks in cardiomyocytes and endothelial cells.

Cardiogenesis relies on the integrated interplay between cardiac transcription factors and signaling pathways. Here, we uncover a role for type IIA procollagen (IIA), an extracellular matrix (ECM) protein encoded by an alternatively spliced Col2a1 transcript, encoding a N-terminal cysteine-rich domain, as a critical regulator in a cardiac gene regulatory feedback loop. The cysteine-rich domain of IIA protein was previously reported to interact with bone morphogenetic proteins (BMPs) and transforming growth factors-beta (TGFβ) in in vitro binding assays and acts as a BMP antagonist in amphibian embryo assays. We show that the Col2a1 gene in mice is activated in the developing heart by core cardiogenic factors (NKX2-5, GATA4, MEF2, and SRF) via cis-regulatory enhancer elements. IIA loss (ΔIIA) in mice results in depletion of Isl1- and Nkx2-5-expressing progenitors, causing outflow tract defects resembling disrupted BMP/TGFβ-SMAD signaling, alongside reduced nuclear pSMAD1/5/8 in cardiac tissues. Compound +/ΔIIA ; Smad4+/− mutants exhibit aggravated malformations. IIA enhances BMP-responsive reporter activity in cells in transactivation assays. We propose that IIA supports a positive functional role on SMAD4-dependent signaling, fine-tuning BMP/TGFβ signaling, thereby regulating GATA4 and NKX2-5 activity during second heart field progenitor specification. These findings position IIA procollagen as a key ECM component that integrates BMP/TGFβ signaling with cardiac transcription factors such as NKX2-5, revealing a feedback loop essential for cardiogenesis. Given its role in cardiac development, IIA emerges as a potential congenital heart disease risk factor.

Congenital heart defects (CHD) occur in ∼1% of live births, with inherited and acquired mutations and environmental factors contributing to causation. However, network perturbations in CHD remain poorly understood. We report an integrated functional-epigenomics approach to CHD, focusing on the cardiac homeodomain (HD) transcription factor NKX2-5, mutations which cause diverse heart structural and conduction defects. We selected twelve NKX2-5 CHD variants affecting different residue classes - homeodomain DNA base-contacting, backbone-contacting and helix-stabilizing, and those affecting other conserved protein:protein interaction (PPI) domains. In HL-1 cardiomyocytes, we profiled genome-wide DNA targets of NKX2-5 wild type (WT) and variants, their DNA binding affinity and specificity, PPI with known NKX2-5 cofactors and chromatin search dynamics. Variants showed diverse yet class-specific behaviours. All variants failed to bind many WT targets but retained binding to a subset of core cardiomyocyte-related targets, and bound hundreds of unique “off-targets” via changes to DNA binding site specificity, homodimerization, cofactor interactions and chromatin search functions. Our data suggest that complex residue-by-residue scale epigenomic, biochemical and chromatin search defects involving both loss-and gain-of-function contribute to CHD. These findings may inform precision molecular therapeutic approaches in patients with CHD.

Aims: The highly conserved long non-coding RNA (lncRNA) MIR505HG has been primarily recognized as a precursor for microRNAs (miR)-424 and miR-503. However, studies have since demonstrated that MIR503HG has distinct functions from its associated miRNAs, playing important roles in cell proliferation, invasion, apoptosis, and differentiation. While these miRNAs are known to influence cardiomyocyte differentiation, the specific role of MIR503HG in heart development remains unexplored. We seek to determine how MIR503HG deletion impacts ventricular chamber development and to identify underlying molecular mechanisms. Methods and results: To study the role of the lncRNA in vivo, we generated a functional MIR503HG knockout mouse model (MIR503HG−/−) using a synthetic polyadenylation signal to terminate MIR503HG transcription without affecting miR-424/503 expression. We performed morphological analyses on embryonic and adult hearts using microCT along with cardiac functional analysis via transthoracic echocardiography. We further apply single-nuclei RNA sequencing (snRNA-seq) on adult hearts to identify potential molecular mechanisms underlying the observed phenotypes. Functional deletion of MIR503HG alone was associated with reduced compact myocardium thickness and increased trabecular myocardium in the left ventricle (LV) at embryonic day 17.5 compared to wild-type mice, indicating a LV non-compaction (LVNC) phenotype. Moreover, adult MIR503HG−/− mutant hearts showed increased trabecular complexity, impaired LV relaxation, and mitral valve regurgitation. SnRNA-seq further revealed altered expression of several genes associated with cardiomyocyte function and LVNC, including Actc1, Mib1, Mybpc3, and Myh7. Lastly, Notch1 activity was also significantly increased in mutant hearts which has been previously associated with LVNC. Conclusion: MIR503HG plays a role in ventricular chamber development, and its deletion leads to an LVNC phenotype independent of the miRNA cluster within its locus, highlighting its importance in cardiac development and disease. We further suggest that abnormal Notch1 activity may underpin the LVNC phenotype presented.

5-Ethynyl-2’-deoxyuridine (EdU) has transformed DNA replication and cell cycle analyses through fast and efficient click chemistry detection. However, commercial EdU kits are expensive, contain proprietary reagents, are suboptimal for antibody multiplexing, and are challenging to use with larger biological specimens, highlighting the need for innovation. Here, we report Open-source EdU Multiplexing Methodology for Understanding DNA replication dynamics (OpenEMMU), an optimized, affordable, and user-friendly click chemistry resource using off-the-shelf reagents. OpenEMMU improves the efficiency, brightness, and multiplexing capabilities of EdU thymidine analog staining with both non-conjugated and conjugated antibodies across various cell types. We validated its effectiveness for fluorescent imaging of nascent DNA in developing embryos and organs, including the embryonic heart and forelimbs, and in 3D hiPSC-derived cardiac organoids. OpenEMMU also enabled 3D imaging of DNA synthesis in zebrafish larvae at fine resolution. This opens new avenues for insights into organismal development and growth, cell proliferation, and DNA replication, with precision and flexibility that surpass traditional methods. Teaser: An open-source and cost-effective resource for DNA replication profiling and cell cycle analysis using click chemistry.

Front Cover: The cover image is based on the article Skull base surgery for malignant tumors: The 2nd international collaborative study (1995–2015) by Jatin P. Shah MD et al., https://doi.org/10.1002/hed.27746. image