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TranscriptomicsCTCF binding polarity determines chromatin looping [4C]
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentall...
ORGANISM(S): Mus musculus 
2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress
TranscriptomicsVariegated gene expression caused by cell-specific long-range DNA interactions
Mammalian genomes contain numerous DNA elements with potential transcription regulatory function but unknown target genes. We used transgenic, gain-of-function mice with an ectopic copy of the beta-globin locus control region (LCR) to better understand how regulatory elements dynamically search the ...
ORGANISM(S): Mus musculus 
2011-06-15 | E-GEOD-24614 | biostudies-arrayexpress
TranscriptomicsMaintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription.
A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transc...
ORGANISM(S): Mus musculus 
2010-05-26 | E-GEOD-10170 | biostudies-arrayexpress
GenomicsThe inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.
3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps...
ORGANISM(S): Mus musculus 
2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress
TranscriptomicsExpression data for resting and activated B and T cells
The IgH locus encodes for part of the antibody exposed by B cells and is important for the immune system. In B cells, one allele produces protein, the other must remain silenced. It was proposed that both alleles reside in different nuclear compartments and that this is important to maintain mono-al...
ORGANISM(S): Mus musculus 
2013-06-01 | E-GEOD-46865 | biostudies-arrayexpress
TranscriptomicsAllele specific analysis of the immunoglobulin heavy chain locus
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2013-06-01 | E-GEOD-47129 | biostudies-arrayexpress
TranscriptomicsAllele specific analysis of the immunoglobulin heavy chain locus by simultaneous analysis of the productive and the non-productive allele through paired-end 4C sequencing analysis in mature B cells
In developing B cells the immunoglobulin heavy chain (IgH) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH a...
ORGANISM(S): Mus musculus 
2013-06-01 | E-GEOD-47128 | biostudies-arrayexpress
TranscriptomicsInteractions among Polycomb domains are guided by chromosome architecture
Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal in...
ORGANISM(S): Drosophila melanogaster 
2011-05-09 | E-GEOD-23166 | biostudies-arrayexpress
TranscriptomicsGene expression profiling in wild type and In(3LR)sep larval brain tissue (Drosophila)
We performed a series of microarray expression profile experiments in central brain tissue from 3rd instar larvae, interrogating expression differences between wild type and In(3LR)sep strains. Since our 4C data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23166), demonstrated dramatic chan...
ORGANISM(S): Drosophila melanogaster 
2011-05-09 | E-GEOD-26693 | biostudies-arrayexpress
TranscriptomicsCell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [Expression]
We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific geno...
ORGANISM(S): Mus musculus 
2016-03-01 | E-GEOD-76480 | biostudies-arrayexpress
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