ChIP Sequencing of Crispr corrected Bloom Syndrome patient cell line using antibody against BLM
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB50464 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8137450.fastq.gz | Fastqsanger.gz | |||
| ERR8137451.fastq.gz | Fastqsanger.gz | |||
| ERR8137452.fastq.gz | Fastqsanger.gz | |||
| ERR8137453.fastq.gz | Fastqsanger.gz | |||
| ERR8137454.fastq.gz | Fastqsanger.gz |
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Project description:BLM protein has been shown to play an important role in homologous recombination (HR) repair. We report that BLM interacts with RAD54 (another HR repair protein) to enhance its chromatin remodeling function. This experiment identifies that BLM gets recruited to different genetic loci even in the absence of damage, possibly along with RAD54 chromatin remodeler.
2024-04-03 | E-MTAB-11372 | biostudies-arrayexpress
Project description:Bloom syndrome is a rare autosomal recessive genetic instability and cancer predisposition syndrome caused by loss of function mutations in the BLM RECQ helicase gene. To ask if some of the distinctive pathological features of Bloom syndrome might reflect altered gene expression, we analyzed global mRNA and miRNA expression in fibroblasts from 16 patients and 15 matched normal controls, and in control primary diploid fibroblasts depleted of the BLM protein. We document significant differential expression of both protein-coding genes and miRNAs with well-characterized cancer associations in BLM-deficient cells. Differences in expression correlated significantly with G4 motifs, which are associated with potential to form G-quadruplex structures. These results indicate that BLM helicase may modulate gene expression by regulating the in vivo stability of G-quadruplex structures, and identify sets of genes and miRNAs whose expression, when altered, may drive the pathogenesis of Bloom syndrome and associated cancers.
2014-06-12 | GSE54502 | GEO
Project description:Bloom syndrome is a rare autosomal recessive genetic instability and cancer predisposition syndrome caused by loss of function mutations in the BLM RECQ helicase gene. To ask if some of the distinctive pathological features of Bloom syndrome might reflect altered gene expression, we analyzed global mRNA and miRNA expression in fibroblasts from 16 patients and 15 matched normal controls, and in control primary diploid fibroblasts depleted of the BLM protein. We document significant differential expression of both protein-coding genes and miRNAs with well-characterized cancer associations in BLM-deficient cells. Differences in expression correlated significantly with G4 motifs, which are associated with potential to form G-quadruplex structures. These results indicate that BLM helicase may modulate gene expression by regulating the in vivo stability of G-quadruplex structures, and identify sets of genes and miRNAs whose expression, when altered, may drive the pathogenesis of Bloom syndrome and associated cancers. Global profiling of mRNA and miRNA expression was analyzed in primary fibroblasts from 16 patients and 15 matched normal controls, and in 9 primary diploid fibroblasts depleted of BLM protein by BLM-specific (3), control (3) and scrambled (3) shRNA.
2014-06-12 | E-GEOD-54502 | biostudies-arrayexpress
Project description:The Bloom syndrome DNA helicase BLM contributes to chromosome stability through its roles in double-strand break repair by homologous recombination and DNA replication fork restart during the replication stress response. Loss of BLM activity leads to Bloom syndrome, which is characterized by extraordinary cancer risk and small stature. Here, we have analyzed the composition of the BLM complex in unperturbed cells and identified a direct physical interaction with the Mcm6 subunit of the minichromosome maintenance (MCM) complex by co-immunopecipitations using endogenous and recombinant proteins as well as two-hybrid analysis.
2022-02-15 | PXD018823 | Pride
Project description:Cellular innate immune sensors of DNA are essential for host defense against invading pathogens. However, the presence of self-derived DNA inside cells poses a biological risk of triggering an inappropriate immune response. The mechanisms limiting induction of inflammation by self nucleic acids are poorly understood. BLM RecQ like helicase is essential for the maintenance of genome integrity and deficient in Bloom syndrome, a rare genetic disease characterized by genome instability, susceptibility to cancer and immunodeficiency. Here, we show that BLM-deficient cells exhibit a constitutively upregulated inflammatory interferon-stimulated gene (ISG) signature. Restoring BLM expression reverts ISG expression to baseline. ISG expression in BLM-deficient fibroblasts is mediated by the cGAS-STING-IRF3 cytosolic DNA sensing pathway. Increased DNA damage or downregulation of the cytoplasmic exonuclease TREX1 enhances ISG expression in BS fibroblasts, and cytoplasmic micronuclei positive for cGAS are increased in BLM-deficient fibroblasts. Finally, BS patients demonstrate elevated ISG expression in peripheral blood. We conclude that BLM is essential to limit the expression of pro-inflammatory genes resulting from the sensing of DNA damage products by the cGAS-STING-IRF3 pathway. These results reveal an unexpected role for BLM in limiting ISG induction, thus connecting DNA damage to innate immunity, which may contribute to human pathogenesis.
