Biology subjects

Tanigawa, M.

Publications and source records attributed to Tanigawa, M..

3 recordsLinked to original sources

bioRxiv2026

Compartment-dependent selection regimes maintain the G-quadruplex paradox across the eukaryotic kingdoms

G-quadruplex (G4) DNA structures are depleted from coding sequences (CDS) and enriched in regulatory regions across diverse genomes (the "G4 paradox"), but the selection regime maintaining this architecture across eukaryotes remains unclear. Analysing 198 reference genomes balanced across the four kingdoms (Animalia 86, Fungi 49, Plantae 33, Protozoa 30), we pro-pose a two-regime architecture in which the dominant selective force depends on the genomic compartment. In CDS, codon-adaptation selection takes priority: naive Nei-Gojobori comparison shows 5-16% synonymous-rate (dS) suppression at G4 codons in six of seven unsaturated species pairs, but the signal is absorbed by per-gene codon-adaptation-index (CAI) adjustment (0/7 pairs retain a G4 odds ratio below 1; five reverse to OR > 1). In introns and promoters, where no codons exist, selection acts directly on G4 structure: phylogenetic generalised least-squares (PGLS) yields five Benjamini-Hochberg-significant kingdom-specific helicase associations (q < 0.10), all at intronic or promoter G4s, including context-dependent FANCJ/BRIP1 ({beta} = +1.60, q = 0.057 for intron G4 in Plantae; {beta} = -2.49, q = 0.004 for promoter G4 in Proto-zoa); three of five remain significant on an independent Open Tree of Life backbone. Intronic G4 are concentrated in deeply conserved orthologue groups ([≥] 87% in every kingdom), consistent with maintenance of regulatory G4 host-gene context since early eukaryotic evolution. Interim-correction notice (bioRxiv v3, 2026-08-03)This preprint version corrects a set of documentation-level errors identified in a coauthor audit of the analysis pipeline (available as AUDIT_REPORT.md in the Zenodo deposit). Several central analytical claims of this manuscript -- the definition of the log2 IRR (density-vs. fraction-ratio), the downstream use of consensus-stable versus candidate G4 motifs, the CAI-controlled dS adjustment model, the filter chain in the stable-G4 classifier, and the reconciliation of PGLS output across main, alternative-tree, robustness, and Supplementary Information files -- are currently under clean-environment re-verification. The outcome of that re-verification may change specific numerical values, the direction of some regional sign summaries, and the framing of downstream conclusions in a subsequent version. Readers should treat the present version as an interim documentation correction, not as a fully verified revision. Users planning to build on the deposited results should consult CORRECTION_NOTES.md and AUDIT_REPORT.md in the Zenodo deposit for the current list of open methodology-level issues.

genomics↗

bioRxiv2025

Sugar-mediated control of ATG101 modulates carbon deficiency-induced autophagy in Arabidopsis

Autophagy is a major eukaryotic degradation and recycling pathway, which eliminates damaged cellular components and provides energy and building blocks especially under adverse environmental conditions. While the core autophagy machinery has been extensively studied, autophagy initiation and regulation remain less understood. In this study, we show that genes encoding the core autophagy initiation complex, ATG1, ATG11, ATG13, and ATG101, are transcriptionally regulated by sugars. To analyze the expression of these genes, we took advantage of Arabidopsis thaliana accessions, which display strong variations in their responses to darkness-induced fixed carbon deprivation. One of the components of the initiation complex, ATG101, has multiple sugar-related elements, and was repressed by sugar. Moreover, ATG101 was induced stronger upon starvation in carbon starvation-resistant accessions when compared to carbon starvation-sensitive accessions. We identified three single nucleotide polymorphisms in the genomic region of ATG101 which are associated with the carbon-starvation phenotype. Further analyses through complementation of the atg101 mutant with different variants of ATG101 demonstrated that the single nucleotide polymorphism alleles contribute differently to ATG101 expression regulation, response to sugar, and phenotype recovery. Taken together, our data suggest that modulation of ATG101 by sugar is part of a multi-layered mechanism regulating the sensitivity to carbon starvation in Arabidopsis.

plant biology↗

bioRxiv2017

Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers

Non-membrane bound, hydrogel-like entities, such as RNA granules, nucleate essential cellular functions through their unique physico-chemical properties. However, these intracellular hydrogels have not been as extensively studied as their extracellular counterparts, primarily due to technical challenges in probing these materials in situ. Here, by taking advantage of a chemically inducible dimerization paradigm, we developed iPOLYMER, a strategy for rapid induction of protein-based hydrogels inside living cells. A series of biochemical and biophysical characterizations, in conjunction with computational modeling, revealed that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that behaves as a size-dependent molecular sieve. We studied several properties of the gel and functionalized it with RNA binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. Therefore, we here demonstrate that iPOLYMER presents a unique and powerful approach to synthetically reconstitute hydrogel-like structures including RNA granules in intact cells.

synthetic biology↗