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Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes
Recent efforts have shown that structural variations (SVs) can disrupt three-dimensional genome organization and induce enhancer hijacking, yet no...
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Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at...
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Super enhancer lncRNAs: a novel hallmark in cancer
Super enhancers (SEs) consist of clusters of enhancers, harboring an unusually high density of transcription factors, mediator coactivators and...
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Etiology of super-enhancer reprogramming and activation in cancer
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by...
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MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming
Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27...
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The super-enhancer-driven lncRNA LINC00880 acts as a scaffold between CDK1 and PRDX1 to sustain the malignance of lung adenocarcinoma
Super-enhancers (SEs) are regulatory element clusters related to cell identity and disease. While the studies illustrating the function of...
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An oncogenic viral interferon regulatory factor upregulates CUB domain-containing protein 1 to promote angiogenesis by hijacking transcription factor lymphoid enhancer-binding factor 1 and metastasis suppressor CD82
Kaposi’s sarcoma (KS), a highly angiogenic and invasive vascular tumor, is the most common AIDS-associated cancer caused by KS-associated herpesvirus...
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Current challenges in understanding the role of enhancers in disease
Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are...
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Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis
BackgroundSharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China. Three-dimensional genome...
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Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution...
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SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints
BackgroundCombined whole-genome sequencing (WGS) and RNA sequencing of cancers offer the opportunity to identify genes with altered expression due to...
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Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes
The cancer-specific fusion oncoprotein SS18–SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to...
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Correction: An oncogenic viral interferon regulatory factor upregulates CUB domain-containing protein 1 to promote angiogenesis by hijacking transcription factor lymphoid enhancer-binding factor 1 and metastasis suppressor CD82
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Gene regulation on extrachromosomal DNA
Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer and is associated with poor outcomes. Clonal, megabase-sized...
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Human cytomegalovirus hijacks host stress response fueling replication stress and genome instability
Viral infections enhance cancer risk and threaten host genome integrity. Although human cytomegalovirus (HCMV) proteins have been detected in a wide...
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Roles of transposable elements in the regulation of mammalian transcription
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription...
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Structural variants shape driver combinations and outcomes in pediatric high-grade glioma
We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs...
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Loss of CASZ1 tumor suppressor linked to oncogenic subversion of neuroblastoma core regulatory circuitry
The neural crest lineage regulatory transcription factors (TFs) form a core regulatory circuitry (CRC) in neuroblastoma (NB) to specify a...
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The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which...
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