Regulation of Chromatin Structure and Function

Displaying 1 - 46 of 46CSV
Suter, T., Friedman, M. J., Tazearslan, C., Merkurjev, D., Ohgi, K., Meluzzi, D., Rosenfeld, M. G., & Suh, Y. (2025). Ligand-specific regulation of a binary enhancer code dictating cellular senescence. Proceedings of the National Academy of Sciences, 122(24). https://doi.org/10.1073/pnas.2506321122
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Triplett, M. K., Ahmed, I., Shekharan, S., & Symington, L. S. (2025). The Slx4-Rad1-Rad10 nuclease differentially regulates deletions and duplications induced by a replication fork barrier. PLOS Genetics, 21(5), e1011720. https://doi.org/10.1371/journal.pgen.1011720
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Barua, S., Murty, V. V., Iglesias, A., & Liao, J. (2025). A Novel EP300 Variant in an African American Girl With Global Developmental Delay and Leukemia. Molecular Genetics & Genomic Medicine, 13(6). Portico. https://doi.org/10.1002/mgg3.70102
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Uwibambe, E., Yalcouyé, A., Aboagye, E. T., Xhakaza, L., Popel, K., Dukuze, N., Bharadwaj, T., de Kock, C., Schrauwen, I., Leal, S. M., Mutesa, L., & Wonkam, A. (2025). Exome sequencing revealed a novel homozygous variant in TRMT61 A in a multiplex family with atypical Cornelia de Lange Syndrome from Rwanda. BMC Medical Genomics, 18(1). https://doi.org/10.1186/s12920-025-02153-0
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Mangione, R. M., Pierce, S., Zheng, M., Martin, R. M., Goncalves, C., Kumar, A., Scaglione, S., de Sousa Morgado, C., Penzo, A., Lancrey, A., Reid, R. J. D., Lautier, O., Gaillard, P.-H., Stirling, P. C., de Almeida, S. F., Rothstein, R., & Palancade, B. (2025). DNA lesions can frequently precede DNA:RNA hybrid accumulation. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57588-x
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Vann, K. R., Sharma, R., Hsu, C.-C., Devoucoux, M., Tencer, A. H., Zeng, L., Lin, K., Zhu, L., Li, Q., Lachance, C., Ospina, R. R., Tong, Q., Cheung, K. L., Yang, S., Biswas, S., Xuan, H., Gatchalian, J., Alamillo, L., Wang, J., … Kutateladze, T. G. (2025). Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57556-5
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Borck, P. C., Boyle, I., Jankovic, K., Bick, N., Foster, K., Lau, A. C., Parker-Burns, L. I., Lubicki, D. A., Li, T., Borah, A. A., Lofaso, N. J., Das Sharma, S., Chan, T., Kishen, R. V., Adeagbo, A., Raghavan, S., Aquilanti, E., Prensner, J. R., Krill-Burger, J. M., … Vazquez, F. (2025). SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO. Nature, 638(8052), 1104–1111. https://doi.org/10.1038/s41586-024-08509-3
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Shi, X., Li, Y., Zhou, H., Hou, X., Yang, J., Malik, V., Faiola, F., Ding, J., Bao, X., Modic, M., Zhang, W., Chen, L., Mahmood, S. R., Apostolou, E., Yang, F.-C., Xu, M., Xie, W., Huang, X., Chen, Y., & Wang, J. (2024). DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-55054-8
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Mackay, H. L., Stone, H. R., Ronson, G. E., Ellis, K., Lanz, A., Aghabi, Y., Walker, A. K., Starowicz, K., Garvin, A. J., Van Eijk, P., Koestler, S. A., Anthony, E. J., Piberger, A. L., Chauhan, A. S., Conway-Thomas, P., Vaitsiankova, A., Vijayendran, S., Beesley, J. F., Petermann, E., … Morris, J. R. (2024). USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-52250-4
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Daly, A. F., Dunnington, L. A., Rodriguez-Buritica, D. F., Spiegel, E., Brancati, F., Mantovani, G., Rawal, V. M., Faucz, F. R., Hijazi, H., Caberg, J.-H., Nardone, A. M., Bengala, M., Fortugno, P., Del Sindaco, G., Ragonese, M., Gould, H., Cannavò, S., Pétrossians, P., Lania, A., … Franke, M. (2024). Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus. Genome Medicine, 16(1). https://doi.org/10.1186/s13073-024-01378-5
