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GenomicsHot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [rDNA units]
4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected inside IGS. Our data indicate that mostly rDNA units exhibit close proximity with pericentromeric regions in different chromosomes. We also detected the contacts within a rDNA uni...
ORGANISM(S): Homo sapiens 
2014-10-04 | E-GEOD-49193 | biostudies-arrayexpress
TranscriptomicsHot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [DSBs]
Eukaryotic chromosomes are subjected to spontaneous fragmentation even under quick isolation of DNA in a solid phase by strong treatment with 0.1 M EDTA, 1% SDS and proteinase K (1 mg/ml). The long DNA fragments of excised chromosomal DNA were denoted as forum domains. Mostly forum domains are of 50...
ORGANISM(S): Homo sapiens 
2014-10-04 | E-GEOD-49302 | biostudies-arrayexpress
TranscriptomicsGenome-wide replication analysis of a yeast eco1 mutant by deep sequencing.
Eco1 is the acetyltransferase that establishes sister-chromatid cohesion during DNA replication. Budding yeast with an eco1 mutation that genocopies Roberts syndrome displaysreduced ribosomal DNA (rDNA) transcription and a transcriptional signature of starvation. Weshow that deleting FOB1, a gene en...
ORGANISM(S): Saccharomyces cerevisiae 
2014-04-03 | E-GEOD-54742 | biostudies-arrayexpress
GenomicsGenomic distribution of linker histone varinat H1T
We report genome-wide distribution of germ cell-specific linker histone variant H1T in cancer cell line AGS, MDA-MB-231, and mouse embryonic stem cells (mESCs). We found that H1T expressed not only testis but also non-germ cells such as cancer cells and pluripotent stem cells and showed the biased d...
ORGANISM(S): Homo sapiens 
2016-03-30 | E-GEOD-75287 | biostudies-arrayexpress
TranscriptomicsThe cohesin acetyltransferase Eco1 coordinates rDNA replication and transcription
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Saccharomyces cerevisiae 
2014-04-03 | E-GEOD-54743 | biostudies-arrayexpress
ProteomicsIdentification of proteins bound with RPA194 at rDNA loci post radiation in breast cancer cells
Following radiation damage, cells resume ribosome biogenesis for survival. We combined chromatin immunoprecipitation (ChIP) with mass spectrometry to identify key binding partners of RPA194 (the major subunit of RNA polI) at the rDNA loci in response to irradiation.
ORGANISM(S): Homo sapiens (Human) 
2023-07-20 | PXD041472 | Pride
Breast cancer Rdna Rpa194 Radiation Chip-ms Ir 
TranscriptomicsY-linked rDNA deletions in Drosophila melanogaster
Please see publication. These experiments were performed to ascertain the contribution of Y-linked rDNA copy number variation in the modulation of gene expression. Males (XY) and female (XXY) genotypes were probed. Dye swaps and direct comparisons within each sex
ORGANISM(S): Drosophila melanogaster 
2011-07-31 | E-GEOD-27695 | biostudies-arrayexpress
GenomicsGenome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria
During transcription the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout budding yeast genome. In wild-type strains, R-loops were readily detected over...
ORGANISM(S): Saccharomyces cerevisiae 
2014-11-03 | E-GEOD-53420 | biostudies-arrayexpress
Transcriptomics16S rDNA sequencing of BALB/c and C57BL/7 mouse gut microbiomes
Age-dependent changes of the gut-associated microbiome have been linked to increased frailty and systemic inflammation. This study found that age-associated changes of the gut microbiome of BALB/c and C57BL/6 mice could be reverted by co-housing of aged (22 months old) and adult (3 months old) mice ...
ORGANISM(S): Mus musculus 
2019-05-08 | E-MTAB-7750 | biostudies-arrayexpress
GenomicsGlycogen synthase kinase (GSK) 3β phosphorylates and protects nuclear myosin 1c from proteasome-mediated degradation to activate rDNA transcription in early G1 cells
Nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by facilitating PCAF-mediated H3K9 acetylation, but the molecular mechanism by which NM1 is regulated remains unclear. Here, we report that at early G1 the glycogen synthase kinase (GSK) 3β ...
ORGANISM(S): Mus musculus 
2014-05-02 | E-GEOD-57153 | biostudies-arrayexpress
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