Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.

Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.

Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure.

NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure.

Targeted DNA demethylation of the Fgf21 promoter by CRISPR/dCas9-mediated epigenome editing.

Recently, we reported PPARα-dependent DNA demethylation of the Fgf21 promoter in the postnatal mouse liver, where reduced DNA methylation is associated with enhanced gene expression after PPARα activation. However, there is no direct evidence for the effect of site-specific DNA methylation on gene expression. We employed the dCas9-SunTag and single-chain variable fragment (scFv)-TET1 catalytic domain (TET1CD) system to induce targeted DNA methylation of the Fgf21 promoter both in vitro and in vivo. We succeeded in targeted DNA demethylation of the Fgf 21 promoter both in Hepa1-6 cells and PPARα-deficient mice, with increased gene expression response to PPARα synthetic ligand administration and fasting, respectively. This study provides direct evidence that the DNA methylation status of a particular gene may determine the magnitude of the gene expression response to activation cues.

Prostaglandin E2 and its receptor EP2 trigger signaling that contributes to YAP-mediated cell competition.

Cell competition is a biological process by which unfit cells are eliminated from "cell society." We previously showed that cultured mammalian epithelial Madin-Darby canine kidney (MDCK) cells expressing constitutively active YAP were eliminated by apical extrusion when surrounded by "normal" MDCK cells. However, the molecular mechanism underlying the elimination of active YAP-expressing cells was unknown. Here, we used high-throughput chemical compound screening to identify cyclooxygenase-2 (COX-2) as a key molecule triggering cell competition. Our work shows that COX-2-mediated PGE2 secretion engages its receptor EP2 on abnormal and nearby normal cells. This engagement of EP2 triggers downstream signaling via an adenylyl cyclase-cyclic AMP-PKA pathway that, in the presence of active YAP, induces E-cadherin internalization leading to apical extrusion. Thus, COX-2-induced PGE2 appears a warning signal to both abnormal and surrounding normal cells to drive cell competition.

Ultrafast intramolecular relaxation dynamics of Mg- and Zn-bacteriochlorophyll a.

Ultrafast excited-state dynamics of the photosynthetic pigment (Mg-)bacteriochlorophyll a and its Zn-substituted form were investigated by steady-state absorption∕fluorescence and femtosecond pump-probe spectroscopic measurements. The obtained steady-state absorption and fluorescence spectra of bacteriochlorophyll a in solution showed that the central metal compound significantly affects the energy of the Qx state, but has almost no effect on the Qy state. Photo-induced absorption spectra were recorded upon excitation of Mg- and Zn-bacteriochlorophyll a into either their Qx or Qy state. By comparing the kinetic traces of transient absorption, ground-state beaching, and stimulated emission after excitation to the Qx or Qy state, we showed that the Qx state was substantially incorporated in the ultrafast excited-state dynamics of bacteriochlorophyll a. Based on these observations, the lifetime of the Qx state was determined to be 50 and 70 fs for Mg- and Zn-bacteriochlorophyll a, respectively, indicating that the lifetime was influenced by the central metal atom due to the change of the energy gap between the Qx and Qy states.

Ultrafast excited state dynamics of spirilloxanthin in solution and bound to core antenna complexes: identification of the S∗ and T1 states.

Ultrafast excited state dynamics of spirilloxanthin in solution and bound to the light-harvesting core antenna complexes from Rhodospirillum rubrum S1 were investigated by means of femtosecond pump-probe spectroscopic measurements. The previously proposed S∗ state of spirilloxanthin was clearly observed both in solution and bound to the light-harvesting core antenna complexes, while the lowest triplet excited state appeared only with spirilloxanthin bound to the protein complexes. Ultrafast formation of triplet spirilloxanthin bound to the protein complexes was observed upon excitation of either spirilloxanthin or bacteriochlorophyll-a. The anomalous reaction of the ultrafast triplet formation is discussed in terms of ultrafast energy transfer between spirilloxanthin and bacteriochlorophyll-a.