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Gretarsson, K. H., Abini-Agbomson, S., Gloor, S. L., Weinberg, D. N., McCuiston, J. L., Kumary, V. U. S., Hickman, A. R., Sahu, V., Lee, R., Xu, X., Lipieta, N., Flashner, S., Adeleke, O. A., Popova, I. K., Taylor, H. F., Noll, K., Windham, C. L., Maryanski, D. N., Venters, B. J., … Lu, C. (2024). Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. Science Advances, 10(35). https://doi.org/10.1126/sciadv.adp0975
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Lu, Z., Wang, Y., Assumpção, A. L. F. V., Liu, P., Kopp, A., Saka, S., Mcilwain, S. J., Viny, A. D., Brand, M., & Pan, X. (2024). Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Advances, 8(12), 3076–3091. https://doi.org/10.1182/bloodadvances.2023011411
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Fang, Y., Hua, X., Shan, C.-M., Toda, T., Qiao, F., Zhang, Z., & Jia, S. (2024). Coordination of histone chaperones for parental histone segregation and epigenetic inheritance. Genes & Development, 38(3–4), 189–204. https://doi.org/10.1101/gad.351278.123
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Mendelson, K., Martin, T. C., Nguyen, C. B., Hsu, M., Xu, J., Lang, C. C. V., Dummer, R., Saenger, Y., Messina, J. L., Sondak, V. K., Desman, G., Hasson, D., Bernstein, E., Parsons, R. E., & Celebi, J. T. (2024). Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation. JCI Insight. https://doi.org/10.1172/jci.insight.166611
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Abela, L., Gianfrancesco, L., Tagliatti, E., Rossignoli, G., Barwick, K., Zourray, C., Reid, K. M., Budinger, D., Ng, J., Counsell, J., Simpson, A., Pearson, T. S., Edvardson, S., Elpeleg, O., Brodsky, F. M., Lignani, G., Barral, S., & Kurian, M. A. (2024). Neurodevelopmental and synaptic defects in DNAJC6 parkinsonism, amenable to gene therapy. Brain, 147(6), 2023–2037. https://doi.org/10.1093/brain/awae020
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Giacomini, G., Piquet, S., Chevallier, O., Dabin, J., Bai, S.-K., Kim, B., Siddaway, R., Raught, B., Coyaud, E., Shan, C.-M., Reid, R. J. D., Toda, T., Rothstein, R., Barra, V., Wilhelm, T., Hamadat, S., Bertin, C., Crane, A., Dubois, F., … Polo, S. E. (2024). Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors. Nucleic Acids Research, 52(5), 2372–2388. https://doi.org/10.1093/nar/gkad1257
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Xiao, M., Kondo, S., Nomura, M., Kato, S., Nishimura, K., Zang, W., Zhang, Y., Akashi, T., Viny, A., Shigehiro, T., Ikawa, T., Yamazaki, H., Fukumoto, M., Tanaka, A., Hayashi, Y., Koike, Y., Aoyama, Y., Ito, H., Nishikawa, H., … Inoue, D. (2023). BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-44081-6
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Chen, X., Li, Y., Zhu, F., Xu, X., Estrella, B., Pazos, M. A., McGuire, J. T., Karagiannis, D., Sahu, V., Mustafokulov, M., Scuoppo, C., Sánchez-Rivera, F. J., Soto-Feliciano, Y. M., Pasqualucci, L., Ciccia, A., Amengual, J. E., & Lu, C. (2023). Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39990-5
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Gaspary, A., Laureau, R., Dyatel, A., Dursuk, G., Simon, Y., & Berchowitz, L. E. (2023). Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision. Journal of Cell Biology, 222(11). https://doi.org/10.1083/jcb.202302074
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Xu, J. J., Chen, Y., Pantazi, J., Fernando, S., Alija, B., Sudunagunta, V., Bhagat, G., & Viny, A. D. (2023). Synergy of Stag2-Cohesin Loss Results in Expansion of Npm1c-Mutant Hematopoietic Stem and Progenitor Cells. Blood, 142(Supplement 1), 954–954. https://doi.org/10.1182/blood-2023-190627
