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ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing

ABSTRACT: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing

PROVIDER: PRJNA378257 | ENA |

REPOSITORIES: ENA

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ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (RRBS-Seq)

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ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-03-07 | GSE95747 | GEO

Epigenetic alterations of a DNMT3B-mutant ICF patient at base-pair resolution

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Genome-wide maps of rH2A.X in wildtype and DNMT3b-KO HCT116 lines

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.

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