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TranscriptomicsA comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of inte...
ORGANISM(S): Mus musculus 
2015-06-19 | E-GEOD-67516 | biostudies-arrayexpress
TranscriptomicsMapping nucleosome resolution chromosome folding in yeast by Micro-C
We describe a Hi-C based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported...
ORGANISM(S): Saccharomyces cerevisiae 
2015-06-25 | E-GEOD-68016 | biostudies-arrayexpress
GenomicsPrinciples of 3D chromosome folding and evolutionary genome reshuffling in mammals
Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals
PRJNA849168 | ENA
TranscriptomicsChromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
In recent years there has been considerable and growing interest in the 3-dimensional organization of genomes. In yeast this has included detailed FISH studies that show a surprising degree of spatial clustering of the tRNA genes, the localization of telomeres, centromere positioning, and global stu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-07-18 | E-GEOD-33018 | 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
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
GenomicsInterphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [CUT&Run]
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [CUT&Run]
PRJNA1332800 | ENA
GenomicsInterphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [ATAC-seq]
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [ATAC-seq]
PRJNA1163687 | ENA
GenomicsInterphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [SLAM-seq]
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [SLAM-seq]
PRJNA1336532 | ENA
GenomicsReplication dynamics identifies the folding principles of the inactive X chromosome
Replication dynamics identifies the folding principles of the inactive X chromosome
PRJNA870918 | ENA
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