Takayo Sasaki

This study shows that microhomology-mediated end joining (MMEJ) repairs single-ended DSBs at replication forks, working with BIR and being regulated by ATR and Pol{theta}.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper identifies subERCEs as master transcription factor binding sites that drive early replication timing and transcription in mESCs, functioning as both enhancers and structural chromatin organizers.

This study identifies RIF1's role in restoring H3K9me3 post-replication by facilitating SUV39H1, HP1, and PP1 recruitment and restraining Aurora kinase activity.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

The paper manipulates transcription to show it can advance replication timing but is not required for the switch to early replication.

The paper uses TSA-seq to map genomic regions near nucleoli and pericentric heterochromatin in human cell lines, revealing variable heterochromatin localization and complex nuclear organization.

The paper investigates how strand-asymmetric processes like replication and transcription influence DNA damage, repair, and mutagenesis, revealing mechanisms that shape cancer genome evolution.

This study shows that Brd2 depletion does not alter genome replication timing or A/B compartmentalization in mouse embryonic stem cells.

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

This study shows that replication timing (RT) is essential for maintaining the global epigenetic state and genome compartmentalization in human cells, with RIF1 playing a central role in this process.

The paper introduces SPIN, a method to identify genome-wide nuclear spatial localization patterns by integrating nuclear compartment mapping and chromatin interaction data.

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

The paper defines the temporal choreography of DNA replication in mammalian cells using High Resolution Repli-Seq, revealing conserved replication timing patterns and cell-type-specific correlations with chromatin features.

The paper identifies a fragility signature linked to replication stress and transcription in chromosomal instability by analyzing replication timing and gene expression.

The paper compares DNA replication timing profiles of BCP-ALL leukemic samples with normal B-lineage differentiation stages to identify clinically relevant features.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

This paper introduces a probabilistic model to compare multi-species functional genomic data, showing it can identify genomic regions with distinct evolutionary patterns of DNA replication timing across primates.

This paper introduces a protocol and computational tools for genome-wide replication timing analysis using next-generation sequencing.