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Timothy J. Richmond, Ph.D. - Related publications

Affiliations: 
Institute of Molecular Biology & Biophysics Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
Area:
Nucleosome structure
Website:
http://www.mol.biol.ethz.ch/groups/richmond
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Morgunova E, Taipale J. Structural insights into the interaction between transcription factors and the nucleosome. Current Opinion in Structural Biology. 71: 171-179. PMID 34364091 DOI: 10.1016/j.sbi.2021.06.016   
2021 Peng Y, Li S, Onufriev A, Landsman D, Panchenko AR. Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. Nature Communications. 12: 5280. PMID 34489435 DOI: 10.1038/s41467-021-25568-6   
2021 Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Molecular Cell. PMID 34478647 DOI: 10.1016/j.molcel.2021.08.010   
2021 Kumar VC, Pai R. Genes of the month: H3.3 histone genes: H3F3A and H3F3B. Journal of Clinical Pathology. PMID 34667098 DOI: 10.1136/jclinpath-2021-207857   
2021 Du W, Pan D, Xiang P, Xiong C, Zhang M, Zhang Q, Tian Y, Zhang Z, Chen B, Luo K, Gong Q, Tian X. Terpyridine Zn(II) Complexes with Azide Units for Visualization of Histone Deacetylation in Living Cells under STED Nanoscopy. Acs Sensors. PMID 34498846 DOI: 10.1021/acssensors.1c01287   
2021 Bates DA, Bates CE, Earl AS, Skousen C, Fetbrandt AN, Ritchie J, Bodily PM, Johnson SM. Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis. Plos One. 16: e0258737. PMID 34673804 DOI: 10.1371/journal.pone.0258737   
2021 Jing Y, Tian G, Qin X, Liu Z, Li XD. Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2-nucleosome association. Rsc Chemical Biology. 2: 1257-1262. PMID 34458839 DOI: 10.1039/d1cb00070e   
2021 Zhao H, Guo M, Zhang F, Shao X, Liu G, Xing Y, Zhao X, Luo L, Cai L. Nucleosome Assembly and Disassembly Are Governed by Chemical Kinetic Principles. Frontiers in Cell and Developmental Biology. 9: 762571. PMID 34692710 DOI: 10.3389/fcell.2021.762571   
2021 Lewis TS, Sokolova V, Jung H, Ng H, Tan D. Structural basis of chromatin regulation by histone variant H2A.Z. Nucleic Acids Research. PMID 34643712 DOI: 10.1093/nar/gkab907   
2021 Ahmad S, Côté V, Côté J. DNA damage-induced phosphorylation of histone H2A at serine 15 is linked to DNA end resection. Molecular and Cellular Biology. MCB0005621. PMID 34570618 DOI: 10.1128/MCB.00056-21   
2021 Quan H, Tian H, Liu S, Xue Y, Zhang Y, Xie W, Gao YQ. Progressive Domain Segregation in Early Embryonic Development and Underlying Correlation to Genetic and Epigenetic Changes. Cells. 10. PMID 34685501 DOI: 10.3390/cells10102521   
2021 Beel AJ, Azubel M, Matteï PJ, Kornberg RD. Structure of mitotic chromosomes. Molecular Cell. PMID 34520722 DOI: 10.1016/j.molcel.2021.08.020   
2021 Sears TK, Horbinski CM, Woolard KD. IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat. Journal of Neuro-Oncology. PMID 34424450 DOI: 10.1007/s11060-021-03829-0   
2021 Ide S, Sasaki A, Kawamoto Y, Bando T, Sugiyama H, Maeshima K. Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs. Epigenetics & Chromatin. 14: 46. PMID 34627342 DOI: 10.1186/s13072-021-00421-8   
2021 Bhagwat M, Nagar S, Kaur P, Mehta R, Vancurova I, Vancura A. Replication stress inhibits synthesis of histone mRNAs in yeast by removing Spt10p and Spt21p from the histone promoters. The Journal of Biological Chemistry. 101246. PMID 34582893 DOI: 10.1016/j.jbc.2021.101246   
2021 Lövkvist C, Mikulski P, Reeck S, Hartley M, Dean C, Howard M. Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory. Elife. 10. PMID 34473050 DOI: 10.7554/eLife.66454   
2021 Yan H, Surovtsev I, Williams JF, Bailey MLP, King MC, Mochrie SGJ. Extrusion of chromatin loops by a composite loop extrusion factor. Physical Review. E. 104: 024414. PMID 34525654 DOI: 10.1103/PhysRevE.104.024414   
