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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells
BackgroundHigher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breastExpand
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  • Open Access
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
Gateway-compatible yeast one-hybrid (Y1H) assays provide a convenient gene-centered (DNA to protein) approach to identify transcription factors that can bind a DNA sequence of interest. We presentExpand
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  • Open Access
Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging: SNP-CLING
Imaging and chromatin capture techniques have provided important insights into our understanding of nuclear organization. A limitation of these techniques is the inability to resolve allele-specificExpand
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RUNX1 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 remodelingExpand
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C‐ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher‐Order Chromatin Organization
Three‐dimensional organization of the chromatin has important roles in transcription, replication, DNA repair, and pathologic events such as translocations. There are two fundamental ways to studyExpand
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Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region.
Runx2 is a developmentally regulated gene in vertebrates and is essential for bone formation and skeletal homeostasis. The induction of runx2-P1 isoform transcripts is a hallmark of earlyExpand
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A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genomeExpand
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The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter
Three-dimensional organization of chromatin is fundamental for transcriptional regulation. Tissue-specific transcriptional programs are orchestrated by transcription factors and epigeneticExpand
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  • Open Access
Epigenetic Control of Cell Cycle-Dependent Histone Gene Expression Is a Principal Component of the Abbreviated Pluripotent Cell Cycle
ABSTRACT Self-renewal of human pluripotent embryonic stem cells proceeds via an abbreviated cell cycle with a shortened G1 phase. We examined which genes are modulated in this abbreviated period andExpand
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Enhancers in the Peril lincRNA locus regulate distant but not local genes
BackgroundRecently, it has become clear that some promoters function as long-range regulators of gene expression. However, direct and quantitative assessment of enhancer activity at long intergenicExpand
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