Biology subjects

Takizawa, Y.

Publications and source records attributed to Takizawa, Y..

6 recordsLinked to original sources

bioRxiv2026

Loss of NKX2-1 predisposes thyroid to neoplasm development through regulation of oxidative stress

Many factors including ionizing radiation and iodine deficiency are known to increase thyroid carcinogenesis risk. Our dataset analysis of The Cancer Genome Atlas (TCGA) showed that lower mRNA expression of NK2 homeobox 1 (NKX2-1) transcription factor, a master regulator of genesis, homeostasis, and function of thyroid, is linked to poor prognosis of papillary thyroid cancer patients. Here we provide the findings that thyroid-specific Nkx2-1 conditional knockout (Nkx2-1{Delta}T) mice develop thyroid adenoma and carcinoma in higher frequency with combined exposure to radiation and iodine deficiency than control Nkx2-1fl/fl mice. Iodine deficiency caused oxidative stress, which subsequently resulted in DNA damage, leading to transformation of thyroid follicular cells. RNA-seq gene set enrichment analysis indicated higher production of reactive oxygen species (ROS) in the thyroids of Nkx2-1{Delta}T as compared to Nkx2-1fl/fl mice with combined exposure to radiation and iodine deficiency. This was accompanied by a feedback induction of SOD3 (superoxide dismutase 3) and GPX2 (glutathione peroxidase 2). These antioxidants were naturally expressed at higher levels in the thyroids of Nkx2-1{Delta}T than Nkx2-1fl/fl mice without iodine deficiency or radiation. Nkx2-1{Delta}T thyroids exhibited abnormal follicle architecture and up-regulation of Acox2 (encoding acyl-CoA oxidase 2), which produces hydrogen peroxide. These results suggest that loss of NKX2-1 may contribute to excess ROS production, which elevates basal oxidative stress resulting in the promotion of ROS-induced carcinogenesis. We propose a role for NKX2-1 as a regulator of ROS production homeostasis in the thyroid. Its disturbance would dispose thyroid follicular cells more vulnerable to the ROS-producing carcinogens.

cancer biology↗

bioRxiv2026

Structural basis for site-specific histone H3 acetylation-dependent regulation of RNAPII transcription through nucleosomes

Acetylation of histone H3 regulates chromatin dynamics and transcription, but how specific acetylation sites affect RNA polymerase II (RNAPII) transcription through nucleosomes remains unclear. Here, we found that H3 acetylation at Lys56 and Lys122 markedly enhances RNAPII transcription through nucleosomes, whereas acetylation at Lys64 has little effect. To elucidate the structural basis for these functional differences, we determined cryo-electron microscopy (cryo-EM) structures of nucleosomes bearing site-specific acetylation at H3K56, H3K64, or H3K122. The cryo-EM structures revealed that H3K56ac and H3K122ac locally weaken histone-DNA interactions at the DNA entry/exit region and near the dyad, respectively, while H3K64ac induces no detectable structural changes. These structural differences correlate with the observed transcriptional outcomes, indicating that acetylation at H3K56 and H3K122, but not H3K64, alleviates the nucleosomal barrier to RNAPII progression. Our findings provide direct structural evidence that specific acetylations within the histone fold domain of H3 finetune nucleosome dynamics to facilitate RNAPII transcription.

molecular biology↗

bioRxiv2025

Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome

The overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, likely through chromatin remodeling activity, and has been proposed to act as a transient regulatory intermediate during transcription. However, how RNA polymerase II (RNAPII) engages with and transcribes through this unusual structure remains unclear. Here, we reconstituted OLDNs in vitro and performed transcription assays with RNAPII. We found that transcription efficiency was markedly higher when RNAPII initiated from the hexasome side than from the octasome side. Cryo-electron microscopy further revealed that transcription from the hexasome side induced pronounced conformational rearrangements, in which RNAPII progression dramatically opened the hexasome-octasome interface. These results uncover the mechanism by which RNAPII senses the intrinsic transcriptional polarity of OLDNs and suggest that OLDNs function as dynamic, directionally sensitive regulators of transcription elongation.

molecular biology↗

bioRxiv2025

Structural basis of RNA polymerase II transcription on the H3-H4 octasome

The H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each H3-H4 tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNAPII transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL) -4 in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-electron microscopy analysis revealed that two H3-H4 tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal H3-H4 tetramer was disassembled but the distal H3-H4 tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise H3-H4 tetramer disassembly.

molecular biology↗

bioRxiv2023

Molecular and structural basis of the heterochromatin-specific chromatin remodeling activity by Arabidopsis DDM1

The chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) deposits the histone H2A variant H2A.W and silences transposons in Arabidopsis thaliana. However, the molecular mechanisms by which DDM1 specifically targets the nucleosome containing H2A.W and allows chromatin writers to access heterochromatin remained elusive. Here, we show that DDM1 promotes remodeling of the H2A.W nucleosome and requires interactions with the H2A.W-specific C-terminal tail. The cryo-EM structure of the DDM1-H2A.W nucleosome complex revealed that DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA. Comparison with the cryo-EM structure of the nucleosome containing H2A.W suggested that DDM1 increases the DNA end flexibility of nucleosomes. Based on these biochemical and structural results, we propose that the chromatin remodeling activity of DDM1 with the heterochromatin-specific H2A.W contributes to the maintenance of repressive epigenetic marks in heterochromatin by providing DNA methyltransferases with access to nucleosomal DNA.

molecular biology↗

bioRxiv2021

Cryo-electron microscopy structure of the H3-H4 octasome without histones H2A and H2B

The canonical nucleosome, which represents the predominant packaging unit in eukaryotic chromatin, has an octameric core made up of two histone H2A-H2B and H3-H4 dimers with ~147 base-pair (bp) DNA wrapping around it. Non-nucleosome particles with alterative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Here we solved the structure of the H3-H4 octasome, which is a nucleosome-like particle with a core made up of four H3-H4 dimers. Two conformations, open and closed, are determined at 3.9 [A] and 3.6 [A] resolutions by cryo-electron microscopy, respectively. The H3-H4 octasome, made up of a di-tetrameric core, is wrapped by ~120 bp DNA in 1.5 negative superhelical turns. The symmetrical halves are connected by a unique H4-H4 interface along the dyad axis. In vivo crosslinking of cysteine probes placed at another unique H3-H3 interface demonstrated the existence of the H3-H4 octasome in cells.

biochemistry↗