Chronic traumatic encephalopathy (CTE) is a neurodegenerative tauopathy associated with repetitive head impact (RHI) exposure. Genetic variation in the 17q21.31 region, containing microtubule-associated protein tau (M...
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Polycomb group(PcG)ring finger protein 6(PCGF6),though known as a member of the transcription-re-pressing complexes,PcG,also has activation function in regulating pluripotency gene ***,the mechanism underlying the act...
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Polycomb group(PcG)ring finger protein 6(PCGF6),though known as a member of the transcription-re-pressing complexes,PcG,also has activation function in regulating pluripotency gene ***,the mechanism underlying the activation function of PCGF6 is poorly ***,we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as *** addition,PCGF6 was recruited to a subset of the super-enhancer(SE)regions upstream of cell cycle-associated genes by OCT4,and increased their *** combining with promoter capture Hi-C data,we found that PCGF6 activates cell cycle genes by regulating SE-promoter interactions via 3D *** fin dings highlight a novel mechanism of PcG protein in regulating pluripotency,and provide a research basis for the therapeutic application of pluripotent stem cells.
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo D...
In cardiac progenitor cells (CPCs), retinoic acid (RA) signaling induces atrial lineage gene expression and acquisition of an atrial cell fate. To achieve this, RA coordinates a complex regulatory network of downstrea...
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We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, u...
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We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.
Interest in cryo-Electron Microscopy (EM) imaging has skyrocketed in recent years due to its pristine views of macromolecules and materials. As advances in instrumentation and computing algorithms spurred this progres...
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Metabolism is a molecular, cellular, ecological and planetary phenomenon, whose fundamental principles are likely at the heart of what makes living matter different from inanimate one. Systems biology approaches devel...
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