Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

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Items 201–269 of 269

1. Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development
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3. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility
   Meijer, Mandy, Agirre, Eneritz, Kabbe, Mukund, van Tuijn, Cassandra A., Heskol, Abeer, Zheng, Chao, Mendanha Falcão, Ana, Bartosovic, Marek, Kirby, Leslie, Calini, Daniela et al. · 2022 · Neuron
4. HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes
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5. Disruption of <i>SUV39H1</i> -Mediated H3K9 Methylation Sustains CAR T-cell Function
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6. CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
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7. Using single‐cell multiple omics approaches to resolve tumor heterogeneity
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8. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
   Bravo González-Blas, Carmen, Matetovici, Irina, Hillen, Hanne, Taskiran, Ibrahim Ihsan, Vandepoel, Roel, Christiaens, Valerie, Sansores-García, Leticia, Verboven, Elisabeth, Hulselmans, Gert, Poovathingal, Suresh et al. · 2024 · Nature Cell Biology
9. ATF3 drives senescence by reconstructing accessible chromatin profiles
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10. ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
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11. Behavior-related gene regulatory networks: A new level of organization in the brain
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12. Time-resolved single-cell RNA-seq using metabolic RNA labelling
    Erhard, Florian, Saliba, Antoine-Emmanuel, Lusser, Alexandra, Toussaint, Christophe, Hennig, Thomas, Prusty, Bhupesh K., Kirschenbaum, Daniel, Abadie, Kathleen, Miska, Eric A., Friedel, Caroline C. et al. · 2022 · Nature Reviews Methods Primers
13. Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis
    Shcherbina, Anna, Larouche, Jacqueline, Fraczek, Paula, Yang, Benjamin A., Brown, Lemuel A., Markworth, James F., Chung, Carolina H., Khaliq, Mehwish, de Silva, Kanishka, Choi, Jeongmoon J. et al. · 2020 · Cell Reports
14. Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1)
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15. The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages
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16. Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation
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17. Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition
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18. Dedifferentiation and neuronal repression define familial Alzheimer’s disease
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19. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility
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20. MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors
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21. Rbpj expression in regulatory T cells is critical for restraining TH2 responses
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22. Targeting epigenetically maladapted vascular niche alleviates liver fibrosis in nonalcoholic steatohepatitis
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23. Phosphoinositide 3-kinase signaling can modulate MHC class I and II expression
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24. Persistent JunB activation in fibroblasts disrupts stem cell niche interactions enforcing skin aging
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25. Epigenetics of T cell aging
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26. Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils
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27. BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes
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28. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
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29. DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency
    Taguchi, Jumpei, Shibata, Hirofumi, Kabata, Mio, Kato, Masaki, Fukuda, Kei, Tanaka, Akito, Ohta, Sho, Ukai, Tomoyo, Mitsunaga, Kanae, Yamada, Yosuke et al. · 2021 · Nature Communications
30. Multifaceted role for p53 in pancreatic cancer suppression
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31. Arid1a restrains Kras-dependent changes in acinar cell identity
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32. Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes
    Lee, Qian Yi, Mall, Moritz, Chanda, Soham, Zhou, Bo, Sharma, Kylesh S., Schaukowitch, Katie, Adrian-Segarra, Juan M., Grieder, Sarah D., Kareta, Michael S., Wapinski, Orly L. et al. · 2020 · Nature Cell Biology
33. Human iPSC-derived Down syndrome astrocytes display genome-wide perturbations in gene expression, an altered adhesion profile, and increased cellular dynamics
    Ponroy Bally, Blandine, Farmer, W Todd, Jones, Emma V, Jessa, Selin, Kacerovsky, J Benjamin, Mayran, Alexandre, Peng, Huashan, Lefebvre, Julie L, Drouin, Jacques, Hayer, Arnold et al. · 2020 · Human Molecular Genetics
34. Analyzing Circulating Tumor Cells One at a Time
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35. Vitamin C–dependent lysine demethylase 6 (KDM6)-mediated demethylation promotes a chromatin state that supports the endothelial-to-hematopoietic transition
    Zhang, Tian, Huang, Ke, Zhu, Yanling, Wang, Tianyu, Shan, Yongli, Long, Bing, Li, Yuhang, Chen, Qianyu, Wang, Pengtao, Zhao, Shaoyang et al. · 2019 · Journal of Biological Chemistry
36. A cell-type-specific error-correction signal in the posterior parietal cortex
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37. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer
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38. Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes
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39. Graph neural networks for single-cell omics data: a review of approaches and applications
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40. Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL
    Schmidl, Christian, Vladimer, Gregory I., Rendeiro, André F., Schnabl, Susanne, Krausgruber, Thomas, Taubert, Christina, Krall, Nikolaus, Pemovska, Tea, Araghi, Mohammad, Snijder, Berend et al. · 2019 · Nature Chemical Biology
41. T-box transcription factor 3 governs a transcriptional program for the function of the mouse atrioventricular conduction system
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42. A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function
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43. SOX9 reprograms endothelial cells by altering the chromatin landscape
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44. The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level
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46. Single cell epigenomic atlas of the developing human brain and organoids
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48. Reduction of lamin B receptor levels by miR-340-5p disrupts chromatin, promotes cell senescence and enhances senolysis
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49. Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
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51. Angiopoietin–TIE2 feedforward circuit promotes PIK3CA-driven venous malformations
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52. Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age
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54. Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation
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55. Pharmacological Restriction of Genomic Binding Sites Redirects PU.1 Pioneer Transcription Factor Activity
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56. Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells
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65. Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer
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66. HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements
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67. Evaluation of chromatin accessibility in prefrontal cortex of schizophrenia cases and controls
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68. Enhancer grammar of liver cell types and hepatocyte zonation states
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69. Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription
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