Nucleosome reorganisation in breast cancer tissues

Shtumpf M, Piroeva KV, Agrawal SP, Jacob DR, Teif VB. NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma. 2022;131(1–2):19–28.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther. 2019;20(8):1057–67.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164(1–2):57–68.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Hofer T, Rippe K. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol. 2012;19(11):1185–92.

Article  CAS  PubMed  Google Scholar 

Cole L, Kurscheid S, Nekrasov M, Domaschenz R, Vera DL, Dennis JH, Tremethick DJ. Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nat Commun. 2021;12(1):2524.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol. 2016;17:36.

Article  PubMed  PubMed Central  Google Scholar 

Bansal N, Petrie K, Christova R, Chung CY, Leibovitch BA, Howell L, Gil V, Sbirkov Y, Lee E, Wexler J, et al. Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer. Oncotarget. 2015;6(33):34087–105.

Article  PubMed  PubMed Central  Google Scholar 

Shimbo T, Du Y, Grimm SA, Dhasarathy A, Mav D, Shah RR, Shi H, Wade PA. MBD3 localizes at promoters, gene bodies and enhancers of active genes. PLoS Genet. 2013;9(12):e1004028.

Article  PubMed  PubMed Central  Google Scholar 

Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res. 2010;20(10):1361–8.

Article  PubMed  PubMed Central  Google Scholar 

Yang X, Cai G-X, Han B-W, Guo Z-W, Wu Y-S, Lyu X, Huang L-M, Zhang Y-B, Li X, Ye G-L, et al. Association between the nucleosome footprint of plasma DNA and neoadjuvant chemotherapy response for breast cancer. npj Breast Cancer. 2021;7(1):35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lavender CA, Cannady KR, Hoffman JA, Trotter KW, Gilchrist DA, Bennett BD, Burkholder AB, Burd CJ, Fargo DC, Archer TK. Downstream antisense transcription predicts genomic features that define the specific chromatin environment at mammalian promoters. PLoS Genet. 2016;12(8):e1006224.

Article  PubMed  PubMed Central  Google Scholar 

Piroeva KV, McDonald C, Xanthopoulos C, Fox C, Clarkson CT, Mallm J-P, Vainshtein Y, Ruje L, Klett LC, Stilgenbauer S, et al. Nucleosome repositioning in chronic lymphocytic leukaemia. Genome Res. 2023;33:1649–61.

Article  PubMed  PubMed Central  Google Scholar 

Compton JL, Bellard M, Chambon P. Biochemical evidence of variability in the DNA repeat length in the chromatin of higher eukaryotes. Proc Natl Acad Sci USA. 1976;73(12):4382–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Docquier F, Kita G-X, Farrar D, Jat P, O’Hare M, Chernukhin I, Gretton S, Mandal A, Alldridge L, Klenova E. Decreased poly(ADP-Ribosyl)ation of CTCF, a transcription factor, is associated with breast cancer phenotype and cell proliferation. Clin Cancer Res. 2009;15(18):5762–71.

Article  CAS  PubMed  Google Scholar 

Docquier F, Farrar D, D’Arcy V, Chernukhin I, Robinson AF, Loukinov D, Vatolin S, Pack S, Mackay A, Harris RA, et al. Heightened expression of CTCF in breast cancer cells is associated with resistance to apoptosis. Can Res. 2005;65(12):5112–22.

Article  CAS  Google Scholar 

D’Arcy V, Pore N, Docquier F, Abdullaev ZK, Chernukhin I, Kita GX, Rai S, Smart M, Farrar D, Pack S, et al. BORIS, a paralogue of the transcription factor, CTCF, is aberrantly expressed in breast tumours. Br J Cancer. 2008;98(3):571–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.

Article  PubMed  PubMed Central  Google Scholar 

Vainshtein Y, Rippe K, Teif VB. NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics. 2017;18(1):158.

Article  PubMed  PubMed Central  Google Scholar 

Quinlan AR. BEDTools: the swiss-army tool for genome feature analysis. Curr Protoc Bioinform. 2014;47(1):11–2.

Article  Google Scholar 

Brooke GN, Powell SM, Lavery DN, Waxman J, Buluwela L, Ali S, Bevan CL. Engineered repressors are potent inhibitors of androgen receptor activity. Oncotarget. 2014;5(4):959–69.

Article  PubMed  PubMed Central  Google Scholar 

Leach DA, Mohr A, Giotis ES, Cil E, Isac AM, Yates LL, Barclay WS, Zwacka RM, Bevan CL, Brooke GN. The antiandrogen enzalutamide downregulates TMPRSS2 and reduces cellular entry of SARS-CoV-2 in human lung cells. Nat Commun. 2021;12(1):4068.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Serna-Pujol N, Salinas-Pena M, Mugianesi F, Le Dily F, Marti-Renom MA, Jordan A. Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. Nucleic Acids Res. 2022;50(7):3892–910.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Achinger-Kawecka J, Valdes-Mora F, Luu P-L, Giles KA, Caldon CE, Qu W, Nair S, Soto S, Locke WJ, Yeo-Teh NS. Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Nat Commun. 2020;11(1):1–17.

Article  Google Scholar 

Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, Sedlazeck FJ, Hansen KD, Simpson JT, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods. 2020;17(12):1191–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lyu R, Zhu X, Shen Y, Xiong L, Liu L, Liu H, Wu F, Argueta C, Tan L. Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells. Epigenetics. 2021;10:1–15.

Google Scholar 

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.

Article  Google Scholar 

Severson TM, Kim Y, Joosten SEP, Schuurman K, van der Groep P, Moelans CB, Ter Hoeve ND, Manson QF, Martens JW, van Deurzen CHM, et al. Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer. Nat Commun. 2018;9(1):482.

Article  PubMed  PubMed Central  Google Scholar 

Santana-Garcia W, Castro-Mondragon JA, Padilla-Galvez M, Nguyen NTT, Elizondo-Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras-Moreira B, et al. RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Res. 2022;50(W1):W670–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell. 2018;173(2):291–304.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH. Nucleosome organization in human embryonic stem cells. PLoS ONE. 2015;10(8):e0136314.

Article  PubMed  PubMed Central  Google Scholar 

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011;474(7352):516–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clarkson CT, Deeks EA, Samarista R, Mamayusupova H, Zhurkin VB, Teif VB. CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Res. 2019;47(21):11181–96.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019;29(5):750–61.

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