Biology subjects

Saitoh, N.

Publications and source records attributed to Saitoh, N..

9 recordsLinked to original sources

bioRxiv2026

Repeat element-anchored enhancer-promoter interactions (REEPIs) shape the regulatory landscape of hormone-resistant breast cancer

Repeat elements (REs) comprise over half of the human genome and are increasingly recognized as regulatory components, yet their role in therapy resistance remains unclear. Here, we integrate CAGE and RADICL-seq to map regulatory elements and RNA-chromatin interactions in estrogen receptor-positive breast cancer cells (MCF7) and their long-term estrogen-deprived (LTED) derivatives. We identify repeat element-anchored enhancer-promoter interactions (REEPIs), defined by the presence of annotated REs at both enhancer and promoter sites. In LTED cells, REEPIs are enriched for ERV1 and ERVL elements and involve specific repeat pairings associated with transcription factor combinations such as SP1-SMAD3 and SP1-NFYC. At the gene level, these REEPIs are preferentially linked to genes involved in chromatin remodeling, DNA repair, and lineage plasticity. Our findings reveal a repeat-guided regulatory architecture associated with transcriptional adaptation in endocrine resistance and identify REEPIs as a previously underexplored component of regulatory reprogramming in hormone-resistant breast cancer.

cancer biology↗

bioRxiv2025

Breast cancer identity is defined by specialized enhancer sets via lysine deacetylation

Breast cancer subtypes are defined by distinct transcriptional programs, yet the epigenetic mechanisms underlying subtype-specific gene regulation remain unclear. Enhancers, key regulators of gene expression and cell identity, are well positioned to define breast cancer subtypes. Here, we identify a previously unrecognized class of enhancers, termed hypoacetylation-defined (HD) enhancers, that regulate cancer-related genes in a luminal breast cancer cell line. HD enhancers are defined by RNA polymerase II dissociation upon lysine deacetylase inhibition, and bidirectional eRNA transcription. They are distinct from super-enhancers, require a specific Mediator subunit for gene-specific transcription, and form extensive chromatin interactions suggestive of a hub-like architecture. Analyses of clinical datasets further identified a subset of HD enhancers, termed HD cluster 1 enhancers, which classify patients into breast cancer subtypes and are associated with expression quantitative trait loci linked to subtype-specific gene expression. This study identifies the lysine deacetylation-regulated cell identity enhancers, which are potential therapeutic targets.

cancer biology↗

bioRxiv2025

Condensin II collaborates with cohesin to establish and maintain interphase chromosome territories

Despite the well-established role of condensin II in mitotic chromosome assembly, its function in interphase chromosome organization remains poorly understood. Here, we applied multiscale fluorescence in situ hybridization (FISH) techniques to human cell lines engineered for single or double depletion of condensin II and cohesin, and examined their functional interplay at two distinct stages of the cell cycle. Our results demonstrate that a functional "handover" from condensin II to cohesin during the mitosis-to-G1 transition is critical for establishing chromosome territories (CTs) in the newly assembling nucleus. During G2 phase, condensin II and cohesin cooperate to maintain global CT morphology, although they act at different genomic scales. Strikingly, double depletion of both complexes causes CTs to collapse and accumulate abnormally at the nucleolar periphery. Based on these findings, we will discuss how the condensin and cohesin complexes act in an orderly and cooperative manner to orchestrate chromatin dynamics across genomic scales, thereby supporting higher-order chromosome organization throughout the cell cycle.

cell biology↗

bioRxiv2023

Mathematical model of nuclear speckle morphology

Nuclear speckles are nuclear bodies consisting of populations of small and irregularly shaped droplet-like molecular condensates that contain various splicing factors. Recent experiments have shown the following morphological features of nuclear speckles: (I) Each molecular condensate contains SON and SRRM2 proteins, and MALAT1 non-coding RNA surrounds these condensates; (II) In the normal interphase of the cell cycle, these condensates are broadly distributed throughout the nucleus in multicellular organisms. In contrast, the fusion of condensates leads to the formation of strongly condensed spherical droplets when cell transcription is suppressed; (III) SON is dispersed spatially in MALAT1 knocked-down cells, whereas MALAT1 is dispersed in SON knocked-down cells by the collapse of nuclear speckles. However, the detailed interactions among molecules that reveal the mechanisms of this rich variety of morphologies remain unknown. In this study, a coarse-grained molecular dynamics model of the nuclear speckle was developed considering the dynamics of SON, SRRM2 or SRSF2, MALAT1, and pre-mRNA as representative components of condensates. The simulations reproduced the abovementioned morphological changes, by which the interaction strength among the representative components of the condensates was predicted.

