プロモーター領域中の塩基置換が転写活性化能へ与える影響の網羅的解析

学位の種別: 課程博士審査委員会委員 : （主査）東京大学教授 菅野 純夫, 東京大学教授 中井 謙太, 東京大学教授 松田 浩一, 東京大学准教授 佐藤 均, 九州工業大学教授 矢田 哲士University of Tokyo(東京大学

Evidence for Efficient Pathway to Produce Slow Electrons by Ground-state Dication in Clusters

We present an experimental evidence for a so-far unobserved, but potentially very important step relaxation cascades following inner-shell ionization of a composite system: Multiply charged ionic states created after Auger decay may be neutralized by electron transfer from a neighboring species, producing at the same time a low-energy free electron. This electron transfer-mediated decay (ETMD) called process is effective even after Auger decay into the dicationic ground state. Here, we report the ETMD of Ne2+ produced after Ne 1s photoionization in Ne-Kr mixed clusters

Improved accuracy in high-frequency AC transport measurements in pulsed high magnetic fields

We show theoretically and experimentally that accurate transport measurements are possible even within the short time provided by pulsed magnetic fields. For this purpose, a new method has been devised, which removes the noise component of a specific frequency from the signal by taking a linear combination of the results of numerical phase detection using multiple integer periods. We also established a method to unambiguously determine the phase rotation angle in AC transport measurements using a frequency range of tens of kilohertz. We revealed that the dominant noise in low-frequency transport measurements in pulsed magnetic fields is the electromagnetic induction caused by mechanical vibrations of wire loops in inhomogeneous magnetic fields. These results strongly suggest that accurate transport measurements in short-pulsed magnets are possible when mechanical vibrations are well suppressed

Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome

In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G + C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome

Fully gapped superconductivity with no sign change in the prototypical heavy-fermion CeCu2Si2

In exotic superconductors including high-$T_c$ copper-oxides, the interactions mediating electron Cooper-pairing are widely considered to have a magnetic rather than the conventional electron-phonon origin. Interest in such exotic pairing was initiated by the 1979 discovery of heavy-fermion superconductivity in CeCu$_2$Si$_2$, which exhibits strong antiferromagnetic fluctuations. A hallmark of unconventional pairing by anisotropic repulsive interactions is that the superconducting energy gap changes sign as a function of the electron momentum, often leading to nodes where the gap goes to zero. Here, we report low-temperature specific heat, thermal conductivity and magnetic penetration depth measurements in CeCu$_2$Si$_2$, demonstrating the absence of gap nodes at any point on the Fermi surface. Moreover, electron-irradiation experiments reveal that the superconductivity survives even when the electron mean free path becomes substantially shorter than the superconducting coherence length. This indicates that superconductivity is robust against impurities, implying that there is no sign change in the gap function. These results show that, contrary to long-standing belief, heavy electrons with extremely strong Coulomb repulsions can condense into a fully-gapped s-wave superconducting state, which has an on-site attractive pairing interaction.Comment: 8 pages, 5 figures + Supplement (3 pages, 5 figures

Following the Birth of a Nanoplasma Produced by an Ultrashort Hard-X-Ray Laser in Xenon Clusters

X-ray free-electron lasers (XFELs) made available a new regime of x-ray intensities, revolutionizing the ultrafast structure determination and laying the foundations of the novel field of nonlinear x-ray optics. Although earlier studies revealed nanoplasma formation when an XFEL pulse interacts with any nanometer-scale matter, the formation process itself has never been decrypted and its timescale was unknown. Here we show that time-resolved ion yield measurements combined with a near-infrared laser probe reveal a surprisingly ultrafast population (similar to 12 fs), followed by a slower depopulation (similar to 250 fs) of highly excited states of atomic fragments generated in the process of XFEL-induced nanoplasma formation. Inelastic scattering of Auger electrons and interatomic Coulombic decay are suggested as the mechanisms populating and depopulating, respectively, these excited states. The observed response occurs within the typical x-ray pulse durations and affects x-ray scattering, thus providing key information on the foundations of x-ray imaging with XFELs

Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in realtime. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (similar to 20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (similar to 100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Bromodomain and extraterminal domain inhibition synergizes with WEE1-inhibitor AZD1775 effect by impairing nonhomologous end joining and enhancing DNA damage in nonsmall cell lung cancer

Bromodomain and extraterminal domain (BET) inhibitors are broadly active against distinct types of cancer, including nonsmall cell lung cancer (NSCLC). Previous studies have addressed the effect of BET-inhibiting drugs on the expression of oncogenes such as c-Myc, but DNA damage repair pathways have also been reported to be involved in the efficacy of these drugs. AZD1775, an inhibitor of the G2-M cell cycle checkpoint kinase WEE1, induces DNA damage by promoting premature mitotic entry. Thus, we hypothesized that BET inhibition would increase AZD1775-induced cytotoxicity by impairing DNA damage repair. Here, we demonstrate that combined inhibition of BET and WEE1 synergistically suppresses NSCLC growth both in vitro and in vivo. Two BET inhibitors, JQ1 and AZD5153, increased and prolonged AZD1775-induced DNA double-strand breaks (DSBs) and concomitantly repressed genes related to nonhomologous end joining (NHEJ), including XRCC4 and SHLD1. Furthermore, pharmaceutical inhibition of BET or knockdown of the BET protein BRD4 markedly diminished NHEJ activity, and the BET-inhibitor treatment also repressed myelin transcription factor 1 (MYT1) expression and promoted mitotic entry with subsequent mitotic catastrophe when combined with WEE1 inhibition. Our findings reveal that BET proteins, predominantly BRD4, play an essential role in DSB repair through the NHEJ pathway, and further suggest that combined inhibition of BET and WEE1 could serve as a novel therapeutic strategy for NSCLC