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2022/12/06

Katsuhiko Minami in Genome Dynamics Laboratory won the “MBSJ2022 Science Pitch Award” at the 45th Annual Meeting of the Molecular Biology Society of Japan

Katsuhiko Minami, D5 student and SOKENDAI Special Researcher in Genome Dynamics Laboratory, received the “MBSJ2022 Science Pitch Award” at the 45th Annual Meeting of the Molecular Biology Society of Japan held in Makuhari, Chiba, Japan, on November 30 – December 2.

Awarded presentation title:

 Replication dependent histone labeling enables euchromatin/heterochromatin specific single nucleosome imaging.

About Science Pitch

The 45th Annual Meeting of the Molecular Biology Society of Japan

Genome Dynamics Laboratory

Katsuhiko Minami
Katsuhiko Minami
2022/12/06

A single-stranded DNA segment in rDNA for bacterial DNA condensation

Niki Group / Microbial Physiology Laboratory

Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin

Koichi Yano, Hideki Noguchi, Hironori Niki

iScience (2022) 25, 105504 DOI:10.1016/j.isci.2022.105504

Bacterial condensin preferentially loads onto single-stranded DNA (ssDNA) in vitro and onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the loading of bacterial condensin. We attempted to detect the ssDNA region in the rrnI gene in situ. Non-denaturing sodium bisulfite treatment catalyzed the conversion of cytosines to thymines (CT-conversion) at the melted DNA of a genome. Using next-generation sequencing, we generated an average of 11,000 reads covering each cytosine on the rDNA segment. In principle, the CT-conversion rate is an accurate guide to detect ssDNA segment. We detected multiple ssDNA segments throughout the rDNA. The deletion mutations of the rDNA hindered the ssDNA formation at the 100-500 bp segment downstream of the promoter. These data support the idea that the ssDNA segment plays a crucial role as the condensin-loading site and suggest the mechanism of condensin loading onto rDNA.

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Figure: The CT conversion rate to determine a single-stranded DNA segment in a bacterial genome, and a model of the DNA loading mechanism of bacterial condensin
2022/12/01

New assistant professor joins NIG

New assistant professor joins NIG as of December 1, 2022.

MATSUMOTO, Akihiro : Yonehara Group • Multiscale Sensory Structure Laboratory

2022/12/01

Faculty member KUBO at the Center for Frontier Research has been awarded tenure

KUBO, Fumi tenure track associate professor at the Center for Frontier Research, has been awarded tenure as of December 1, 2022.

KUBO, Fumi: Systems Neuroscience Laboratory

KUBO, Fumi
Associate Professor
2022/11/24

The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites

The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites

Nozomu Sakurai*†, Shinichi Yamazaki†, Kunihiro Suda, Ai Hosoki, Nayumi Akimoto, Haruya Takahashi, Daisuke Shibata and Yuichi Aoki*
* Corresponding authors† First authors

Nucleic Acids Research (Database Issue) 2022 November 24 DOI:10.1093/nar/gkac1058

Press release (In Japanese only)

The identification of unknown chemicals has emerged as a significant issue in untargeted metabolome analysis owing to the limited availability of purified standards for identification; this is a major bottleneck for the accumulation of reusable metabolome data in systems biology. Public resources for discovering and prioritizing the unknowns that should be subject to practical identification, as well as further detailed study of spending costs and the risks of misprediction, are lacking. As such a resource, we released databases, Food-, Plant-, and Thing- Metabolome Repository (http://metabolites.in/foods, http://metabolites.in/plants, and http://metabolites.in/things, referred to as XMRs) in which the sample-specific localization of unknowns detected by liquid chromatography–mass spectrometry in a wide variety of samples can be examined, helping to discover and prioritize the unknowns. A set of application programming interfaces for the XMRs facilitates the use of metabolome data for large-scale analysis and data mining. Several applications of XMRs, including integrated metabolome and genome analyses, are presented. Expanding the concept of XMRs will accelerate the identification of unknowns and increase the discovery of new knowledge.