2021 Sharma R, Choi KJ, Quan MD, Sharma S, Sankaran B, Park H, LaGrone A, Kim JJ, MacKenzie KR, Ferreon ACM, Kim C, Ferreon JC. Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization. Nature Communications. 12: 5579. PMID 34552088 DOI: 10.1038/s41467-021-25761-7   
2021 He XL, Li JH, Wu Q. [Combinatorial CRISPR inversions of CTCF sites in cluster reveal complex insulator function]. Yi Chuan = Hereditas. 43: 758-774. PMID 34413016 DOI: 10.16288/j.yczz.21-131   
2021 Reddy D, Bhattacharya S, Shah S, Rashid M, Gupta S. DNA methylation mediated downregulation of histone H3 variant H3.3 affects cell proliferation contributing to the development of HCC. Biochimica Et Biophysica Acta. Molecular Basis of Disease. 1868: 166284. PMID 34626773 DOI: 10.1016/j.bbadis.2021.166284   
2021 Cheung KL, Kim C, Zhou MM. The Functions of BET Proteins in Gene Transcription of Biology and Diseases. Frontiers in Molecular Biosciences. 8: 728777. PMID 34540900 DOI: 10.3389/fmolb.2021.728777   
2021 Rippe K. Liquid-Liquid Phase Separation in Chromatin. Cold Spring Harbor Perspectives in Biology. PMID 34127447 DOI: 10.1101/cshperspect.a040683   
2021 Casari E, Gobbini E, Gnugnoli M, Mangiagalli M, Clerici M, Longhese MP. Dpb4 promotes resection of DNA double-strand breaks and checkpoint activation by acting in two different protein complexes. Nature Communications. 12: 4750. PMID 34362907 DOI: 10.1038/s41467-021-25090-9   
2021 Sudhamalla B, Barman S, Roy A, Bardhan I, Kandasamy T, Shivani S. Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain. Chemistry, An Asian Journal. PMID 34448544 DOI: 10.1002/asia.202100793   
2021 Jos S, Gogoi H, Prasad TK, Hurakadli MA, Kamariah N, Padmanabhan B, Padavattan S. Molecular insights into α-synuclein interaction with individual human core histones, linker histone, and dsDNA. Protein Science : a Publication of the Protein Society. 30: 2121-2131. PMID 34382268 DOI: 10.1002/pro.4167   
2021 Tian H, Yang J, Guo AD, Ran Y, Yang YZ, Yang B, Huang R, Liu H, Chen XH. Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells. Acs Chemical Biology. PMID 34618427 DOI: 10.1021/acschembio.1c00614   
2021 Yoneda M, Yasui K, Nakagawa T, Hattori N, Ito T. Nucleosome assembly protein 1 (NAP-1) is a regulator of histone H1 acetylation. Journal of Biochemistry. PMID 34551067 DOI: 10.1093/jb/mvab098   
2021 Van Rechem C, Ji F, Chakraborty D, Black JC, Sadreyev RI, Whetstine JR. Collective regulation of chromatin modifications predicts replication timing during cell cycle. Cell Reports. 37: 109799. PMID 34610305 DOI: 10.1016/j.celrep.2021.109799   
2021 Fulton MD, Cao M, Ho MC, Zhao X, Zheng YG. The Macromolecular Complexes of Histones Affect Protein Arginine Methyltransferase Activities. The Journal of Biological Chemistry. 101123. PMID 34492270 DOI: 10.1016/j.jbc.2021.101123   
2021 Shirra MK, Kocik RA, Ellison MA, Arndt KM. Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. G3 (Bethesda, Md.). PMID 34499735 DOI: 10.1093/g3journal/jkab298   
2021 Huang R, Huang T, Irish VF. Do Epigenetic Timers Control Petal Development? Frontiers in Plant Science. 12: 709360. PMID 34295349 DOI: 10.3389/fpls.2021.709360   
2021 Enríquez P, Krajewski K, Strahl BD, Rothbart SB, Dowen RH, Rose RB. Binding specificity and function of the SWI/SNF subunit SMARCA4 bromodomain interaction with acetylated histone H3K14. The Journal of Biological Chemistry. 101145. PMID 34473995 DOI: 10.1016/j.jbc.2021.101145   
2021 Chacin E, Bansal P, Reusswig KU, Diaz-Santin LM, Ortega P, Vizjak P, Gómez-González B, Müller-Planitz F, Aguilera A, Pfander B, Cheung ACM, Kurat CF. A CDK-regulated chromatin segregase promoting chromosome replication. Nature Communications. 12: 5224. PMID 34471130 DOI: 10.1038/s41467-021-25424-7   
