An Oestrogen Receptor α-bound Human Chromatin Interactome

By Melissa Jane Fullwood, Mei Hui Liu, Y. Pan, Jun Liu, Xu Han, Yusoff Bin Mohamed, Y. Orlov, S. Velkov, Andrea Ho, Poh Huay Mei and 31 more. Nature, 2009

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Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/306cd4af0a5337139b38578ea09f6b269eaa6c15

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Citations in the corpus

Genome-wide mapping and analysis of chromosome architecture (2016, background): “Following proximity ligation, the ligation products are biotin-labelled at the ligation junctions 22,23 .”
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts (2014, methodology): “High-confidence Hi-C contacts capture interactions identified by ChIA-PET in mouse embryonic stem cells Several lines of evidence suggest that the 3D proximity of en-hancerstotargetpromotersplaysa roleingeneexpression(Tolhuis et al. 2002; Ferraiuolo et al. 2010; Shen et al. 2012).”
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, methodology): “ChIA-PET SMC1 ChIA-PET was performed as previously described (Chepelev et al., 2012; Fullwood et al., 2009; Goh et al., 2012; Li et al., 2012).”
Three-dimensional folding and functional organization principles of the Drosophila genome. (2012, methodology): “…sequencing to globally map chromatin contacts in human (Lieberman-Aiden et al., 2009; the Hi-C method) and yeast (Duan et al., 2010; Tanizawa et al., 2010), or of subsets of genomic interactions between regions bound by regulatory factors (Fullwood et al., 2009; Handoko et al., 2011).”
Next-Generation Genomics: an Integrative Approach (2010, positive): “However, recently developed methods have demonstrated the identification of long-range genomic interactions at a genomic scale through high-throughput, paired-end sequencing of the DNA fragments generated by the 3C metho”
The long-range interaction landscape of gene promoters (2012, background): “Previous studies have been limited to analysis of single loci 5–8 , interactions that involve a single protein of interest 9 , or to analysis of genome-wide folding of chromosomes at a resolution that cannot detect specific looping interactions between genes and functional elements 10 .”
Transcriptional enhancers: from properties to genome-wide predictions (2014, methodology): “A variant method, chromatin interaction analysis with paired‑end tag sequencing (ChIA–PET) 105 , essentially couples 3C-based methods to ChIP, thereby probing chromosomal contacts that involve certain protein factors.”
Charting histone modifications and the functional organization of mammalian genomes (2011, methodology): “scaled the technology of a related approach that also incorporates an immunoprecipitation step (chromatin interaction analysis using paired-end tag sequencing; ChIA–PET”
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development (2011, background): “More recent work has shown that clustering of genes with related gene expression patterns is common and is also associated with clustered binding of chromatin organizing proteins, patterns of histone modification and the tendency of regions to be physically close to one another in the nucleus [53-56”
Regulation of disease-associated gene expression in the 3D genome (2016, positive): “C provides an analysis of contacts among all genomic fragments 59,160 ; and chromatin interaction analysis by paired‑end tag (ChIA‑PET) combines 3C with chromatin immunoprecipitation (ChIP) to analyse the contacts of sequences bound by a protein of interest 161 .”
High-Throughput Sequencing Technologies (2015, background): “Recent advancements to the Hi-C technique combined with extremely deep sequencing (billions of reads per sample) have produced much higher resolution contact maps ( 1 kb), which refine TAD domain size from 1 Mb to less than 200 kb (Rao et al., 2014).”