Nergiz Dogan, Ph.D. - Related publications

Affiliations: 
2014 Biochemistry, Microbiology, and Molecular biology Pennsylvania State University, State College, PA, United States 
 2016- Princess Margaret Cancer Centre, Toronto 
Area:
Biochemistry, Molecular Biology, Genetics, Cancer Genomics
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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 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 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 Gowthaman U, Ivanov M, Schwarz I, Patel HP, Müller NA, García-Pichardo D, Lenstra TL, Marquardt S. The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency. The Embo Journal. e108903. PMID 34661296 DOI: 10.15252/embj.2021108903   
2021 Rippe K. Liquid-Liquid Phase Separation in Chromatin. Cold Spring Harbor Perspectives in Biology. PMID 34127447 DOI: 10.1101/cshperspect.a040683   
2021 Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG. Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 34647658 DOI: 10.1002/dvdy.430   
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 Nirala NK, Li Q, Ghule PN, Chen HJ, Li R, Zhu LJ, Wang R, Rice NP, Mao J, Stein JL, Stein GS, van Wijnen AJ, Ip YT. Hinfp is a guardian of the somatic genome by repressing transposable elements. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34620709 DOI: 10.1073/pnas.2100839118   
2021 Mashtalir N, Dao HT, Sankar A, Liu H, Corin AJ, Bagert JD, Ge EJ, D'Avino AR, Filipovski M, Michel BC, Dann GP, Muir TW, Kadoch C. Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes. Science (New York, N.Y.). 373: 306-315. PMID 34437148 DOI: 10.1126/science.abf8705   
2021 Frank L, Weinmann R, Erdel F, Trojanowski J, Rippe K. Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators. Methods in Molecular Biology (Clifton, N.J.). 2351: 307-320. PMID 34382197 DOI: 10.1007/978-1-0716-1597-3_17   
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 Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. International Journal of Molecular Sciences. 22. PMID 34445507 DOI: 10.3390/ijms22168809   
2021 Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription. 1-37. PMID 34499567 DOI: 10.1080/21541264.2021.1973865   
2021 Finke D, Schanze LM, Schreiter F, Kreußer MM, Katus HA, Backs J, Lehmann LH. Histone deacetylase 4 deletion broadly affects cardiac epigenetic repression and regulates transcriptional susceptibility via H3K9 methylation. Journal of Molecular and Cellular Cardiology. PMID 34492228 DOI: 10.1016/j.yjmcc.2021.09.001   
2021 Dai Y, Wei T, Shen Z, Bei Y, Lin H, Dai H. Classical HDACs in the regulation of neuroinflammation. Neurochemistry International. 105182. PMID 34509559 DOI: 10.1016/j.neuint.2021.105182   
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 Ozturk N, Dansranjavin T, Gies S, Calay D, Shiplu S, Creppe C, Hendrickx J, Schagdarsurengin U. H4K20me3 marks distal intergenic and repetitive regions in human mature spermatozoa. Development (Cambridge, England). 148. PMID 34345914 DOI: 10.1242/dev.196477   
2021 Shaukat A, Khan MHF, Ahmad H, Umer Z, Tariq M. Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in . Frontiers in Cell and Developmental Biology. 9: 740866. PMID 34650987 DOI: 10.3389/fcell.2021.740866   
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   
2021 Zhang Z, Liu L, Shen Y, Meng Z, Chen M, Lu Z, Zhang X. Characterization of chromatin accessibility in psoriasis. Frontiers of Medicine. PMID 34669155 DOI: 10.1007/s11684-021-0872-3   
2021 Suganuma T, Workman JL. Nucleotide Metabolism Behind Epigenetics. Frontiers in Endocrinology. 12: 731648. PMID 34526971 DOI: 10.3389/fendo.2021.731648   
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 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 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 Dochnal SA, Francois AK, Cliffe AR. De Novo Polycomb Recruitment: Lessons from Latent Herpesviruses. Viruses. 13. PMID 34452335 DOI: 10.3390/v13081470   
2021 Doane AS, Chu CS, Di Giammartino DC, Rivas MA, Hellmuth JC, Jiang Y, Yusufova N, Alonso A, Roeder RG, Apostolou E, Melnick AM, Elemento O. OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nature Immunology. PMID 34556886 DOI: 10.1038/s41590-021-01025-w   
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 Xu B, Wang H, Wright S, Hyle J, Zhang Y, Shao Y, Niu M, Fan Y, Rosikiewicz W, Djekidel MN, Peng J, Lu R, Li C. Acute depletion of CTCF rewires genome-wide chromatin accessibility. Genome Biology. 22: 244. PMID 34429148 DOI: 10.1186/s13059-021-02466-0   
2021 Kong NR, Chai L, Tenen DG, Bassal MA. A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines. Star Protocols. 2: 100750. PMID 34458869 DOI: 10.1016/j.xpro.2021.100750   
2021 Feng J, Gao Y, Wang K, Jiang M. A Novel Epigenetic Regulator ZRF1: Insight into Its Functions in Plants. Genes. 12. PMID 34440419 DOI: 10.3390/genes12081245   
2021 Mohan C, Das C, Tyler J. Histone and Chromatin Dynamics Facilitating DNA repair. Dna Repair. 107: 103183. PMID 34419698 DOI: 10.1016/j.dnarep.2021.103183   
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 Wu PS, Grosser J, Cameron DP, Baranello L, Ström L. Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion. Plos Genetics. 17: e1009763. PMID 34499654 DOI: 10.1371/journal.pgen.1009763   
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 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 Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Frontiers in Cell and Developmental Biology. 9: 723859. PMID 34422840 DOI: 10.3389/fcell.2021.723859   
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 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 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 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 Liu S, Trejo-Arellano MS, Qiu Y, Eklund DM, Köhler C, Hennig L. H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha. Genome Biology. 22: 253. PMID 34465381 DOI: 10.1186/s13059-021-02476-y   
2021 Ding H, Zhang L, Yang Q, Zhang X, Li X. Epigenetics in kidney diseases. Advances in Clinical Chemistry. 104: 233-297. PMID 34462056 DOI: 10.1016/bs.acc.2020.09.005   
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 Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M. SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nature Methods. PMID 34446921 DOI: 10.1038/s41592-021-01231-2   
2021 Cheon Y, Han S, Kim T, Hwang D, Lee D. The chromatin remodeler Ino80 mediates RNAPII pausing site determination. Genome Biology. 22: 294. PMID 34663418 DOI: 10.1186/s13059-021-02500-1   
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 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 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 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 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