2021 Niederacher G, Urwin D, Dijkwel Y, Tremethick DJ, Rosengren KJ, Becker CFW, Conibear AC. Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications. Rsc Chemical Biology. 2: 537-550. PMID 34458797 DOI: 10.1039/d0cb00175a   
2021 Shi J, Xu J, Chen YE, Li JS, Cui Y, Shen L, Li JJ, Li W. The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nature Communications. 12: 5285. PMID 34489442 DOI: 10.1038/s41467-021-25521-7   
2021 Kumar D, Cinghu S, Oldfield AJ, Yang P, Jothi R. Decoding the function of bivalent chromatin in development and cancer. Genome Research. PMID 34667120 DOI: 10.1101/gr.275736.121   
2021 Chen Z, Zhang Y, Guan Q, Zhang H, Luo J, Li J, Wei W, Xu X, Liao L, Wong J, Li J. Linking nuclear matrix-localized PIAS1 to chromatin SUMOylation via direct binding of histones H3 and H2A.Z. The Journal of Biological Chemistry. 101200. PMID 34537242 DOI: 10.1016/j.jbc.2021.101200   
2021 Barnes T, Korber P. The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo. International Journal of Molecular Sciences. 22. PMID 34360997 DOI: 10.3390/ijms22158233   
2021 Zhang S, Zhan L, Li X, Yang Z, Luo Y, Zhao H. Preclinical and clinical progress for HDAC as a putative target for epigenetic remodeling and functionality of immune cells. International Journal of Biological Sciences. 17: 3381-3400. PMID 34512154 DOI: 10.7150/ijbs.62001   
2021 Fang K, Li T, Huang Y, Jin VX. NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality. Genome Biology. 22: 250. PMID 34446075 DOI: 10.1186/s13059-021-02465-1   
2021 Katheeja MN, Das SP, Laha S. The budding yeast protein Chl1p is required for delaying progression through G1/S phase after DNA damage. Cell Division. 16: 4. PMID 34493312 DOI: 10.1186/s13008-021-00072-x   
2021 Park TL, Lee Y, Cho WK. Visualization of chromatin higher-order structures and dynamics in live cells. Bmb Reports. PMID 34488934   
2021 Zhang X, Wang T. Plant 3-D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years. Plant & Cell Physiology. PMID 34486654 DOI: 10.1093/pcp/pcab134   
2021 Tamburri S, Conway E, Pasini D. Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer. Trends in Genetics : Tig. PMID 34426021 DOI: 10.1016/j.tig.2021.07.011   
2021 Chen X, Li Y, Rubio K, Deng B, Li Y, Tang Q, Mao C, Liu S, Xiao D, Barreto G, Tao Y. Lymphoid-specific helicase in epigenetics, DNA repair and cancer. British Journal of Cancer. PMID 34493821 DOI: 10.1038/s41416-021-01543-2   
2021 Guttzeit S, Backs J. Post-translational modifications talk and crosstalk to class IIa histone deacetylases. Journal of Molecular and Cellular Cardiology. PMID 34416247 DOI: 10.1016/j.yjmcc.2021.08.007   
2021 Wang W, Chen X, Yang Z, Chen X, Li C, Wang M. Crystal structure of histone chaperone Vps75 from Candida albicans. Biochemical and Biophysical Research Communications. 578: 136-141. PMID 34562653 DOI: 10.1016/j.bbrc.2021.09.030   
2021 Stirpe A, Guidotti N, Northall SJ, Kilic S, Hainard A, Vadas O, Fierz B, Schalch T. SUV39 SET domains mediate crosstalk of heterochromatic histone marks. Elife. 10. PMID 34524082 DOI: 10.7554/eLife.62682   
2021 Gautam P, Sharma A, Bhatnagar A. Global histone modification analysis reveals hypoacetylated H3 and H4 histones in B Cells from systemic lupus erythematosus patients. Immunology Letters. 240: 41-45. PMID 34614442 DOI: 10.1016/j.imlet.2021.09.007   
2021 Wang T, Perazza D, Boussouar F, Cattaneo M, Bougdour A, Chuffart F, Barral S, Vargas A, Liakopoulou A, Puthier D, Bargier L, Morozumi Y, Jamshidikia M, Garcia-Saez I, Petosa C, et al. ATAD2 controls chromatin-bound HIRA turnover. Life Science Alliance. 4. PMID 34580178 DOI: 10.26508/lsa.202101151