論文 - 中谷　庸寿

RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organization

Tsunetoshi Nakatani, Tamas Schauer, Mrinmoy Pal, Andreas Ettinger, Luis Altamirano-Pacheco, Julia Zorn, David M. Gilbert, Maria-Elena Torres-Padilla

Developmental Cell （Elsevier BV）  2025年04月

筆頭著者,  ISSN  1534-5807

• Access to Document (DOI)

The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways

Mrinmoy Pal, Tamas Schauer, Adam Burton, Tsunetoshi Nakatani, Federico Pecori, Alicia Hernández-Giménez, Iliya Nadelson, Marc A. Marti-Renom, Maria-Elena Torres-Padilla

Cell （Elsevier BV）  2025年04月

ISSN  0092-8674

• Access to Document (DOI)

Dynamics of replication timing during mammalian development

Tsunetoshi Nakatani

Trends in Genetics （Elsevier BV）  2025年03月

筆頭著者, 責任著者,  ISSN  0168-9525

• Access to Document (DOI)

The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation

Clara Hermant, Carlos Michel Mourra-Díaz, Marlies E. Oomen, Luis Altamirano-Pacheco, Mrinmoy Pal, Tsunetoshi Nakatani, Maria-Elena Torres-Padilla

Genes & Development （Cold Spring Harbor Laboratory）  39 （ 7-8 ） 490 - 509 2025年02月

ISSN  0890-9369

　概要を見る

The regulatory circuitry of cell-specific transcriptional programs is thought to be influenced by transposable elements (TEs), whereby TEs serve as raw material for the diversification and genome-wide distribution of genetic elements that containcis-regulatory activity. However, the transcriptional activators of TEs in relevant physiological contexts are largely unknown. Here, we undertook an evolutionary approach to identify regulators of two main families of MERVL, a major regulator of transcription during early mouse development. Using a combination of phyloregulatory, transcriptomic, and loss-of-function approaches, we demonstrate that SRF is a novel regulator of MERVL and embryonic transcription during zygotic genome activation. By resolving the phylogenetic history of two major MERVL families, we delineate the evolutionary acquisition of SRF and DUX binding sites and show that the acquisition of the SRF site precedes that of DUX. SRF contributes to embryonic transcription through the regulation of MERVLs, which in turn serve as promoters for host genes. Our work identifies new transcriptional regulators and TEs that shape the gene expression programs in early embryos and highlights the process of TE domestication via the sequential acquisition of transcription factor binding sites and coevolution with the host.

• Access to Document (DOI)

An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development

Marlies E. Oomen, Diego Rodriguez-Terrones, Mayuko Kurome, Valeri Zakhartchenko, Lorenza Mottes, Kilian Simmet, Camille Noll, Tsunetoshi Nakatani, Carlos Michel Mourra-Diaz, Irene Aksoy, Pierre Savatier, Jonathan Göke, Eckhard Wolf, Henrik Kaessmann, Maria-Elena Torres-Padilla

Cell （Elsevier BV）  188 （ 4 ） 1156 - 1174.e20 2025年02月

ISSN  0092-8674

• Access to Document (DOI)

Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy

Anastasia E. Hains, Kashish Chetal, Tsunetoshi Nakatani, Joana G. Marques, Andreas Ettinger, Carlos A. O. Biagi Junior, Adriana Gonzalez-Sandoval, Renjitha Pillai, Mariella G. Filbin, Maria-Elena Torres-Padilla, Ruslan I. Sadreyev, Capucine Van Rechem

Genome Biology （Springer Science and Business Media LLC）  25 （ 1 ）  2024年12月

　概要を見る

Abstract

Background

The fatal diffuse midline gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling differentiation. The identification of targetable pathways remains very poorly explored. Toward this goal, we undertake a multi-omics approach to evaluate replication timing profiles, transcriptomics, and cell cycle features in DMG cells from both H3.1K27M and H3.3K27M subgroups and perform a comparative, integrative data analysis with healthy brain tissue.

Results

DMG cells present differential replication timing in each subgroup, which, in turn, correlates with significant differential gene expression. Differentially expressed genes in S phase are involved in various pathways related to DNA replication. We detect increased expression of DNA replication genes earlier in the cell cycle in DMG cell lines compared to normal brain cells. Furthermore, the distance between origins of replication in DMG cells is smaller than in normal brain cells and their fork speed is slower, a read-out of replication stress. Consistent with these findings, DMG tumors present high replication stress signatures in comparison to normal brain cells. Finally, DMG cells are specifically sensitive to replication stress therapy.

Conclusions

This whole genome multi-omics approach provides insights into the cell cycle regulation of DMG via the H3K27M mutations and establishes a pharmacologic vulnerability in DNA replication, which resolves a potentially novel therapeutic strategy for this non-curable disease.

