Project description:Dysfunction of DNA methyltransferase 3b (DNMT3b) causes centromere instability but the underlying mechanism is unclear. We found that enforced expression of RNase H1 that removes R-loops, nucleic structures comprising an DNA-RNA hybrid, was sufficient to abolish DNA double-strand breaks (DSBs) at (peri-)centromeric sites in immunodeficiency-centromeric instability-facial anomalies (ICF) patient cells carrying DNMT3b mutation. However, ICF cells had lower steady-state level of centromeric R-loops than normal cells. Simultaneous knockdown of two DNA endonucleases, XPG and XPF, restored centromeric R-loops in ICF cells while reducing DSBs and chromosome segregation error. This suggests that (peri-)centromeric R-loops are more vulnerable to XPG or XPF in ICF cells, thus increasing centromeric breaks. This mechanism is recapitulated in DNMT3b-knockout HCT116 cells. Moreover, we present evidence for the choice of alternative end-joining (alt-EJ) repair of (peri-)centromeric breaks in ICF cells. Thus, DNA cleavages of (peri-)centromeric R-loops and mutagenic alt-EJ repair undermine centromere stability in DNMT3b defective cells.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection,Tumor tissue were isolated from infected recipients,and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer,especially for cell adhension
Project description:RNA-seq was performed on parental HCT116 colon cancer cell line and on HCT116 DKO (double knock-out) cell line, which contains genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-).
Project description:RNAseq was performed by to compare gene expression between wildtype and Smchd1 KO ES cells, the gene expression pattern in Dux KO mutants , Double KO mutant Tet-TKO mutants and Tet TKO plus SMCKHD1 KO mutants were analyzed by RNAseq.
Project description:mRNA was sequenced from HCT116 MYC 3' TBE1 (WT) and KO cells to identify genes differentially expressed after deletion of the MYC 3' TBE1
Project description:Genome-wide DNA methylation profiling of HCT116 WT, HCT116 DNMT1 and DNMT3B double KO, and breast cancer tumors by next generation Infinium assay