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Xu, J. J., Chen, Y., Pantazi, J., Fernando, S., Alija, B., Sudunagunta, V., Bhagat, G., Bowman, R. L., & Viny, A. D. (2023). Stag2-Cohesin Loss Attenuates Flt3 ITD Myeloid Blast Expansion Yet Preserves Mutant HSC. Blood, 142(Supplement 1), 2756–2756. https://doi.org/10.1182/blood-2023-190702
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Bosch, E., Popp, B., Güse, E., Skinner, C., van der Sluijs, P. J., Maystadt, I., Pinto, A. M., Renieri, A., Bruno, L. P., Granata, S., Marcelis, C., Baysal, Ö., Hartwich, D., Holthöfer, L., Isidor, B., Cogne, B., Wieczorek, D., Capra, V., Scala, M., … Vasileiou, G. (2023). Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals. Genetics in Medicine, 25(11), 100950. https://doi.org/10.1016/j.gim.2023.100950
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Trauernicht, M., Rastogi, C., Manzo, S. G., Bussemaker, H. J., & van Steensel, B. (2023). Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Research, 51(18), 9690–9702. https://doi.org/10.1093/nar/gkad718
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Abini-Agbomson, S., Gretarsson, K., Shih, R. M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M. D., Armache, J.-P., Nudler, E., Narlikar, G., Liu, S., Lu, C., & Armache, K.-J. (2023). Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell, 83(16), 2872-2883.e7. https://doi.org/10.1016/j.molcel.2023.07.020
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FitzPatrick, V. D., Leemans, C., van Arensbergen, J., van Steensel, B., & Bussemaker, H. J. (2023). Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR. Nucleic Acids Research, 51(11), 5499–5511. https://doi.org/10.1093/nar/gkad232
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Gnügge, R., Reginato, G., Cejka, P., & Symington, L. S. (2023). Sequence and chromatin features guide DNA double-strand break resection initiation. Molecular Cell, 83(8), 1237-1250.e15. https://doi.org/10.1016/j.molcel.2023.02.010
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Yi, J., Zhao, X., Noell, C. R., Helmer, P., Solmaz, S. R., & Vallee, R. B. (2023). Role of Nesprin-2 and RanBP2 in BICD2-associated brain developmental disorders. PLOS Genetics, 19(3), e1010642. https://doi.org/10.1371/journal.pgen.1010642
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Sheppard, S. E., Bryant, L., Wickramasekara, R. N., Vaccaro, C., Robertson, B., Hallgren, J., Hulen, J., Watson, C. J., Faundes, V., Duffourd, Y., Lee, P., Simon, M. C., de la Cruz, X., Padilla, N., Flores-Mendez, M., Akizu, N., Smiler, J., Pellegrino Da Silva, R., Li, D., … Stessman, H. A. F. (2023). Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. Science Advances, 9(10). https://doi.org/10.1126/sciadv.ade1463
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Ganapathi, M., Buchovecky, C. M., Cristo, F., Ahimaz, P., Ruzal-Shapiro, C., Wou, K., Inácio, J. M., Iglesias, A., Belo, J. A., & Jobanputra, V. (2022). A novel biallelic loss-of-function variant inDAND5causes heterotaxy syndrome. Molecular Case Studies, 8(7), a006248. https://doi.org/10.1101/mcs.a006248
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Kim, M., Singh, M., Lee, B.-K., Hibbs, M., Richardson, K., Ellies, L., Wintle, L., Stuart, L. M., Wang, J. Y., Voon, D. C., Blancafort, P., Wang, J., Kim, J., Leedman, P. J., & Woo, A. J. (2022). A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer. Oncogenesis, 11(1). https://doi.org/10.1038/s41389-022-00435-1
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Malik, V., Zang, R., Fuentes-Iglesias, A., Huang, X., Li, D., Fidalgo, M., Zhou, H., & Wang, J. (2022). Comparative functional genomics identifies unique molecular features of EPSCs. Life Science Alliance, 5(11), e202201608. https://doi.org/10.26508/lsa.202201608