• Access to Document (DOI)

Emergence of replication timing during early mammalian development

Tsunetoshi Nakatani, Tamas Schauer, Luis Altamirano-Pacheco, Kyle N. Klein, Andreas Ettinger, Mrinmoy Pal, David M. Gilbert, Maria-Elena Torres-Padilla

Nature （Springer Science and Business Media LLC）  625 （ 7994 ） 401 - 409 2023年12月

筆頭著者,  ISSN  0028-0836

　概要を見る

Abstract

DNA replication enables genetic inheritance across the kingdoms of life. Replication occurs with a defined temporal order known as the replication timing (RT) programme, leading to organization of the genome into early- or late-replicating regions. RT is cell-type specific, is tightly linked to the three-dimensional nuclear organization of the genome^1,2 and is considered an epigenetic fingerprint³. In spite of its importance in maintaining the epigenome⁴, the developmental regulation of RT in mammals in vivo has not been explored. Here, using single-cell Repli-seq⁵, we generated genome-wide RT maps of mouse embryos from the zygote to the blastocyst stage. Our data show that RT is initially not well defined but becomes defined progressively from the 4-cell stage, coinciding with strengthening of the A and B compartments. We show that transcription contributes to the precision of the RT programme and that the difference in RT between the A and B compartments depends on RNA polymerase II at zygotic genome activation. Our data indicate that the establishment of nuclear organization precedes the acquisition of defined RT features and primes the partitioning of the genome into early- and late-replicating domains. Our work sheds light on the establishment of the epigenome at the beginning of mammalian development and reveals the organizing principles of genome organization.

• Access to Document (DOI)

Regulation of mammalian totipotency: a molecular perspective from in vivo and in vitro studies.

Nakatani T, Torres-Padilla ME

Current opinion in genetics & development 2023年07月

筆頭著者

　概要を見る

In mammals, cells acquire totipotency at fertilization. Embryonic genome activation (EGA), which occurs at the 2-cell stage in the mouse and 4- to 8-cell stage in humans, occurs during the time window at which embryonic cells are totipotent and thus it is thought that EGA is mechanistically linked to the foundations of totipotency. The molecular mechanisms that lead to the establishment of totipotency and EGA had been elusive for a long time, however, recent advances have been achieved with the establishment of new cell lines with greater developmental potential and the application of novel low-input high-throughput techniques in embryos. These have unveiled several principles of totipotency related to its epigenetic makeup but also to characteristic features of totipotent cells. In this review, we summarize and discuss current views exploring some of the key drivers of totipotency from both in vitro cell culture models and embryogenesis in vivo.

• Access to Document (DOI)

A change in biophysical properties accompanies heterochromatin formation in mouse embryos.

Manuel Guthmann, Chen Qian, Irene Gialdini, Tsunetoshi Nakatani, Andreas Ettinger, Tamas Schauer, Igor Kukhtevich, Robert Schneider, Don C Lamb, Adam Burton, Maria-Elena Torres-Padilla

Genes & development 37 （ 7-8 ） 336 - 350 2023年04月

　概要を見る

The majority of our genome is composed of repeated DNA sequences that assemble into heterochromatin, a highly compacted structure that constrains their mutational potential. How heterochromatin forms during development and how its structure is maintained are not fully understood. Here, we show that mouse heterochromatin phase-separates after fertilization, during the earliest stages of mammalian embryogenesis. Using high-resolution quantitative imaging and molecular biology approaches, we show that pericentromeric heterochromatin displays properties consistent with a liquid-like state at the two-cell stage, which change at the four-cell stage, when chromocenters mature and heterochromatin becomes silent. Disrupting the condensates results in altered transcript levels of pericentromeric heterochromatin, suggesting a functional role for phase separation in heterochromatin function. Thus, our work shows that mouse heterochromatin forms membrane-less compartments with biophysical properties that change during development and provides new insights into the self-organization of chromatin domains during mammalian embryogenesis.

• Access to Document (DOI)

DNA replication fork speed underlies cell fate changes and promotes reprogramming.

Tsunetoshi Nakatani, Jiangwei Lin, Fei Ji, Andreas Ettinger, Julien Pontabry, Mikiko Tokoro, Luis Altamirano-Pacheco, Jonathan Fiorentino, Elmir Mahammadov, Yu Hatano, Capucine Van Rechem, Damayanti Chakraborty, Elias R Ruiz-Morales, Paola Y Arguello Pascualli, Antonio Scialdone, Kazuo Yamagata, Johnathan R Whetstine, Ruslan I Sadreyev, Maria-Elena Torres-Padilla

Nature genetics 54 （ 3 ） 318 - 327 2022年03月

筆頭著者

　概要を見る

Totipotency emerges in early embryogenesis, but its molecular underpinnings remain poorly characterized. In the present study, we employed DNA fiber analysis to investigate how pluripotent stem cells are reprogrammed into totipotent-like 2-cell-like cells (2CLCs). We show that totipotent cells of the early mouse embryo have slow DNA replication fork speed and that 2CLCs recapitulate this feature, suggesting that fork speed underlies the transition to a totipotent-like state. 2CLCs emerge concomitant with DNA replication and display changes in replication timing (RT), particularly during the early S-phase. RT changes occur prior to 2CLC emergence, suggesting that RT may predispose to gene expression changes and consequent reprogramming of cell fate. Slowing down replication fork speed experimentally induces 2CLCs. In vivo, slowing fork speed improves the reprogramming efficiency of somatic cell nuclear transfer. Our data suggest that fork speed regulates cellular plasticity and that remodeling of replication features leads to changes in cell fate and reprogramming.

• Access to Document (DOI)