Source: N. Sakurai et al., DOI: 10.1093/nar/gkac1058

FoodMR

PlantMR

ThingMR

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Figure1: The top page of the database
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Figure2: Metabolite and gene candidates found in the integrated metabolome and genome analysis.
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Figure3: Change of the contents profiles between immature soybeans and fermented soybeans
2022/11/02

Shiori Iida in Genome Dynamics Laboratory won the Student Presentation Award at the 60th Annual Meeting of the Biophysical Society of Japan

Shiori Iida

Shiori Iida , D3 student and SOKENDAI Special Researcher in Genome Dynamics Laboratory, received the Student Presentation Award at the 60th Annual Meeting of the Biophysical Society of Japan held in Hakodate, Japan, on September 28 – 30.

Awarded poster title:

 Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells

Award Winners’ list

The 60th Annual Meeting of the Biophysical Society of Japan

Genome Dynamics Laboratory

2022/11/01

New assistant professor joins NIG

New assistant professor joins NIG as of November 1, 2022.

KOSHIMIZU, Shizuka : Arita Group • Biological Networks Laboratory

2022/10/26

Rice GLUCAN SYNTHASE-LIKE5 promotes anther callose deposition to maintain meiosis initiation and progression

Rice GLUCAN SYNTHASE-LIKE5 promotes anther callose deposition to maintain meiosis initiation and progression

H. Somashekar, M. Mimura, K. Tsuda, K. I. Nonomura

Plant Physiology 2022 October 22 DOI:10.1093/plphys/kiac488

Press release (In Japanese only)

Callose is a plant cell-wall polysaccharide whose deposition is spatiotemporally regulated in various developmental processes and environmental stress responses. Appearance of callose in premeiotic anthers is a prominent histological hallmark for the onset of meiosis in flowering plants; however, the biological role of callose in meiosis remains unknown. Here we show that rice (Oryza sativa) GLUCAN SYNTHASE LIKE5 (OsGSL5), a callose synthase, localizes on the plasma membrane of pollen mother cells (PMCs) and is responsible for biogenesis of callose in anther locules through premeiotic and meiotic stages. In Osgsl5 mutant anthers mostly lacking callose deposition, aberrant PMCs accompanied by aggregated, unpaired or multivalent chromosomes were frequently observed, and furthermore, a considerable number of mutant PMCs had untimely progress into meiosis compared to that of wild-type PMCs. Immunostaining of meiosis-specific protein HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS2 (PAIR2) in premeiotic PMCs revealed precocious meiosis entry in Osgsl5 mutant anthers. These findings provide insights into the function of callose in controlling the timing of male meiosis initiation and progression, in addition to roles in microsporogenesis, in flowering plants.

Source: H. Somashekar et al., DOI: 10.1093/plphys/kiac488

Figure1
2022/10/26

How to build the cellular machine for error-free chromosome segregation

Morphological growth dynamics, mechanical stability, and active microtubule mechanics underlying spindle self-organization

T. Fukuyama, L. Yan, M. Tanaka, M. Yamaoka, K. Saito, SC. Ti, CC. Liao, KC. Hsia, YT. Maeda, Y. Shimamoto

PNAS (2022) 119, e2209053119 DOI:10.1073/pnas.2209053119

Press release (In Japanese only)

Each time a cell divides in our body, it builds a tiny micron-sized machine called the spindle. The spindle passes the copied DNA from a parental cell to the newly-created two daughter cells and should have a bipolar, football-like shape for evenly splitting the chromosomes that carry the DNA. Disrupted spindle shapes can cause errors in chromosome splitting and malfunctions in the cell offspring.

Now, a new study reveals how the shaping of this tiny segregation machine succeeds and when it ends up with failure. A team of biophysics groups in Japan (Yuta Shimamoto’s lab at the National Institute of Genetics and Yusuke Maeda’s lab at Kyushu University) and biochemistry groups abroad (Kuo-Chiang Hsia’s group at Academia Sinica and Jeff Ti’s group at the University of Hong Kong) develop a computer-based algorithm and fluorescence microscopy to track at an unprecedented resolution the way in which the machine is built from scratch. They find the unique “assembly instruction” for making the spindle with the correct shape and one for making the spindle with unfavored shapes. The team also uncovers a memory form-like material property of the spindle, which appears to be a key that separates success from failure in assembling the machine.

