{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T05:32:31Z","timestamp":1788845551475,"version":"build-2803163510"},"reference-count":110,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Yong Dai Academician\u2019s Workstation","award":["317"],"award-info":[{"award-number":["317"]}]},{"name":"Graduate Innovation Fund Project of Anhui University of Science & Technology\n              https:\/\/ror.org\/00q9atg80","award":["2024cx2204"],"award-info":[{"award-number":["2024cx2204"]}]},{"name":"Graduate Innovation Fund Project of Hefei National Research Center for Health Science & Technology Joint Research Center for Occupational Medicine and Health Open Fund","award":["OMH-2023-04"],"award-info":[{"award-number":["OMH-2023-04"]}]},{"name":"Clinical and Translational Research Project of Anhui Province","award":["202427610020132"],"award-info":[{"award-number":["202427610020132"]}]},{"name":"Natural Science Research Project of Anhui Educational Committee","award":["2023AH051200"],"award-info":[{"award-number":["2023AH051200"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Cardiac embryonic development is a highly coordinated and dynamic process governed by precise spatiotemporal gene regulation. Increasing evidence indicates that cellular heterogeneity and lineage specification during heart development are tightly controlled by complex gene regulatory networks (GRNs) and epigenetic mechanisms. Recent advances in single-cell multi-omics technologies provide unprecedented resolution to dissect these regulatory processes. This review aims to summarise current applications of single-cell multi-omics approaches to elucidate gene regulatory mechanisms underlying cardiac embryogenesis and their implications for congenital heart disease (CHD). Methods: We systematically reviewed recent literature on single-cell RNA sequencing (scRNA-seq), single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), spatial transcriptomics, and integrative multi-omics analyses applied to embryonic heart development. Studies were analysed to evaluate how these technologies contribute to cell-type identification, lineage trajectory reconstruction, GRN inference, and epigenetic landscape characterisation. Results: Single-cell multi-omics approaches have enabled the construction of high-resolution cardiac cell atlases, revealing previously unrecognised cellular heterogeneity and transitional states during heart development. Integrative analyses of transcriptomic and chromatin accessibility data have provided insights into lineage commitment, key transcription factors, enhancer\u2013promoter interactions, and dynamic GRNs. These findings have advanced understanding of developmental genetics in cardiac morphogenesis and offered new perspectives on the molecular mechanisms underlying CHD. Conclusions: Single-cell multi-omics technologies provide a powerful framework for investigating gene regulatory mechanisms during cardiac embryogenesis. Continued methodological refinement and integrative analyses are expected to further clarify developmental processes and facilitate translational insights into CHD.<\/jats:p>","DOI":"10.3390\/genes17040414","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T16:34:08Z","timestamp":1774974848000},"page":"414","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Single-Cell Multi-Omics Reveal Gene Regulatory Mechanisms Underlying Cardiac Embryonic Development"],"prefix":"10.3390","volume":"17","author":[{"given":"Enqi","family":"Feng","sequence":"first","affiliation":[{"name":"School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuejia","family":"Zheng","sequence":"additional","affiliation":[{"name":"The First Hospital, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"The First Hospital, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Xiang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengcheng","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leping","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Big Data, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanni","family":"Cao","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence, Anhui University of Science & Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Dai","sequence":"additional","affiliation":[{"name":"School of Medicine, Anhui University of Science & Technology, Huainan 232001, China"},{"name":"Anhui Provincial Academician Workstation of Anhui University of Science & Technology for Autoimmune Disease Diagnostic Technology, Huainan 232001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"a008292","DOI":"10.1101\/cshperspect.a008292","article-title":"Signaling and transcriptional networks in heart development and regeneration","volume":"5","author":"Bruneau","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2533","DOI":"10.1016\/j.devcel.2022.10.009","article-title":"Essential role of MESP1-RING1A complex in cardiac differentiation","volume":"57","author":"Liang","year":"2022","journal-title":"Dev. Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-019-1414-x","article-title":"Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects","volume":"572","author":"Ranade","year":"2019","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e178355","DOI":"10.1172\/JCI178355","article-title":"Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL","volume":"135","author":"Li","year":"2024","journal-title":"J. Clin. Investig."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"7960","DOI":"10.1038\/s41467-022-35691-7","article-title":"Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages","volume":"13","author":"Feng","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/s41586-024-07171-z","article-title":"Spatially organized cellular communities form the developing human heart","volume":"627","author":"Farah","year":"2024","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Elorbany, R., Popp, J.M., Rhodes, K., Strober, B.J., Barr, K., Qi, G., Gilad, Y., and Battle, A. (2022). Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet., 18.","DOI":"10.1371\/journal.pgen.1009666"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"111596","DOI":"10.1016\/j.isci.2024.111596","article-title":"Elucidating cardiomyocyte heterogeneity and maturation dynamics through integrated single-cell and spatial transcriptomics","volume":"28","author":"Wang","year":"2025","journal-title":"iScience"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Shang, M., Hu, Y., Cao, H., Lin, Q., Yi, N., Zhang, J., Gu, Y., Yang, Y., He, S., and Lu, M. (2022). Concordant and Heterogeneity of Single-Cell Transcriptome in Cardiac Development of Human and Mouse. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.892766"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41422-019-0168-1","article-title":"Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate","volume":"29","author":"Gao","year":"2019","journal-title":"Cell Res."},{"key":"ref_11","unstructured":"Chang, A.C., Schlegel, B.T., Carleton, N., McAuliffe, P.F., Oesterreich, S., Schwartz, R., and Lee, A.V. (2025). CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends. bioRxiv, (Preprint)."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1038\/s41597-025-05838-4","article-title":"A dataset of spatially resolved transcriptomics of post-natal cardiac development in mice","volume":"12","author":"Zheng","year":"2025","journal-title":"Sci. Data"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Nguyen, Q., Tung, L.W., Lin, B., Sivakumar, R., Sar, F., Singhera, G., Wang, Y., Parker, J., Le Bihan, S., and Singh, A. (2025). Spatial Transcriptomics in Human Cardiac Tissue. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26030995"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1934","DOI":"10.1016\/j.celrep.2019.01.079","article-title":"Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart","volume":"26","author":"Cui","year":"2019","journal-title":"Cell Rep."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1161\/CIRCRESAHA.119.315243","article-title":"Single-Cell Transcriptomics Reveals Chemotaxis-Mediated Intraorgan Crosstalk During Cardiogenesis","volume":"125","author":"Xiong","year":"2019","journal-title":"Circ. Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"110083","DOI":"10.1016\/j.isci.2024.110083","article-title":"scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation","volume":"27","author":"Sulej","year":"2024","journal-title":"iScience"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nprot.2014.006","article-title":"Full-length RNA-seq from single cells using Smart-seq2","volume":"9","author":"Picelli","year":"2014","journal-title":"Nat. Protoc."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1038\/nmeth.2639","article-title":"Smart-seq2 for sensitive full-length transcriptome profiling in single cells","volume":"10","author":"Picelli","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.slast.2021.10.018","article-title":"Automation enables high-throughput and reproducible single-cell transcriptomics library preparation","volume":"27","author":"Kind","year":"2022","journal-title":"SLAS Technol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"106302","DOI":"10.1016\/j.isci.2023.106302","article-title":"Single-cell RNA sequencing reveals maturation trajectory in human pluripotent stem cell-derived cardiomyocytes in engineered tissues","volume":"26","author":"Cheng","year":"2023","journal-title":"iScience"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1038\/s41467-021-21892-z","article-title":"Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis","volume":"12","author":"Mantri","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"108472","DOI":"10.1016\/j.celrep.2020.108472","article-title":"Cell-Type-Specific Gene Regulatory Networks Underlying Murine Neonatal Heart Regeneration at Single-Cell Resolution","volume":"33","author":"Wang","year":"2020","journal-title":"Cell Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4877","DOI":"10.1038\/s41467-018-07307-6","article-title":"Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement","volume":"9","author":"Jia","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1126\/science.aab1601","article-title":"Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing","volume":"348","author":"Cusanovich","year":"2015","journal-title":"Science"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1161\/CIRCULATIONAHA.122.061955","article-title":"In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen- Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity","volume":"147","author":"Cao","year":"2023","journal-title":"Circulation"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41594-025-01704-4","article-title":"Mechanisms of DNMT3A-3L-mediated de novo DNA methylation on chromatin","volume":"33","author":"Yan","year":"2025","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2437","DOI":"10.1002\/jcb.24570","article-title":"SWI\/SNF in cardiac progenitor cell differentiation","volume":"114","author":"Lei","year":"2013","journal-title":"J. Cell. Biochem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.devcel.2016.01.009","article-title":"The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation","volume":"36","author":"Waldron","year":"2016","journal-title":"Dev. Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/s44161-023-00334-7","article-title":"Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network","volume":"2","author":"Sweat","year":"2023","journal-title":"Nat. Cardiovasc. Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1006\/bbrc.2001.5863","article-title":"5-Aza-2\u2032-deoxycytidine induces histone hyperacetylation of mouse centromeric heterochromatin by a mechanism independent of DNA demethylation","volume":"288","author":"Takebayashi","year":"2001","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41587-021-01006-2","article-title":"Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis","volume":"40","author":"Lohoff","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1186\/s13059-025-03633-3","article-title":"Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors","volume":"26","author":"He","year":"2025","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4754","DOI":"10.1016\/j.cell.2025.05.035","article-title":"Digital reconstruction of full embryos during early mouse organogenesis","volume":"188","author":"Xie","year":"2025","journal-title":"Cell"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/s41586-023-06812-z","article-title":"A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain","volume":"624","author":"Yao","year":"2023","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1146\/annurev-pathol-012615-044336","article-title":"Genetics of Cardiac Developmental Disorders: Cardiomyocyte Proliferation and Growth and Relevance to Heart Failure","volume":"11","author":"Wilsbacher","year":"2016","journal-title":"Annu. Rev. Pathol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4937","DOI":"10.1016\/j.cell.2022.11.028","article-title":"Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease","volume":"185","author":"Ameen","year":"2022","journal-title":"Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"100953","DOI":"10.1016\/j.xcrm.2023.100953","article-title":"Gestational palmitic acid suppresses embryonic GATA-binding protein 4 signaling and causes congenital heart disease","volume":"4","author":"Zhao","year":"2023","journal-title":"Cell Rep. Med."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"eadk4694","DOI":"10.1126\/sciadv.adk4694","article-title":"Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells","volume":"10","author":"Dong","year":"2024","journal-title":"Sci. Adv."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.devcel.2024.09.018","article-title":"RNA splicing controls organ-wide maturation of postnatal heart in mice","volume":"60","author":"Li","year":"2025","journal-title":"Dev. Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1126\/science.aao4174","article-title":"Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq","volume":"359","author":"Lescroart","year":"2018","journal-title":"Science"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"dev182097","DOI":"10.1242\/dev.182097","article-title":"Single cell transcriptome dynamics from pluripotency to FLK1+ mesoderm","volume":"146","author":"Zhao","year":"2019","journal-title":"Development"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/dvdy.24349","article-title":"cis-Regulatory control of Mesp1 expression by YY1 and SP1 during mouse embryogenesis","volume":"245","author":"Beketaev","year":"2016","journal-title":"Dev. Dyn."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3254","DOI":"10.1002\/stem.2111","article-title":"Genome-Wide Identification of MESP1 Targets Demonstrates Primary Regulation over Mesendoderm Gene Activity","volume":"33","author":"Soibam","year":"2015","journal-title":"Stem Cells"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.ydbio.2008.09.012","article-title":"A novel activity of the Dickkopf-1 amino terminal domain promotes axial and heart development independently of canonical Wnt inhibition","volume":"324","author":"Korol","year":"2008","journal-title":"Dev. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ydbio.2015.02.014","article-title":"Mesenchymal Wnt signaling promotes formation of sternum and thoracic body wall","volume":"401","author":"Snowball","year":"2015","journal-title":"Dev. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"6930","DOI":"10.1038\/ncomms7930","article-title":"PDGFR\u03b1 demarcates the cardiogenic clonogenic Sca1+ stem\/progenitor cell in adult murine myocardium","volume":"6","author":"Noseda","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1016\/j.cell.2019.11.025","article-title":"A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart","volume":"179","author":"Asp","year":"2019","journal-title":"Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"bio059941","DOI":"10.1242\/bio.059941","article-title":"Population-level antagonism between FGF and BMP signaling steers mesoderm differentiation in embryonic stem cells","volume":"12","author":"Gattiglio","year":"2023","journal-title":"Biol. Open"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e31018","DOI":"10.7554\/eLife.31018","article-title":"BMP and FGF signaling interact to pattern mesoderm by controlling basic helix-loop-helix transcription factor activity","volume":"7","author":"Row","year":"2018","journal-title":"eLife"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/ncb3280","article-title":"Sequential Notch activation regulates ventricular chamber development","volume":"18","author":"Luxan","year":"2016","journal-title":"Nat. Cell Biol."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Wang, Y., Wu, B., Chamberlain, A.A., Lui, W., Koirala, P., Susztak, K., Klein, D., Taylor, V., and Zhou, B. (2013). Endocardial to myocardial notch-wnt-bmp axis regulates early heart valve development. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0060244"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Padula, S.L., Velayutham, N., and Yutzey, K.E. (2021). Transcriptional Regulation of Postnatal Cardiomyocyte Maturation and Regeneration. