Liu, Y. j. | bioRxiv Science

bioRxiv2025

Transposon targeting non-coding RNA transcription targets G/C-rich tracts and is facilitated by an intrinsically disordered protein in Tetrahymena

Tetrahymena is a well-established ciliate model organism, known for its nuclear dualism and unique mechanism for transposon defense, wherein transposons are kept within the highly heterochromatinized micronucleus (MIC), which is transcriptionally inert except during meiosis. The discovery of preferential transcription in the meiotic MIC at regions enriched with transposons, and the identification of MIC transcription regulatory proteins, emphasizes the necessity to elucidate the underlying mechanisms driving this process. In this study, we demonstrate that G/C-rich tracts are overrepresented in meiotic non-coding RNA (ncRNA) transcription regions and that RNA polymerase II (Pol II) is highly enriched at and around these tracts. Further analysis revealed that Pol IIs association with G/C-rich tracts is not abolished in cells lacking Rib1, a Mediator complex-associated protein essential for MIC ncRNA biogenesis. Nevertheless, in the absence of Rib1, Pol II showed abnormal association with the meiotic MIC chromatin, suggesting that Rib1 is critical for maintaining Pol IIs binding specificity. Through Rib1 truncation analysis, we found that the intrinsically disordered region, which contains putative phase-separating peptides, is crucial for its function. Disruption of phase-separation, either by deleting these peptides or by treating cells with a phase-separation disruption reagent, leads to aberrant localization of both Rib1 and Pol II on the MIC chromatin, implicating that Rib1 likely facilitates the MIC ncRNA transcription via phase-separation.

molecular biology↗

bioRxiv2025

A pair of readers of histone H3K4 methylation recruit Polycomb repressive complex 2 to regulate photoperiodic flowering

In flowering plants, the transition from vegetative growth to reproduction or flowering, is often timed by seasonal changes in day length (photoperiod). In the model flowering plant Arabidopsis thaliana, the photoperiodic cue increasing day length or long day, through the photoperiod pathway, induces a daily rhythmic activation of the florigen gene FLOWERING LOCUS T (FT) to promote flowering. Under inductive long days (LDs), FT expression is activated around dusk, but to be repressed overnight and into the early afternoon the next day. The mechanism underlying the daily oscillation of FT repression to ensure long-day induction of flowering remains unclear. Here, we report that AtING1 and AtING2, Arabidopsis homologs of the mammalian Inhibitor of Growth (ING) proteins, read di- and tri-methylated histone 3 lysine 4 (H3K4me2/me3) on FT chromatin and further recruit Polycomb-repressive complex 2 (PRC2) to repress FT expression at night and into the early afternoon the next day, following FT activation at dusk in LDs. This prevents precocious flowering under inductive LDs. Our study reveals that a previously-undescribed chromatin-regulatory module: H3K4me2/me3-ING1/2-PRC2, which timely represses FT expression following the daily rhythmic FT activation at dusk by the long-day pathway, to prevent excessive FT expression and thus precisely control the timing of the transition to flowering in response to inductive photoperiodic signals.

plant biology↗