Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

By Jennifer E. Phillips-Cremins, M. Sauria, Amartya Sanyal, T. Gerasimova, B. Lajoie, J. Bell, Chin-Tong Ong, Tracy A. Hookway, Changying Guo, Yuhua Sun and 8 more. Cell, 2013

1,149 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/38ba662946f15c5156c56412802bb8a1d832a86c

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Citations in the corpus

Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “A classic example of this is seen at the Drosophila bithorax complex (BX-C), responsible for the restricted expression of Ubx, abd-A, or Abd-B along the fly’s A-P axis.”
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes (2013, background): “Recent work has shown that during neural differentiation, CCCTC binding factor, cohesion and the mediator complex modulate chromosome topology to control development (Millau and Gaudreau, 2011; Phillips-Cremins et al., 2013).”
Mapping nucleosome resolution chromosome folding in yeast by Micro-C (2015, neutral): “…of biological processes, as for example gene loops are proposed to enforce promoter directionality in yeast (Tan-Wong et al., 2012), TADs correspond to regulatory domains in mammals (Symmons et al., 2014), and LADs are correlated with gene silencing during development (Pickersgill et al., 2006).”
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III (2020, background): “A/B Compartments and TAD structures persist after acute depletion of Pol I, Pol II, and Pol III Previous studies on the relationships between transcription and 3D genome usually focused on Pol II [3, 42-44], here we separately investigated Pol I, Pol II,”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “…enhancers and genes within the CTCF-CTCF loops from elements outside those loops (Dixon et al., 2012; Dowen et al., 2014; Hnisz et al., 2016b; Ji et al., 2016; Lupiáñez et al., 2015; Narendra et al., 2015; Nora et al., 2012; Phillips-Cremins et al., 2013; Rao et al., 2014; Tang et al., 2015).”
Topologically-associating domains are stable units of replication-timing regulation (2014, neutral): “However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale 11,12 .”
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, positive): “…previous study suggested that DNA loops mediated by cohesin and CTCF tend to be larger and more shared among multiple cell types than DNA loops associated with cohesin and Mediator, which represent enhancer-promoter interactions that may be cell-type specific (Phillips-Cremins et al., 2013).”
Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes (2015, positive): “…6F), and (3) Topo IIb knockdown precludes the expression of earlyresponse genes following neuronal activity; however, gene expression can be restored under these conditions by the generation of targeted DSBs (Figure 6J). hIP-seq dataset frommouse neural progenitors (Phillips-Cremins et al., 2013).”
Regulation of disease-associated gene expression in the 3D genome (2016, neutral): “SubTADs are believed to be dynamic and often tissuespecific 66 .”