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22063288"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/cvr\/cvac088","article-title":"AP-1 activation mediates post-natal cardiomyocyte maturation","volume":"119","author":"Zhang","year":"2023","journal-title":"Cardiovasc. Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1007\/s11684-023-0987-9","article-title":"Distinct mononuclear diploid cardiac subpopulation with minimal cell-cell communications persists in embryonic and adult mammalian heart","volume":"17","author":"Zhu","year":"2023","journal-title":"Front. Med."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1038\/s44161-024-00565-2","article-title":"The tRNA methyltransferase Mettl1 governs ketogenesis through translational regulation and drives metabolic reprogramming in cardiomyocyte maturation","volume":"3","author":"Du","year":"2024","journal-title":"Nat. Cardiovasc. Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.stem.2022.02.011","article-title":"PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes","volume":"29","author":"Wickramasinghe","year":"2022","journal-title":"Cell Stem Cell"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"bbae711","DOI":"10.1093\/bib\/bbae711","article-title":"Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks","volume":"26","author":"Cai","year":"2024","journal-title":"Brief. Bioinform."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1479-5876-12-31","article-title":"Association of promoter methylation statuses of congenital heart defect candidate genes with Tetralogy of Fallot","volume":"12","author":"Sheng","year":"2014","journal-title":"J. Transl. Med."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.cell.2013.01.003","article-title":"Braveheart, a long noncoding RNA required for cardiovascular lineage commitment","volume":"152","author":"Klattenhoff","year":"2013","journal-title":"Cell"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-019-1850-9","article-title":"A benchmark of batch-effect correction methods for single-cell RNA sequencing data","volume":"21","author":"Tran","year":"2020","journal-title":"Genome Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"giaa151","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"Gigascience"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1186\/s13059-022-02820-w","article-title":"Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics","volume":"23","author":"Subramanian","year":"2022","journal-title":"Genome Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e8746","DOI":"10.15252\/msb.20188746","article-title":"Current best practices in single-cell RNA-seq analysis: A tutorial","volume":"15","author":"Luecken","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","article-title":"Adjusting batch effects in microarray expression data using empirical Bayes methods","volume":"8","author":"Johnson","year":"2007","journal-title":"Biostatistics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive Integration of Single-Cell Data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.semcdb.2007.01.001","article-title":"Transcriptional pathways in second heart field development","volume":"18","author":"Black","year":"2007","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Deng, Z., Wang, Y., and Alobaedy, M.M. (2025). Federated k-means based on clusters backbone. PLoS ONE, 20.","DOI":"10.1371\/journal.pone.0326145"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1093\/bib\/bbz063","article-title":"Machine learning and statistical methods for clustering single-cell RNA-sequencing data","volume":"21","author":"Petegrosso","year":"2020","journal-title":"Brief. Bioinform."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: Guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: Consensus clustering of single-cell RNA-seq data","volume":"14","author":"Kiselev","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/s41592-018-0229-2","article-title":"Deep generative modeling for single-cell transcriptomics","volume":"15","author":"Lopez","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/s41592-018-0230-9","article-title":"Bayesian deep learning for single-cell analysis","volume":"15","author":"Way","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: Single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Zhang, Z., Luo, D., Zhong, X., Choi, J.H., Ma, Y., Wang, S., Mahrt, E., Guo, W., Stawiski, E.W., and Modrusan, Z. (2019). SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. Genes, 10.","DOI":"10.3390\/genes10070531"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"e9620","DOI":"10.15252\/msb.20209620","article-title":"Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models","volume":"17","author":"Xu","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"dev170506","DOI":"10.1242\/dev.170506","article-title":"Concepts and limitations for learning developmental trajectories from single cell genomics","volume":"146","author":"Tritschler","year":"2019","journal-title":"Development"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Ruan, H., Liao, Y., Ren, Z., Mao, L., Yao, F., Yu, P., Ye, Y., Zhang, Z., Li, S., and Xu, H. (2019). Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment. BMC Biol., 17.","DOI":"10.1186\/s12915-019-0709-6"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/nmeth.4402","article-title":"Reversed graph embedding resolves complex single-cell trajectories","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1016\/j.stem.2022.08.007","article-title":"Modeling human multi-lineage heart field development with pluripotent stem cells","volume":"29","author":"Yang","year":"2022","journal-title":"Cell Stem Cell"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13059-019-1663-x","article-title":"PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells","volume":"20","author":"Wolf","year":"2019","journal-title":"Genome Biol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2989","DOI":"10.1093\/bioinformatics\/btv325","article-title":"Diffusion maps for high-dimensional single-cell analysis of differentiation data","volume":"31","author":"Haghverdi","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Street, K., Risso, D., Fletcher, R.B., Das, D., Ngai, J., Yosef, N., Purdom, E., and Dudoit, S. (2018). Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4772-0"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","article-title":"The single-cell transcriptional landscape of mammalian organogenesis","volume":"566","author":"Cao","year":"2019","journal-title":"Nature"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/978-3-031-44087-8_16","article-title":"Cardiac Transcription Factors and Regulatory Networks","volume":"1441","author":"Grunert","year":"2024","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Canac, R., Cimarosti, B., Girardeau, A., Forest, V., Olchesqui, P., Poschmann, J., Redon, R., Lemarchand, P., Gaborit, N., and Lamirault, G. (2022). Deciphering Transcriptional Networks during Human Cardiac Development. Cells, 11.","DOI":"10.1101\/2022.08.11.503560"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"qzaf060","DOI":"10.1093\/gpbjnl\/qzaf060","article-title":"ScReNI: Single-cell Regulatory Network Inference Through Integrating scRNA-seq and scATAC-seq Data","volume":"23","author":"Xu","year":"2025","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1002\/dvdy.22763","article-title":"Transactivation in Drosophila of human enhancers by human transcription factors involved in congenital heart diseases","volume":"241","author":"Amodio","year":"2012","journal-title":"Dev. Dyn."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41592-023-01938-4","article-title":"SCENIC+: Single-cell multiomic inference of enhancers and gene regulatory networks","volume":"20","author":"Hulselmans","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1826","DOI":"10.1038\/s12276-024-01293-0","article-title":"SMC3 contributes to heart development by regulating super-enhancer associated genes","volume":"56","author":"Zhang","year":"2024","journal-title":"Exp. Mol. Med."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1038\/s41586-022-05688-9","article-title":"Dissecting cell identity via network inference and in silico gene perturbation","volume":"614","author":"Kamimoto","year":"2023","journal-title":"Nature"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Cao, C., Li, L., Zhang, Q., Li, H., Wang, Z., Wang, A., and Liu, J. (2023). Nkx2.5: A crucial regulator of cardiac development, regeneration and diseases. Front. Cardiovasc. Med., 10.","DOI":"10.3389\/fcvm.2023.1270951"},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Lv, H., Sun, F., and Chen, Y. (2025). Decoding congenital heart disease: A multi-omic framework for cardiac lineage and regulatory dysfunction. Front. Cell Dev. Biol., 13.","DOI":"10.3389\/fcell.2025.1659884"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"110671","DOI":"10.1016\/j.ygeno.2023.110671","article-title":"Spatial transcriptomics: Technologies, applications and experimental considerations","volume":"115","author":"Wang","year":"2023","journal-title":"Genomics"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1038\/s41586-024-08334-8","article-title":"Spatial transcriptomic clocks reveal cell proximity effects in brain ageing","volume":"638","author":"Sun","year":"2025","journal-title":"Nature"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1038\/s42256-022-00545-w","article-title":"A multi-use deep learning method for CITE-seq and single-cell RNA-seq data integration with cell surface protein prediction and imputation","volume":"4","author":"Lakkis","year":"2022","journal-title":"Nat. Mach. Intell."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41576-019-0093-7","article-title":"Integrative single-cell analysis","volume":"20","author":"Stuart","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/s41467-023-35923-4","article-title":"Transformer for one stop interpretable cell type annotation","volume":"14","author":"Chen","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/s41421-023-00543-1","article-title":"A live-cell image-based machine learning strategy for reducing variability in PSC differentiation systems","volume":"9","author":"Yang","year":"2023","journal-title":"Cell Discov."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.cell.2023.01.001","article-title":"Graded mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart","volume":"186","author":"Dominguez","year":"2023","journal-title":"Cell"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"5587","DOI":"10.1016\/j.cell.2023.10.030","article-title":"Multi-chamber cardioids unravel human heart development and cardiac defects","volume":"186","author":"Schmidt","year":"2023","journal-title":"Cell"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.devcel.2018.06.003","article-title":"A Rapid Method for Directed Gene Knockout for Screening in G0 Zebrafish","volume":"46","author":"Wu","year":"2018","journal-title":"Dev. Cell"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s13073-020-00772-z","article-title":"Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease","volume":"12","author":"Izarzugaza","year":"2020","journal-title":"Genome Med."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/4\/414\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T16:42:47Z","timestamp":1774975367000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/4\/414"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,31]]},"references-count":110,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["genes17040414"],"URL":"https:\/\/doi.org\/10.3390\/genes17040414","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,31]]}}}