Ontology highlight
ABSTRACT:
PROVIDER: PRJNA765341 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2022-06-12 | GSE142376 | GEO
Project description:The biorientation of sister chromatids on the mitotic spindle, essential for accurate sister chromatid segregation, relies on critical centromere components including cohesin, the centromere-specific H3 variant CENP-A, and centromeric DNA. Centromeric DNA is highly variable between chromosomes yet must accomplish a similar function. Moreover, how the 50 nm cohesin ring, proposed to encircle sister chromatids, accommodates inter-sister centromeric distances of hundreds of nanometers on the metaphase spindle is a conundrum. Insight into the 3D organization of centromere components would help resolve how centromeres function on the mitotic spindle. We used ChIP-seq and super-resolution microscopy to examine the geometry of essential centromeric components on human chromosomes. ChIP-seq of SA1, SA2, and Rad21 in human cells demonstrates that cohesin subunits are depleted in -satellite arrays where CENP-A nucleosomes and kinetochores assemble. Cohesin is instead enriched at pericentromeric DNA. Structured illumination microscopy of sister centromeres is consistent, revealing a non-overlapping pattern of CENP-A and cohesin.
2023-10-11 | GSE240957 | GEO
Project description:We report that DNA2 predominantly bound to the centromeric α-satellite regions. The centromeric regions contained 58% of the DNA2-associated DNA, representing a 33.5-fold enrichment over genomic input. To define the under-replicated DNA regions in DNA2-null cells, we conducted whole-genome DNA sequencing of the under-replicated BrdU negative DNA. After normalization to genomic input DNA from the same cells, 12.9% of the peaks from the under-replicated DNA aligned with the centromeric DNA regions, representing an 8.5-fold enrichment. In addition, among the peaks that overlapped between the DNA2 pull-down and under-replicated regions, two thirds fell into the centromeric regions, representing a 48-fold enrichment.
2018-04-10 | GSE108619 | GEO
Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome. We developed in vivo and in vitro Chem-Seq protocols with a biotinylated derivative of small molecules. In the in vivo protocol, Cells were first treated with biotinylated ligand and cross-linked with formaldehyde at the same time. Cells were then lysed, sonicated to shear the DNA, and streptavidin beads were used to isolate biotinylated ligand and associated chromatin fragments. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome. In in vitrol protocol, MM1.S cells were fixed and the derived sonicated lysate incubated with biotinylated drug to enrich for bound chromatin regions in vitro. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome.
2013-05-31 | E-GEOD-44098 | biostudies-arrayexpress
Project description:Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism that underlies centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here we define the SNF2 ATPase ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes efficient deposition of core centromeric factors. Our genomic analyses show that ERCC6L2 deficiency erodes centromeric chromatin, leading to unrestrained replication of centromeric DNA. We also establish that, beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the major DNA replication factor PCNA through an atypical peptide, presented here as a co-crystal structure. Finally, we examine ERCC6L2 activities at DNA breaks, and show that it acts to restrict end resection independently of the 53BP1-REV7-Shieldin complex. Our observations allow us to propose a mechanistic model of ERCC6L2 activity, which reconciles its seemingly distinct functions in DNA repair and DNA replication. Together, these findings provide a new molecular context for studies linking ERCC6L2 to human disease.
2023-04-10 | GSE226152 | GEO
Project description:CDCA7, encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of peri/centromeric satellite DNA. Previous work suggests that the CDCA7 CRD is implicated in DNA binding, which plays a key role in directing the DNA methylation mechinery to peri/centromeric regions. To identify potential genomic targets of CDCA7, we performed ChIP-Seq using CDCA7 knockout (KO) mouse embryonic stem cells (mESCs) stably expressing HA-tagged wild-type (WT) or ICF mutant (R285H) mCDCA7.
2024-07-31 | GSE255395 | GEO
Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting. Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.
2013-07-01 | E-GEOD-48431 | biostudies-arrayexpress
Project description:The reasons why centromeric DNA is often A+T rich are not understood. We have used chromosome engineering to replace native centromeric DNA with different test sequences at native centromeres in two different strains of the fission yeast Schizosaccharomyces pombe and have discovered that A+T rich DNA, whether synthetic or of bacterial origin, will function as a centromere and that the functionality of the A+T rich DNA does not differ substantially from that of native centromeric DNA. Using genome size as a surrogate for the inverse of effective population size (Ne) we also show that the relative A+T content of centromeric DNA scales with Ne across 45 eukaryotic species. This suggests that in most eukaryotes the A+T content of the centromeric DNA is adaptive and that the A+T content of centromeric DNA is determined by a balance between selection and mutation. Combing the experimental results and the evolutionary analyses allows us to conclude that A+T rich DNA of almost any sequence will function as a centromere in most eukaryotes. The fact that many G/C to A/T substitutions are unlikely to be selected against may contribute to the rapid evolution of centromeric DNA. We also show that neo-centromeres are not simply weak versions of native centromeres but that their establishment or inheritance may require factors in addition to those required by native centromeres.
2021-11-26 | GSE181806 | GEO