Abnormally shaped spindles are linked to conditions that impact human life, such as cancer and infertility. The findings of this study should be an important step toward understanding the relevant mechanisms.

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Figure: A dividing cell builds a micron-sized bipolar apparatus, called the spindle, to distribute the copied chromosomes between the newly created two daughter cells (top cartoon; blue, chromosomes). The spindle is built from thousands of microtubule cytoskeletal polymers (red) that are transported and arranged by force-generating proteins called motor proteins (green and yellow). The bipolar shape of the spindle is essential for the even distribution of chromosomes (picture at bottom left). A disruption of the spindle shape (picture at bottom right) can cause errors in chromosome segregation.
2022/10/05

Life cycle and functional genomics of the unicellular red alga Galdieria for elucidating algal and plant evolution and industrial use

Life cycle and functional genomics of the unicellular red alga Galdieria for elucidating algal and plant evolution and industrial use

S. Hirooka, T. Itabashi, T. M. Ichinose, R. Onuma, T. Fujiwara, S. Yamashita, L. W. Jong, R. Tomita, A. H. Iwane. S. Miyagishima

PNAS (2022) 119, e2210665119 DOI:10.1073/pnas.2210665119

Press release (In Japanese only)

Sexual reproduction is widespread in eukaryotes. However, only asexual reproduction has been observed in unicellular red algae, including Galdieria, which branched early in Archaeplastida. Galdieria possesses a small genome; it is polyextremophile, grows either photoautotrophically, mixotrophically, or heterotrophically and is being developed as an industrial source of vitamins and pigments because of its high biomass productivity. Here, we show that Galdieria exhibits a sexual life cycle, alternating between cell-walled diploid and cell wall-less haploid and that both phases can proliferate asexually. The haploid can move over surfaces and undergo self-diploidization or generate heterozygous diploids through mating. Further, we have prepared the whole genome and comparative transcriptome dataset between the diploid and haploid and developed genetic tools for the stable gene expression, gene disruption and selectable marker recycling system using the cell wall-less haploid. The BELL/KNOX and MADS-box transcription factors, which function in haploid-diploid transition and development in plants, are specifically expressed in the haploid and diploid, respectively, and are involved in the haploid-diploid transition in Galdieria, providing information on the missing link of the sexual life cycle evolution in Archaeplastida. Four actin genes are differently involved in motility of the haploid and cytokinesis in the diploid both of which are myosin-independent and likely reflect ancestral roles of actin. We have also generated photosynthesis-deficient mutants such as blue-colored cells, which were depleted in chlorophyll and carotenoids, for industrial pigment production. These features of Galdieria facilitate understanding the evolution of algae and plants and the industrial use of microalgae.

Source: S. Hirooka et al., PNAS DOI: 10.1073/pnas.2210665119

A review by Professor Ursula Goodenough (Washington University in St. Louis) about this article will be published in this journal (PNAS) at a later day.

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Figure: This study revealed that the cell-walled form of Galdieria, previously known as the only form, is diploid. A diploid undergoes meiosis in response to pH drop and generates a cell wall-less haploid which also can proliferate asexually (by cell division). Haploids undergo isogamous sexual reproduction or endoreduplication, generating heterozygous or homozygous diploids, respectively.

▶ The article of EurekAlert! is here

2022/10/03

Spontaneous Activity in Whisker-Innervating Region of Neonatal Mouse Trigeminal Ganglion

Iwasato Group / Laboratory of Mammalian Neural Circuits

Spontaneous Activity in Whisker-Innervating Region of Neonatal Mouse Trigeminal Ganglion.