cell biology↗

bioRxiv2021

Role of the Topoisomerase IIα Chromatin Tether domain in Nucleosome Binding & Chromosome Segregation

Due to the intrinsic nature of DNA replication, replicated genomes retain catenated genomic loci that must be resolved to ensure faithful segregation of sister chromatids in mitosis. Type II DNA Topoisomerase (TopoII) decatenates the catenated genomic DNA through its unique Strand Passage Reaction (SPR). Loss of SPR activity results in anaphase chromosome bridges and formation of Polo-like Kinase Interacting Checkpoint Helicase (PICH)-coated ultra-fine DNA bridges (UFBs) whose timely resolution is required to prevent micronuclei formation. Vertebrates have two TopoII isoforms- TopoII and TopoII{beta}, that share a conserved catalytic core. However, the essential mitotic function of TopoII cannot be compensated by TopoII{beta}, due to differences in their catalytically inert C-terminal domains (CTDs). Using genome-edited human cells, we show that specific binding of TopoII to methylated histone, tri-methylated H3K27 (H3K27me3), via its Chromatin Tether (ChT) domain within the CTD contributes critically to avoid anaphase UFB formation. Reducing H3K27 methylation prior to mitosis increases UFBs, revealing a requirement for proper establishment of H3K27me3 after DNA replication to facilitate TopoII-ChT dependent UFB prevention. We propose that interaction of the TopoII-ChT with H3K27me3 is a key factor that ensures the complete resolution of catenated loci to permit faithful chromosome segregation in human cells. Summary StatementGenomic catenations originating from the DNA replication process must be resolved by DNA Topoisomerase II (TopoII) to permit sister chromatid disjunction. The results show that specific recognition of methylated histone containing chromatin by TopoII is critical for complete resolution of the genome.

cell biology↗

bioRxiv2020

Importin α2 associates with chromatin via a novel DNA binding domain

Nuclear transport of proteins is important for facilitating appropriate nuclear functions. The proteins of the importin family play key roles in nuclear transport as transport receptors for a huge number of nuclear proteins. Additionally, these proteins possess other functions, including chromatin association and gene regulation. However, these non-transport functions of importin are not yet fully understood, especially their molecular-level mechanisms for functioning with chromatin and their consequences. Here, we report the novel molecular characteristics of importin involving binding to diverse sequences in chromatin. We newly identified and characterized a DNA-binding domain--the Nucleic Acid Associating Trolley pole domain (NAAT domain)--in the N-terminal region of importin within the conventional importin {beta} binding (IBB) domain, which was shown to be necessary for nuclear transport of cargo proteins. We propose a stroll and locate model to explain the association of importin with chromatin. This is the first study to delineate the interaction between importin and chromatin DNA via the NAAT domain, indicating the bifunctionality of the importin N-terminal region for nuclear transport and chromatin association.

molecular biology↗

bioRxiv2019

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

Transcriptional bursting is stochastic activation and inactivation of promoters, leading to discontinuous production of mRNA, and is considered to be a contributing factor to cell-to-cell heterogeneity in gene expression. However, it remains elusive how the kinetic properties of transcriptional bursting (e.g., burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing. We found that the kinetics of transcriptional bursting was determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. Furthermore, large-scale CRISPR-Cas9-based screening and functional analysis revealed that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncover key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

systems biology↗

bioRxiv2019

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. We found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the recapitulation of the pre-existing chromatin structure: the genome-wide even distribution of H2A and the exclusion of H2A.Z from the closed chromatin. Intriguingly, an H2A.Z mutant with mutations in the developmentally essential region was incorporated into closed chromatin. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition for maintaining the epigenetic chromatin states.

biochemistry↗

bioRxiv2017

Ki-67 and condensins support the integrity of mitotic chromosomes through distinct mechanisms

Although condensins play essential roles in mitotic chromosome assembly, Ki-67, a protein localizing to the periphery of mitotic chromosomes, had also been shown to make a contribution to the process. To examine their respective roles, we generated a set of HCT116-based cell lines expressing Ki-67 and/or condensin subunits that were fused with an auxin-inducible degron for their conditional degradation. Both the localization and the dynamic behavior of Ki-67 on mitotic chromosomes were not largely affected upon depletion of condensin subunits, and vice versa. When both Ki-67 and SMC2 (a core subunit of condensins) were depleted, ball-like chromosome clusters with no sign of discernible thread-like structures were observed. This severe defective phenotype was distinct from that observed in cells depleted of either Ki-67 or SMC2 alone. Our results show that Ki-67 and condensins, which localize to the external surface and the central axis of mitotic chromosomes, respectively, have independent yet cooperative functions in supporting the structural integrity of mitotic chromosomes.\n\nList of Abbreviations used

cell biology↗