Project description:Laminins are large heterotrimeric cross-shaped extracellular matrix (ECM) glycoproteins with terminal globular domains and a coiled-coil region. We have produced for the first time a recombinant laminin coiled-coil domain and studied the transcriptional profile of cells incubated in coiled-coil-coated wells. Cells were incubated in 24w plates, onto coiled-coil-coated wells or control BSA-coated wells (one each), 24h
Project description:Laminins are large heterotrimeric cross-shaped extracellular matrix (ECM) glycoproteins with terminal globular domains and a coiled-coil region. We have produced for the first time a recombinant laminin coiled-coil domain and studied the transcriptional profile of cells incubated in coiled-coil-coated wells.
Project description:We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility. We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample.
Project description:Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify multiciliated cells in vertebrates. Here, we performed RNAseq on Xenopus laevis ectoderm in the presence of multicilin alone or multicilin and a dominant-negative e2f4 construct. We also performed ChIPseq on e2f4 in the presence or absence of multicilin. Taken together, these data demonstrate how multicilin affects e2f4 genomic targets and their downstream transcription.
Project description:The aim of this pilot study is to establish if a correlation between sub-lingual microcirculation measured by Orthogonal polarization spectral (OPS) imaging and symptoms of postoperative ileus exist in patients undergoing elective colorectal surgery.
Project description:We report a proximity labeling-based orthogonal trap approach for investigation of HDAC8 substrates in living cells. In this strategy, the genetic fusions that coupled the engineering enzyme APEX2 with HDAC8 are designed to trap substrate proteins in cellular context, by which they contribute to the covalent tagging of the transient neighboring binders. The tagged proteins are then employed with an integrated orthogonal enrichment strategy that allows for direct identification of acetylated sites on targets.
Project description:As one of approaches for elucidating the molecular bases which define the difference for counteracting defect of Mbd3-knockout ESCs between MBD3a mutant lacking MBD domain and that lacking coiled-coil domain, we explored the possibility that these two mutants are different in their ability to recruit PRC2 complex in close vicinity by ChIP-sequence analyses.
Project description:Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50 nm long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific cross-linking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.