2019-03-26 | GSE123447 | GEO
Project description:Transcriptionally active loci are particularly prone to breakage and mounting evidence suggest that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncovered a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we found that BLM promotes cell death. We report that upon excessive R-loop accumulation, DNA synthesis is enhanced at DSBs, in a anner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs.
2022-04-13 | E-MTAB-11592 | biostudies-arrayexpress
Project description:Genome modification in mouse embryonic stem cells (mESCs) has provided the versatile platform to analyzing gene functions in mammalian cells. Bloom helicase-deficient mESCs showed elevated rate of loss of heterozygosity (LOH) through mitotic recombination. By utilizing this characteristic of Blm deficiency, we established an efficient method to introduce homozygous mutations into mESCs, which can be used for phenotype-driven recessive screen. It is generally thought that mitotic recombination is initiated by double-strand break. DNA repair machinery, however, possesses mechanisms that suppress deleterious crossovers between homologous chromosomes. Bloom helicase plays a central role to suppress such crossover; hence its deficiency causes elevated frequency of mitotic recombination. To directly answer if DSB can initiate mitotic recombination, we established a reporter cell line, in which the recognition site of I-SceI endonuclease was introduced in the Aprt gene in Blm-deficient mESCs. We used two types of I-SceI expression vectors; one expresses a mammalian codon-optimized I-SceI (ISceIo) and the other expresses I-SceIo fused with N-terminal 110-amino acids of Geminin (Gemi). Geminin-fused I-SceI can be stabilized only in lateS/G2 phase. After I-SceI transfection and subsequent selection, we isolated Aprt-deficient mutants. Half of the mutants showed LOH in the whole telomeric region from I-SceI site, but the other half showed local LOH near the I-SceI site. Further analyses suggested that large deletion was introduced and caused LOH, which was not seen in spontaneous LOH. We designed CGH probes in 300-bp resolution in 8Mb telomeric region of chr 8 (The Aprt gene locates 7Mb from the telomere) to map the deleted regions in these mutants.
2012-11-30 | E-MTAB-1116 | biostudies-arrayexpress
Project description:The human Werner and Bloom syndromes (WS and BS) are caused by deficiencies in the WRN and BLM RecQ helicases, respectively. WRN, BLM and their S. cerevisiae homologue Sgs1, are particularly active in vitro in unwinding G-quadruplex DNA (G4-DNA), a family of non-canonical nucleic acid structures formed by certain G-rich sequences. Recently, mRNA levels from loci containing potential G-quadruplex-forming sequences (PQS) were found to be preferentially altered in sgs1 mutants, suggesting that G4-DNA targeting by Sgs1 directly affects gene expression. Here, we extend these findings to human cells. Using microarrays to measure mRNAs obtained from human fibroblasts deficient for various RecQ family helicases, we observe significant associations between loci that are upregulated in WS or BS cells and loci that have PQS. No such PQS associations were observed for control expression datasets, however. Furthermore, upregulated genes in WS and BS showed no or dramatically reduced associations with sequences similar to PQS but that have considerably reduced potential to form intramolecular G4-DNA. These findings indicate that, like Sgs1, WRN and BLM can regulate transcription globally by targeting G4-DNA.
2009-12-10 | GSE19205 | GEO
Project description:BLM deficient cells responded differently to the temozolomide and olaparib treatment in comparison to the wild type cells. The double treatment evoked cell cycle arrest, cellular senescence or polyploidy in BLM KO LN229 and LN18 cells, respectively.
2023-05-17 | GSE214931 | GEO
Project description:We profiled transcriptomes in human lung cancer cell line A549 when the expression of Bloom was knockdown by the siRNA specific to Bloom.
2018-09-06 | GSE119512 | GEO