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TranscriptomicsChromosomal translocations are guided by the spatial organization of the genome
The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from...
ORGANISM(S): Mus musculus 
2012-02-16 | E-GEOD-35519 | biostudies-arrayexpress
TranscriptomicsSpatial organisation of the X inactivation center
We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomi...
ORGANISM(S): Mus musculus 
2012-04-11 | E-GEOD-35721 | biostudies-arrayexpress
TranscriptomicsChromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
Amartya Sanyal mailto:amartya.sanyal@umassmed.edu (Wet Lab), Bryan R. Lajoie mailto:bryan.lajoie@umassmed.edu, Gaurav Jain mailto:gaurav.jain@umassmed.edu (Dry Lab), Job Dekker mailto:job.dekker@umassmed.edu (Principal Investigator) This track contains chromatin interaction data generated using the...
ORGANISM(S): Homo sapiens 
2012-07-18 | E-GEOD-39510 | biostudies-arrayexpress
GenomicsMus musculus
5C Chromatin interactions in the Igh locus in B cell progenitors
PRJNA306173 | ENA
TranscriptomicsGenome-wide maps of nuclear lamina interactions in single human cells. (Hi-C, KBM7 haploid)
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with hig...
ORGANISM(S): Homo sapiens 
2015-09-24 | E-GEOD-69841 | biostudies-arrayexpress
TranscriptomicsRUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.
RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organiz...
ORGANISM(S): Homo sapiens 
2016-08-23 | E-GEOD-75070 | biostudies-arrayexpress
TranscriptomicsMetaphase-Chromosome-Organization
Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding state...
ORGANISM(S): Homo sapiens 
2013-11-05 | E-MTAB-1948 | biostudies-arrayexpress
GenomicsMORC family ATPases required for heterochromatin condensation and gene silencing
Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, CRT1 and CRH6, which cause de-repression of DNA-methylated genes and TEs, but no losses of DNA or histone methylatio...
ORGANISM(S): Arabidopsis thaliana 
2012-05-02 | E-GEOD-37644 | biostudies-arrayexpress
TranscriptomicsSMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucl...
ORGANISM(S): Homo sapiens 
2016-06-02 | E-GEOD-74716 | biostudies-arrayexpress
TranscriptomicsThe conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer
Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is m...
ORGANISM(S): Saccharomyces cerevisiae 
2015-11-20 | E-GEOD-73890 | biostudies-arrayexpress
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