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Shen, Y., Singh, J., Sah, B., Chen, Z., Ha, W., Henzler, C., Su, T., Xie, L., Deng, Y., Li, G., Guo, H., Hibshoosh, H., & Liu, L. (2022). The Histone Demethylase HR Suppresses Breast Cancer Development through Enhanced CELF2 Tumor Suppressor Activity. Cancers, 14(19), 4648. https://doi.org/10.3390/cancers14194648
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Halder, S., Ranjha, L., Taglialatela, A., Ciccia, A., & Cejka, P. (2022). Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex. Nucleic Acids Research, 50(14), 8008–8022. https://doi.org/10.1093/nar/gkac583
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Alvarez, S., da Silva Almeida, A. C., Albero, R., Biswas, M., Barreto-Galvez, A., Gunning, T. S., Shaikh, A., Aparicio, T., Wendorff, A., Piovan, E., Van Vlierberghe, P., Gygi, S., Gautier, J., Madireddy, A., & A. Ferrando, A. (2022). Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood, 139(23), 3418–3429. https://doi.org/10.1182/blood.2021014103
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Chen, H., Hu, B., Horth, C., Bareke, E., Rosenbaum, P., Kwon, S. Y., Sirois, J., Weinberg, D. N., Robison, F. M., Garcia, B. A., Lu, C., Pastor, W. A., & Majewski, J. (2022). H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Research. https://doi.org/10.1101/gr.276383.121
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Park, D., Gharghabi, M., Reczek, C. R., Plow, R., Yungvirt, C., Aldaz, C. M., & Huebner, K. (2022). Wwox Binding to the Murine Brca1-BRCT Domain Regulates Timing of Brip1 and CtIP Phospho-Protein Interactions with This Domain at DNA Double-Strand Breaks, and Repair Pathway Choice. International Journal of Molecular Sciences, 23(7), 3729. https://doi.org/10.3390/ijms23073729
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Saleh, T., Alhesa, A., El-Sadoni, M., Abu Shahin, N., Alsharaiah, E., Al Shboul, S., Awad, H., Bloukh, S., Al-Balas, M., Alsalem, M., Azab, B., & Aladily, T. N. (2022). The Expression of the Senescence-Associated Biomarker Lamin B1 in Human Breast Cancer. Diagnostics, 12(3), 609. https://doi.org/10.3390/diagnostics12030609
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Wang, Y., Shilagardi, K., Hsu, T., Odinammadu, K. O., Maruyama, T., Wu, W., Lin, C.-S., Damoci, C. B., Spear, E. D., Shin, J.-Y., Hsu, W., Michaelis, S., & Worman, H. J. (2022). Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice. Proceedings of the National Academy of Sciences, 119(9). https://doi.org/10.1073/pnas.2118695119
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Bao, K., Shan, C.-M., Chen, X., Raiymbek, G., Monroe, J. G., Fang, Y., Toda, T., Koutmou, K. S., Ragunathan, K., Lu, C., Berchowitz, L. E., & Jia, S. (2022). The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly. PLOS Genetics, 18(2), e1010049. https://doi.org/10.1371/journal.pgen.1010049
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Kadamb, R., Leibovitch, B. A., Farias, E. F., Dahiya, N., Suryawanshi, H., Bansal, N., & Waxman, S. (2022). Invasive phenotype in triple negative breast cancer is inhibited by blocking SIN3A–PF1 interaction through KLF9 mediated repression of ITGA6 and ITGB1. Translational Oncology, 16, 101320. https://doi.org/10.1016/j.tranon.2021.101320
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Liu, Y., Wu, Z., Zhou, J., Ramadurai, D. K. A., Mortenson, K. L., Aguilera-Jimenez, E., Yan, Y., Yang, X., Taylor, A. M., Varley, K. E., Gertz, J., Choi, P. S., Cherniack, A. D., Chen, X., Bass, A. J., Bailey, S. D., & Zhang, X. (2021). A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-27055-4
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Rivas, M. A., Durmaz, C., Kloetgen, A., Chin, C. R., Chen, Z., Bhinder, B., Koren, A., Viny, A. D., Scharer, C. D., Boss, J. M., Elemento, O., Mason, C. E., & Melnick, A. M. (2021). Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.688493
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