[{"pmid":1,"department":[{"_id":"MaRo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","article_processing_charge":"No","scopus_import":"1","article_type":"letter_note","publication":"Nature Genetics","day":"01","author":[{"first_name":"Elizabeth","last_name":"Ing-Simmons","full_name":"Ing-Simmons, Elizabeth"},{"full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","first_name":"Nick N"},{"first_name":"Juan M.","last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M."}],"title":"Reply to: Revisiting the use of structural similarity index in Hi-C","language":[{"iso":"eng"}],"issue":"12","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"quality_controlled":"1","doi":"10.1038/s41588-023-01595-5","year":"2023","_id":"14689","date_updated":"2023-12-18T08:51:38Z","oa_version":"None","month":"12","type":"journal_article","page":"2053-2055","date_created":"2023-12-17T23:00:53Z","volume":55,"external_id":{"pmid":["38052961"]},"status":"public","citation":{"short":"E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023) 2053–2055.","chicago":"Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-023-01595-5\">https://doi.org/10.1038/s41588-023-01595-5</a>.","ieee":"E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting the use of structural similarity index in Hi-C,” <i>Nature Genetics</i>, vol. 55, no. 12. Springer Nature, pp. 2053–2055, 2023.","apa":"Ing-Simmons, E., Machnik, N. N., &#38; Vaquerizas, J. M. (2023). Reply to: Revisiting the use of structural similarity index in Hi-C. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-023-01595-5\">https://doi.org/10.1038/s41588-023-01595-5</a>","mla":"Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” <i>Nature Genetics</i>, vol. 55, no. 12, Springer Nature, 2023, pp. 2053–55, doi:<a href=\"https://doi.org/10.1038/s41588-023-01595-5\">10.1038/s41588-023-01595-5</a>.","ista":"Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.","ama":"Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. <i>Nature Genetics</i>. 2023;55(12):2053-2055. doi:<a href=\"https://doi.org/10.1038/s41588-023-01595-5\">10.1038/s41588-023-01595-5</a>"},"intvolume":"        55","publication_status":"published","date_published":"2023-12-01T00:00:00Z"},{"month":"02","type":"journal_article","oa_version":"Published Version","date_updated":"2023-02-27T07:48:24Z","abstract":[{"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.","lang":"eng"}],"page":"333-345","date_created":"2023-01-12T12:09:09Z","file_date_updated":"2023-02-27T07:46:45Z","volume":55,"year":"2023","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.","_id":"12158","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570","000"],"date_published":"2023-02-01T00:00:00Z","status":"public","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.","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.","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>","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.","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>."},"intvolume":"        55","file":[{"checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","file_id":"12688","date_updated":"2023-02-27T07:46:45Z","access_level":"open_access","date_created":"2023-02-27T07:46:45Z","file_name":"2023_NatureGenetics_Zeller.pdf","success":1,"creator":"dernst","file_size":21484855,"content_type":"application/pdf","relation":"main_file"}],"day":"01","author":[{"full_name":"Zeller, Peter","first_name":"Peter","last_name":"Zeller"},{"orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","last_name":"Yeung","first_name":"Jake"},{"full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza","first_name":"Helena"},{"full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj","first_name":"Vivek"},{"full_name":"Florescu, Maria","first_name":"Maria","last_name":"Florescu"},{"first_name":"Reinier","last_name":"van der Linden","full_name":"van der Linden, Reinier"},{"last_name":"van Oudenaarden","first_name":"Alexander","full_name":"van Oudenaarden, Alexander"}],"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","department":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"review","scopus_import":"1","article_processing_charge":"No","publication":"Nature Genetics","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"quality_controlled":"1","doi":"10.1038/s41588-022-01260-3","language":[{"iso":"eng"}],"keyword":["Genetics"]},{"author":[{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"last_name":"Aldridge","first_name":"Billy","full_name":"Aldridge, Billy"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"full_name":"Higgins, James D.","last_name":"Higgins","first_name":"James D."},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"}],"day":"18","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","publisher":"Nature Research","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"XiFe"}],"pmid":1,"publication":"Nature Genetics","article_type":"original","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"doi":"10.1038/s41588-017-0008-5","quality_controlled":"1","keyword":["Genetics"],"issue":"1","language":[{"iso":"eng"}],"page":"130-137","oa_version":"None","month":"12","type":"journal_article","date_updated":"2023-10-18T07:21:53Z","abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"volume":50,"date_created":"2023-01-16T09:18:05Z","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","year":"2017","_id":"12193","publication_status":"published","oa":1,"date_published":"2017-12-18T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"external_id":{"pmid":["29255257"]},"status":"public","intvolume":"        50","citation":{"apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017."}},{"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"publication_status":"published","quality_controlled":"1","date_published":"2007-04-01T00:00:00Z","doi":"10.1038/ng0407-442","status":"public","external_id":{"pmid":["17392803"]},"issue":"4","citation":{"short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","chicago":"Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>. Vol. 39. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>.","ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","apa":"Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i> (Vol. 39, pp. 442–443). Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>","mla":"Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>, vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","ama":"Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing Group; 2007:442-443. doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>"},"language":[{"iso":"eng"}],"intvolume":"        39","extern":"1","oa_version":"None","month":"04","type":"other_academic_publication","day":"01","date_updated":"2021-12-14T08:55:46Z","page":"442-443","author":[{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"date_created":"2021-06-07T12:08:24Z","volume":39,"title":"The human promoter methylome","department":[{"_id":"DaZi"}],"year":"2007","pmid":1,"publisher":"Nature Publishing Group","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","_id":"9504","publication":"Nature Genetics"},{"issue":"1","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1038/ng1929","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Nature Genetics","department":[{"_id":"DaZi"}],"pmid":1,"publisher":"Nature Publishing Group","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","day":"26","author":[{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Gehring, Mary","first_name":"Mary","last_name":"Gehring"},{"full_name":"Tran, Robert K.","last_name":"Tran","first_name":"Robert K."},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"citation":{"chicago":"Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>.","ieee":"D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.","short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.","ama":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>","apa":"Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>","mla":"Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>.","ista":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69."},"extern":"1","intvolume":"        39","external_id":{"pmid":["17128275"]},"status":"public","date_published":"2006-11-26T00:00:00Z","publication_status":"published","_id":"9505","year":"2006","date_created":"2021-06-07T12:19:31Z","volume":39,"type":"journal_article","month":"11","oa_version":"None","abstract":[{"text":"Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.","lang":"eng"}],"date_updated":"2021-12-14T09:02:51Z","page":"61-69"}]