The conserved Pre-mRNA PROCESSING FACTOR 21 regulates the abscisic acid response and seed germination in Arabidopsis.

Seed germination is a critical developmental stage in the lifecycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana Pre-mRNA PROCESSING FACTOR 21 (PRP21) is crucial for regulating the abscisic acid (ABA) response and seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene expression, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation.

The influence of homologous recombination repair on temozolomide chemosensitivity in gliomas.

Gliomas represent a prevalent form of primary brain tumors, with temozolomide (TMZ) serving as the established first-line therapeutic option. Nevertheless, the effectiveness of TMZ is hindered by the development of chemoresistance. Recent investigations have underscored the correlation of homologous recombination repair (HRR), a pivotal mechanism responsible for mending DNA double-strand breaks, with TMZ resistance in glioma treatment.

Naturally inspired chimeric quinolone derivatives to reverse bacterial drug resistance.

Antimicrobial resistance poses an urgent threat to global health, underscoring the critical need for new antibacterial drugs. Ciprofloxacin, a third-generation quinolone antibiotic, is used to treat different types of bacterial infections; however, it often results in the rapid emergence of resistance in clinical settings. Inspired by low susceptibility to antimicrobial resistance of natural antimicrobial peptides, we herein propose a host defense peptide-mimicking strategy for designing chimeric quinolone derivatives which may reduce the likelihood of antibacterial resistance.

The Role of FveAFB5 in Auxin-Mediated Responses and Growth in Strawberries.

Auxin is a crucial hormone that regulates various aspects of plant growth and development. It exerts its effects through multiple signaling pathways, including the TIR1/AFB-based transcriptional regulation in the nucleus. However, the specific role of auxin receptors in determining developmental features in the strawberry () remains unclear.

Dual-Domain Reconstruction Network Incorporating Multi-Level Wavelet Transform and Recurrent Convolution for Sparse View Computed Tomography Imaging.

Sparse view computed tomography (SVCT) aims to reduce the number of X-ray projection views required for reconstructing the cross-sectional image of an object. While SVCT significantly reduces X-ray radiation dose and speeds up scanning, insufficient projection data give rise to issues such as severe streak artifacts and blurring in reconstructed images, thereby impacting the diagnostic accuracy of CT detection. To address this challenge, a dual-domain reconstruction network incorporating multi-level wavelet transform and recurrent convolution is proposed in this paper.

ABLs and TMKs are co-receptors for extracellular auxin.

Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin-binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here, we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner.

Sea-ATI unravels novel vocabularies of plant active cistrome.

The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging.

Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

Microglia play an important role in neuroinflammation and neurodegeneration. Here, we report an approach for generating microglia-containing cerebral organoids derived from human pluripotent stem cells involving the supplementation of growth factors (FGF, EGF, heparin) and 10% CO2 culture conditions. Using this platform, Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex (ALS-PDC) cerebral organoids were generated from patient-derived induced pluripotent stem cells (iPSCs).

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response.

Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat.

Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.

Dimethylated histone H3 Lys9 (H3K9me2) is a conserved heterochromatic mark catalyzed by SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) methyltransferases in plants. However, the mechanism underlying the locus specificity of SUVH enzymes has long been elusive. Here, we show that a conserved N-terminal motif is essential for SUVH6-mediated H3K9me2 deposition in planta.

High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis.

Callus induction, which results in fate transition in plant cells, is considered as the first and key step for plant regeneration. This process can be stimulated in different tissues by a callus-inducing medium (CIM), which contains a high concentration of phytohormone auxin. Although a few key regulators for callus induction have been identified, the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation.

Coupling epigenetics and RNA polyadenylation: missing links.

Precise regulation of gene expression is crucial for plant survival. As a cotranscriptional regulatory mechanism, pre-mRNA polyadenylation is essential for fine-tuning gene expression. Polyadenylation can be alternatively projected at various sites of a transcript, which contributes to transcriptome diversity.

Auxin Coordinates Achene and Receptacle Development During Fruit Initiation in .

In strawberries, fruit set is considered as the transition from the quiescent ovary to a rapidly growing fruit. Auxin, which is produced from the fertilized ovule in the achenes, plays a key role in promoting the enlargement of receptacles. However, detailed regulatory mechanisms for fruit set and the mutual regulation between achenes and receptacles are largely unknown.

Divergence in the Regulation of the Salt Tolerant Response Between and Its Halophytic Relative by mRNA Alternative Polyadenylation.

Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in and its halophytic relative with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both and , possesses fewer APA genes than (47% vs.

Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice.

Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development.

QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering.

The dynamic choice of different polyadenylation sites in a gene is referred to as alternative polyadenylation, which functions in many important biological processes. Large-scale messenger RNA 3' end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations.

QPAT-seq, a rapid and deduplicatable method for quantification of poly(A) site usages.

Alternative polyadenylation (APA) is an essential regulatory mechanism for gene expression. The next generation sequencing provides ample opportunity to precisely delineate APA sites genome-wide. Various methods for profiling transcriptome-wide poly(A) sites were developed.

Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in .

Alternative polyadenylation (APA) is a widespread post-transcriptional modification method that changes the 3' ends of transcripts by altering poly(A) site usage. However, the longitudinal transcriptomic 3' end profile and its mechanism of action are poorly understood. We applied diurnal time-course poly(A) tag sequencing (PAT-seq) for and identified 3284 genes that generated both rhythmic and arrhythmic transcripts.

Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis.

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1-AIPP1-EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin-containing genes. However, the genome-wide functions of AAE are still unknown.

HDA6-dependent histone deacetylation regulates mRNA polyadenylation in .

Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on , HDA6 (one of HDACs) was found to be a critical part of many biological processes.

Discovery of alternative polyadenylation dynamics from single cell types.

Alternative polyadenylation (APA) occurs in the process of mRNA maturation by adding a poly(A) tail at different locations, resulting increased diversity of mRNA isoforms and contributing to the complexity of gene regulatory network. Benefit from the development of high-throughput sequencing technologies, we could now delineate APA profiles of transcriptomes at an unprecedented pace. Especially the single cell RNA sequencing (scRNA-seq) technologies provide us opportunities to interrogate biological details of diverse and rare cell types.

Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation.

A crucial step for mRNA polyadenylation is poly(A) signal recognition by -acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (), the flowering time regulator FY is the homolog of WDR33.

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica.

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica.

Alternative polyadenylation is involved in auxin-based plant growth and development.

Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre-mRNA post-transcriptional regulation is mostly unknown.