scholarly journals Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells

2007 ◽  
Vol 36 (3) ◽  
pp. 770-784 ◽  
Author(s):  
Jairo Rodriguez ◽  
Laura Vives ◽  
Mireia Jordà ◽  
Cristina Morales ◽  
Mar Muñoz ◽  
...  
Keyword(s):  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Donguk Kim ◽  
Na Yeon Park ◽  
Keunsoo Kang ◽  
Stuart K. Calderwood ◽  
Dong-Hyung Cho ◽  
...  

AbstractArsenic is reportedly a biphasic inorganic compound for its toxicity and anticancer effects in humans. Recent studies have shown that certain arsenic compounds including arsenic hexoxide (AS4O6; hereafter, AS6) induce programmed cell death and cell cycle arrest in human cancer cells and murine cancer models. However, the mechanisms by which AS6 suppresses cancer cells are incompletely understood. In this study, we report the mechanisms of AS6 through transcriptome analyses. In particular, the cytotoxicity and global gene expression regulation by AS6 were compared in human normal and cancer breast epithelial cells. Using RNA-sequencing and bioinformatics analyses, differentially expressed genes in significantly affected biological pathways in these cell types were validated by real-time quantitative polymerase chain reaction and immunoblotting assays. Our data show markedly differential effects of AS6 on cytotoxicity and gene expression in human mammary epithelial normal cells (HUMEC) and Michigan Cancer Foundation 7 (MCF7), a human mammary epithelial cancer cell line. AS6 selectively arrests cell growth and induces cell death in MCF7 cells without affecting the growth of HUMEC in a dose-dependent manner. AS6 alters the transcription of a large number of genes in MCF7 cells, but much fewer genes in HUMEC. Importantly, we found that the cell proliferation, cell cycle, and DNA repair pathways are significantly suppressed whereas cellular stress response and apoptotic pathways increase in AS6-treated MCF7 cells. Together, we provide the first evidence of differential effects of AS6 on normal and cancerous breast epithelial cells, suggesting that AS6 at moderate concentrations induces cell cycle arrest and apoptosis through modulating genome-wide gene expression, leading to compromised DNA repair and increased genome instability selectively in human breast cancer cells.


2018 ◽  
Vol 9 (24) ◽  
pp. 4762-4773 ◽  
Author(s):  
Wenwen Chien ◽  
Makoto Sudo ◽  
Ling-Wen Ding ◽  
Qiao-Yang Sun ◽  
Peer Wuensche ◽  
...  

2012 ◽  
Vol 13 (7) ◽  
pp. 8259-8272 ◽  
Author(s):  
Sumiyo Morita ◽  
Ryou-u Takahashi ◽  
Riu Yamashita ◽  
Atsushi Toyoda ◽  
Takuro Horii ◽  
...  

2011 ◽  
Vol 205 ◽  
pp. S50 ◽  
Author(s):  
Z. Fernández-Bedmar ◽  
J. Anter ◽  
M. Villatoro-Pulido ◽  
V. Martin-Palanco ◽  
M. Del Río-Celestino ◽  
...  

2018 ◽  
Vol 46 (06) ◽  
pp. 1333-1355 ◽  
Author(s):  
Juyeon Ham ◽  
Seungyeon Lee ◽  
Hyunkyung Lee ◽  
Dawoon Jeong ◽  
Sungbin Park ◽  
...  

Ginsenoside Rg3 is a key metabolite of ginseng and is known to inhibit cancer cell growth. However, the epigenetics of CpG methylation and its regulatory mechanism have yet to be determined. Genome-wide methylation analysis of MCF-7 breast cancer cells treated with Rg3 was performed to identify epigenetically regulated genes and pathways. The effect of Rg3 on apoptosis and cell proliferation was examined by a colony formation assay and a dye-based cell proliferation assay. The association between methylation and gene expression was monitored by RT-PCR and Western blot analysis. Genome-wide methylation analysis identified the “cell morphology”-related pathway as the top network. Rg3 induced late stage apoptosis but inhibited cell proliferation up to 60%. Hypermethylated TRMT1L, PSMC6 and NOX4 were downregulated by Rg3, while hypomethylated ST3GAL4, RNLS and KDM5A were upregulated. In accordance, downregulation of NOX4 by siRNA abrogated the cell growth effect of Rg3, while the effect was opposite for KDM5A. Notably, breast cancer patients with a higher expression of NOX4 and KDM5A showed poor and good prognosis of survival, respectively. In conclusion, Rg3 deregulated tumor-related genes through alteration of the epigenetic methylation level leading to growth inhibition of cancer cells.


2015 ◽  
Vol 9 (6) ◽  
pp. 2319-2324 ◽  
Author(s):  
YUE CHENG ◽  
PAN YU ◽  
XIUZHI DUAN ◽  
CHUNHUA LIU ◽  
SIQI XU ◽  
...  

Cancer Cell ◽  
2013 ◽  
Vol 24 (2) ◽  
pp. 182-196 ◽  
Author(s):  
Fabio Petrocca ◽  
Gabriel Altschuler ◽  
Shen Mynn Tan ◽  
Marc L. Mendillo ◽  
Haoheng Yan ◽  
...  

2009 ◽  
Author(s):  
Wei‐Lin Winnie Wang ◽  
Nick Russell ◽  
Sridar Chittur ◽  
Courtney Ensslin ◽  
Sarah Mordan‐McCombs ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document