P. Banerjee, F. Kubo, H. Nakaoka, R. Ajima, T. Sato, T. Hirata, T. Iwasato.

Scientific Reports (2022) 12, 16311 DOI:10.1038/s41598-022-20068-z

Spontaneous activity is the activity that occurs without any external sensory input. During the early postnatal period in mammals, such activity is thought to be crucial for the establishment of mature neural circuits. It remains unclear if the peripheral structure of the developing somatosensory system exhibits spontaneous activity, similar to that observed in the retina and cochlea of developing visual and auditory systems, respectively. By establishing an ex vivo calcium imaging system, here we discovered that neurons in the whisker-innervating region of the trigeminal ganglion (TG) of neonatal mice generate spontaneous activity. A small percentage of neurons showed some obvious correlated activity, and these neurons were mostly located close to one another. TG spontaneous activity was majorly exhibited by medium-to-large diameter neurons, a characteristic of mechanosensory neurons, and was blocked by chelation of extracellular calcium. Moreover, this activity was diminished by the adult stage. Spontaneous activity in the TG during the first postnatal week could be a source of spontaneous activity observed in the neonatal mouse barrel cortex.

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Figure: Discovery and characterization of spontaneous activity in peripheral sensory neurons across development
Sensory neurons of neonatal mouse trigeminal ganglion (TG) exhibit spontaneous activity ex vivo, which majorly diminishes by adult stage. Violin plot: Correlated neurons are closer to one-another, compared to non-correlated ones (Red arrow: Distance between two neurons).
2022/10/03

Chromatin organization and DNA damage

Maeshima Group / Genome Dynamics Laboratory

Chromatin organization and DNA damage.

K. Minami, S. Iida, K. Maeshima

The Enzymes “DNA Damage and Double Strand Breaks” 2022 September 27 DOI:10.1016/bs.enz.2022.08.003

Free link (until 2022.11.16)

Genomic DNA is organized three-dimensionally in the nucleus as chromatin. Recent accumulating evidence has demonstrated that chromatin organizes into numerous dynamic domains in higher eukaryotic cells, which act as functional units of the genome. However, the cellular genome is constantly threatened by many sources of DNA damage (e.g., radiation). How do cells maintain their genome integrity when subjected to DNA damage?

In this review, we discuss how the compact state of chromatin safeguards the genome from radiation damage and chemical attacks. Together with recent genomics data, our finding (Takata et al. “Chromatin compaction protects genomic DNA from radiation damage”. PLOS ONE (2013). DOI: 10.1371/journal.pone.0075622) suggests that DNA compaction, such as chromatin domain formation, plays a critical role in maintaining genome integrity. But does the formation of such domains limit DNA accessibility inside the domain and hinder the recruitment of repair machinery to the damaged site(s) during DNA repair? To approach this issue, we first describe a sensitive imaging method to detect changes in chromatin states in living cells (single-nucleosome imaging). We then use this method to explain how cells can overcome potential recruiting difficulties; cells can decompact chromatin domains following DNA damage and temporarily increase chromatin motion (∼ DNA accessibility) to perform efficient DNA repair (Iida et al. “Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells” Science Advances (2022). DOI: 10.1126/sciadv.abn5626).

This review article will be published as the 3rd chapter in the book “The Enzymes vol.51: DNA Damage and Double Strand Breaks (Elsevier, 2022)”. This work was supported by JSPS and MEXT KAKENHI grants (19H05273 and 20H05936 to K. Maeshima), the Takeda Science Foundation (to K. Maeshima), and the Uehara Memorial Foundation (to K. Maeshima). K. Minami and S. Iida are SOKENDAI Special Researchers supported by JST SPRING JPMJSP2104.

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Figure: (A) Left: Decondensed chromatin is highly susceptible to reactive radicals (marked with “・OH”) and chemicals like cisplatin (marked with “Pt”). Right: Fewer hydroxyl radicals and chemicals can attack chromatin when it is more densely compacted.
(B) Local chromatin motion persisted throughout interphase of the cell cycle (“steady-state” local chromatin motion; red line) can be transiently increased by a DNA damage response (dashed line). This temporal change in chromatin motion presumably occurs to facilitate access for DNA repair machinery.

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