Author

Chikako Shimura

RIKEN

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Molecular Biology· 5 Developmental Biology· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:gene regulatory network inference· 6 Organism:mouse· 5 Assay:DNA methylation· 4 Approach:experimental assay· 4 Approach:statistical model· 4 Assay:ChIP-seq· 3 Research Focus:differential expression· 3 Research Focus:cell type annotation· 2

Frequent Co-Authors

Kei FukudaiD· 7 shared Yoichi ShinkaiiD· 7 shared Akie Tanigawa· 1 shared Atsuo OguraiD· 1 shared Hisashi MiuraiD· 1 shared Ichiro HirataniiD· 1 shared Jun‐ichi NakayamaiD· 1 shared Kenji IchiyanagiiD· 1 shared

Activity by Year

2021-2025 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

7 shared papersMolecular Biology

Kei FukudaORCID

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1

Taiki Shimizu, Kei Fukuda, Chikako Shimura, Jun‐ichi Nakayama, Masaya Oki, Yoichi Shinkai

This study introduces H3K9 methylation and HP1 into budding yeast to examine their role in heterochromatin formation, finding they do not significantly alter chromatin structure or transcription.

Genes to Cells · Dec 8, 2025Peer-reviewedSynthetic Biology

H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity

Kei Fukuda, Chikako Shimura, Yoichi Shinkai

The paper investigates how H3K9 and H3K27 methylation regulate CTCF binding and 3D genome structure in mouse cells, showing that their loss disrupts chromatin organization and gene expression.

Genome Research · Oct 1, 2025Peer-reviewedMolecular Biology

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin

Kei Fukuda, Kimiko Inoue, Chikako Shimura, Moe Kitazawa, Michiko Hirose, Takashi Ishiuchi, Shogo Matoba, Atsuo Ogura, Yoichi Shinkai

This study shows that Resf1 is essential for placental development and trophoblast cell-specific heterochromatin configuration in mice, with loss of Resf1 leading to retroelement upregulation and developmental defects.

bioRxiv · Sep 25, 2025Developmental Biology

H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation

Kei Fukuda, Chikako Shimura, Yoichi Shinkai

The paper investigates how H3K27me3 and the PRC1-H2AK119ub pathway work together to maintain heterochromatin structure after H3K9 methylation loss in mammalian cells.

Epigenetics & Chromatin · May 1, 2025Peer-reviewedMolecular Biology

Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A

Kei Fukuda, Chikako Shimura, Yoichi Shinkai

The paper investigates the effect of Trichostatin A on nuclear compartments in cells lacking H3K9me, H3K27me3, and uH2A, finding minimal impact on compartment structure despite increased H3K27ac levels.

bioRxiv · Apr 26, 2025 · PreprintMolecular Biology

Transcriptional states of retroelement-inserted regions and KRAB zinc finger protein association regulate DNA methylation of retroelements in human male germ cells

Kei Fukuda, Yoshinori Makino, Satoru Kaneko, Chikako Shimura, Yuki Okada, Kenji Ichiyanagi, Yoichi Shinkai

The paper investigates how transcriptional states and KRAB-ZFPs regulate DNA methylation of retroelements in human male germ cells, revealing inter-individual epigenetic variation in sperm.

eLife · Mar 22, 2022Peer-reviewedMolecular Biology

Functional correlation of H3K9me2 and nuclear compartment formation

Kei Fukuda, Chikako Shimura, Hisashi Miura, Akie Tanigawa, Takehiro Suzuki, Naoshi Dohmae, Ichiro Hiratani, Yoichi Shinkai

The paper investigates the role of H3K9me2 in 3D genome organization by analyzing its distribution, transcriptome, and chromatin structure in mouse embryonic stem cells with altered H3K9 methyltransferase activity.

Communications Biology · May 13, 2021Peer-reviewedMolecular Biology