Coordination of cohesin and DNA replication observed with purified proteins

Yasuto Murayama, Shizuko Endo, Yumiko Kurokawa, Ayako Kurita, Sanae Iwasaki, Hiroyuki Araki

Nature 2024 Jan 24 DOI:10.1038/s41586-023-07003-6

Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication, but how cohesion is established at the replication fork is poorly understood.

Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4, which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1.

Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.

Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago

Luca Nishimura, Akio Tanino, Mayumi Ajimoto, Takafumi Katsumura, Motoyuki Ogawa, Kae Koganebuchi, Daisuke Waku, Masahiko Kumagai, Ryota Sugimoto, Hirofumi Nakaoka, Hiroki Oota, Ituro Inoue

PLOS ONE (2024) 19, e0295924 DOI:10.1371/journal.pone.0295924

Press release (In Japanese only)

The characteristics of the intestinal environment of the Jomon people who lived in the Japanese archipelago thousands of years ago were not known.

In this study, we conducted the first metagenomic analysis in Japan using ancient DNA extracted from four Jomon-period feces fossil (coprolite) samples. Analysis of the large scale DNA data obtained by metagenomic analysis revealed genome sequences derived from bacteria and viruses that are presumed to have existed in the intestines. The results of this analysis may reflect the characteristics of the Jomon people’s intestinal environment.

We plan to conduct similar analyses on other Jomon coprolites to identify more bacteria and viruses, and to elucidate the evolution of intestinal bacteria and viruses from the Jomon period to the present day, as well as the detailed characteristics of the Jomon intestinal environment.

The research was conducted by a joint research group including Luca Nishimura (a graduate student at SOKENDAI) and Project Professor Ituro Inoue from the National Institute of Genetics, Professor Hiroki Oota from Graduate School of Science, The University of Tokyo, and Mayumi Ajimoto, a curator at the Wakasa History Museum in Fukui Prefecture.

The research results were published in the international scientific journal PLOS ONE on January 25, 2024 (JST).

Figure: Classification of viral genome sequences detected in the Jomon coprolites.
The pie chart shows the ratio of virus from eukaryotes as 0.07%, archaea as 0.04%, and viruses infecting bacteria (phage), as 99.89%. You can see that most of the viruses are phages that

• The article of “EurekAlert!” is here.

Kawakami Group / Laboratory of Molecular and Developmental Biology

Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly

Sherman, S., Arnold-Ammer, I., Schneider, M.W., Kawakami, K., and Baier, H.

Nature Communications (2023) 14, 6020 DOI:10.1038/s41467-023-40749-1

Brain development is orchestrated by both innate and experience-dependent mechanisms, but their relative contributions are difficult to disentangle. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum, thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated, the complete set of 77 neuronal types develops in apparently normal proportions, at normal locations, and along normal differentiation trajectories. Strikingly, the cell-cycle exits of proliferating progenitors in these areas are delayed, and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a pre-glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion, we show that signals emitted by retinal axons influence the pace of neuro- genesis in visual brain areas, but do not detectably affect the specification or wiring of downstream neurons.

This study was conducted as collaboration with Baier lab at Max Planck Institute.

Figure: (A)Transgenic zebrafish (HGn12C) expressing GFP in neurons of retinorecipient areas.
(B)The lakritz mutation was introduced into HGn12C (center), and transcriptional profiling analysis of GFP-positive neurons was conducted.

Sakai Group / Model Fish Genetics Laboratory

In vitro storage of functional sperm at room temperature in zebrafish and medaka

Takemoto K, Nishimura T, Kawasaki T, Imai Y, Levy K, Hart N, Olaya I, Burgess SM, Elkouby YM, Tanaka M, Sakai N,

Zebrafish (2023) 20, 229-235 DOI:10.1089/zeb.2023.0054
A PDF of this paper can be downloaded from here.

The longevity of sperm in teleost such as zebrafish and medaka is short when isolated even in saline-balanced solution at a physiological temperature. However, we thought that under suitable conditions sperm could be survived for a longer period of time, and we investigated these conditions. Here, we show that the sperm of zebrafish can survive and maintain fertility in L-15-based storage medium supplemented with 50 Units/ml penicillin, 50 µg/ml streptomycin, 0.5% (w/v) bovine serum albumin, 3% foetal bovine serum, 25 mM glucose, 0.1 mM lactic acid, 10 mM Hepes (pH 7.9), and 22% water for 28 days at room temperature. The fertilized embryos developed to normal fertile adults. This storage medium with increasing lactic acid two-fold was effective in medaka sperm stored for 7 days at room temperature. These results suggest that sperm from external fertilizer zebrafish and medaka has the ability to survive for at least 4 weeks and 1 week, respectively, in the body fluid-like medium at a physiological temperature. This sperm storage method allows researchers to ship sperm by low-cost methods and to investigate key factors for motility and fertile ability in those sperm.

Figure: Zebrafish cover featuring zebrafish and medaka sperm

Kawakami Group/Laboratory of Molecular and Developmental Biology

Determinants of motor neuron functional subtypes important for locomotor speed

Kristen P. D’Elia, Hanna Hameedy, Dena Goldblatt, Paul Frazel, Mercer Kriese, Yunlu Zhu, Kyla R. Hamling, Koichi Kawakami, Shane A. Liddelow, David Schoppik, and Jeremy S. Dasen

Cell Reports (2023) 42, 113049. DOI:10.1016/j.celrep.2023.113049

Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons (MNs). MNs are essential to movement and differentially susceptible in disease, but little is known about how MNs acquire functional subtype-specific features during development. Using single-cell RNA profiling in embryonic and larval zebrafish, we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post- mitotic and mature MNs. Assessing MN development in genetic mutants, we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors, Prdm16 and Mecom, are both functional subtype-specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes.

This study was conducted as collaboration with Schoppik lab at New York University.

Figure1: Zebrafish motor neuron diversity is regulated by the transcription factors prdm16 and mecom. The absence of these transcription factors results in fast motor neurons exhibiting characteristics of slow motor neurons.

Figure2: Overlap of prdm16 and mecom expression in motor neurons using transgenic fish.

A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception

Hidenori Nishihara, Yasuka Toda, Tae Kuramoto, Kota Kamohara, Azusa Goto, Kyoko Hoshino, Shinji Okada, Shigehiro Kuraku, Masataka Okabe, Yoshiro Ishimaru

Nature Ecology & Evolution 2023 Dec 13 DOI:10.1038/s41559-023-02258-8

Press release (In Japanese only)

EurekAlert! link about this artcle

• Unraveling the evolutionary origins of umami and sweet taste preferences

The perception of taste is one of the most important senses and helps us identify beneficial foods and avoid harmful substances. For instance, our fondness for sweet and savory foods results from our need to consume carbohydrates and proteins. Given their importance as an evolutionary trait, researchers around the world are investigating how taste receptors originated and evolved over a period of time. Obtaining these insights into the feeding behavior of organisms can help them paint a picture of the history of life on Earth.　read more>

Figure: A new study led by researchers from Kindai University identified five new groups of umami and sweet taste receptors within the TAS1R family (TAS1R 4, 5, 6, 7, and 8) and also diversity in TAS1R2 and TAS1R3 genes.