[{"day":"01","type":"journal_article","intvolume":"        41","status":"public","publication":"Nature Biotechnology","page":"813–823","file_date_updated":"2023-08-16T11:30:45Z","month":"06","article_type":"original","date_published":"2023-06-01T00:00:00Z","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"ScienComp"}],"date_created":"2023-01-08T23:00:53Z","file":[{"checksum":"668447a1c8d360b68f8aaf9e08ed644f","date_created":"2023-08-16T11:30:45Z","file_size":12040976,"file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","date_updated":"2023-08-16T11:30:45Z","success":1,"creator":"dernst","file_id":"14066","relation":"main_file","content_type":"application/pdf"}],"citation":{"chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"author":[{"orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"first_name":"Max D.","full_name":"Wellenstein, Max D.","last_name":"Wellenstein"},{"first_name":"Alexander","full_name":"Van Oudenaarden, Alexander","last_name":"Van Oudenaarden"}],"article_processing_charge":"No","oa":1,"volume":41,"date_updated":"2023-08-16T11:32:33Z","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"_id":"12106","quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","year":"2023","doi":"10.1038/s41587-022-01560-3","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","external_id":{"isi":["000909067600003"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"ddc":["570"]},{"publisher":"Springer Nature","scopus_import":"1","language":[{"iso":"eng"}],"month":"02","date_published":"2023-02-01T00:00:00Z","article_type":"review","file":[{"success":1,"file_id":"12688","creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","date_created":"2023-02-27T07:46:45Z","file_size":21484855,"file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","date_updated":"2023-02-27T07:46:45Z"}],"date_created":"2023-01-12T12:09:09Z","has_accepted_license":"1","department":[{"_id":"ScienComp"}],"intvolume":"        55","status":"public","day":"01","type":"journal_article","publication":"Nature Genetics","file_date_updated":"2023-02-27T07:46:45Z","page":"333-345","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","doi":"10.1038/s41588-022-01260-3","year":"2023","ddc":["570","000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"keyword":["Genetics"],"author":[{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","last_name":"Yeung","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza","first_name":"Helena"},{"last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton","first_name":"Buys Anton"},{"first_name":"Vivek","full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden"}],"publication_status":"published","citation":{"chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>.","ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>"},"_id":"12158","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","quality_controlled":"1","oa_version":"Published Version","date_updated":"2023-02-27T07:48:24Z","oa":1,"volume":55,"article_processing_charge":"No"}]