microRNA-mediated control of cell fate specification and patterning in Marchantia polymorpha.

Lch-miR156b-directed repression of LcSPL11 regulates flowering in Liriodendron chinense.

MicroRNAs (miRNAs) are small regulatory RNAs that control gene expression through sequence-specific interactions with target transcripts and play pivotal roles in plant developmental phase transitions. Among them, the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module constitutes a conserved regulatory pathway controlling flowering time in diverse species, yet its molecular function in woody perennials with extended juvenile phases remains poorly understood. Here, seven miR156 family members were identified in Liriodendron chinense by small RNA sequencing, and the Lch-miR156b-LcSPL11 regulatory module was functionally characterized. 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) and dual-luciferase assays demonstrated that Lch-miR156b directly cleaves and represses LcSPL11 transcripts. Expression profiling further associated the Lch-miR156b-LcSPL11 module with flowering-time variation in L. chinense. In heterologous assays, ectopic expression of Lch-miR156b in Arabidopsis thaliana delayed flowering, whereas overexpression of LcSPL11, including a miRNA-resistant variant (rLcSPL11), accelerated floral transition. In addition, LcSOC1 and LcFUL showed expression patterns similar to that of LcSPL11, their promoters contained conserved GTAC cis-elements, and yeast one-hybrid assays confirmed direct binding of LcSPL11 to both promoters. Together, these findings reveal a conserved miRNA-mediated regulatory cascade in which Lch-miR156b modulates flowering through LcSPL11 and its downstream targets LcSOC1 and LcFUL, providing mechanistic insight into flowering control in a woody basal angiosperm.

microRNAs affecting development of body pigmentation in adult Drosophila melanogaster.

Phenotypic development is regulated by multiple mechanisms that ensure tight control of gene expression. Post-transcriptional regulation, including the silencing or degradation of messenger RNAs by microRNAs (miRNAs), is an important component of this process. Here, we use gain-of-function and loss-of-function screens to examine the effects of miRNAs on cuticular pigmentation in adult Drosophila melanogaster. We found that 48 of 166 miRNAs ectopically expressed in a stripe along the dorsal side of developing flies were each sufficient to affect pigmentation. We also found that 22 of 41 miRNAs competitively inhibited in the same tissue visibly altered pigmentation, showing that they were necessary for adult pigmentation development. For each of the 15 miRNAs with opposing effects in the gain- and loss-of-function screens, computational tools identified possible targets among 93 genes previously reported to affect adult pigmentation. Using cell culture, we found that one of these miRNAs (miR-8) was able to regulate gene expression through 3' UTR sequences from at least three pigmentation genes: ebony, bric-a-brac 1, and bric-a-brac 2. All three of these genes reduce development of black pigments, suggesting that miR-8 coordinately regulates expression of multiple genes with similar effects on pigmentation. These data show that miRNAs are developmental regulators of body pigmentation, which could also allow them to contribute to pigmentation divergence, as has been shown for miR-193 in butterflies.

Expanding the repertoire of microRNA target mimicry in plants.

microRNAs (miRNAs) are master regulators of gene expression, guiding ARGONAUTE proteins to bind to and repress target RNAs. Interestingly, a special class of target RNAs, termed target mimics (TMs), can in turn trigger miRNA degradation in plants-a process genetically dependent on the F-box protein HAWAIIAN SKIRT (HWS). However, the pairing rules governing effective TM sites remain unclear. Here, we systematically investigate the pairing architectures that enable plant TM-directed miRNA degradation (pTDMD). Using transient expression in Nicotiana benthamiana leaves and validation in stable Arabidopsis thaliana transgenic lines, we demonstrate that effective TM sites contain a central or near-central unpaired region-classified as insertions (I-type), mismatches (X-type), or deletions (D-type)-flanked by complementary segments. I-type sites tolerate considerable variation in bulge size and position, whereas X- and D-types are more constrained. By incorporating these features into a predictive pipeline, we identified endogenous TMs with alternative pairing architectures, including EARLY NODULIN-LIKE PROTEIN5 (ENODL5), which fine-tunes miR159 levels during Arabidopsis floral development in an HWS-dependent manner. Duplex stability and non-coding context also contribute to TM efficacy. Together, our findings establish a robust empirical framework for understanding, designing, and predicting miRNA TMs in plants.

Spatiotemporal Profiling of the Marchantia Sporophyte Reveals Ancestral Meristem Module and Dynamic Epigenetic Reprogramming during Early Embryogenesis

Functions of the plant NuA4-C in shaping developmental gene expression patterns.

Chromatin remodeling plays a central role in regulating plant development and physiology by shaping the gene expression patterns that drive biological processes. Among epigenetic modifications, histone acetylation is particularly relevant as it alters chromatin structure and influences transcriptional activity. MYST-type histone acetyltransferases (HAT) are evolutionarily conserved components of the Nucleosome Acetyltransferase of histone H4 (NuA4) complex, a key regulator that acetylates histones H4, H2A, and the histone variant H2A.Z. Growing evidence supports the presence of a canonical NuA4-C in plants, similar to that described in yeast. In this review, we summarize recent studies that have begun to uncover its broad role in plant biology, highlighting its involvement in diverse processes such as the skoto- to photomorphogenesis switch, chloroplast development, shade avoidance responses, thermomorphogenesis, the vegetative-to-reproductive transition, plant growth, reproduction and hormonal signalling. In addition, we discuss recent advances in understanding the crosstalk of NuA4-C-mediated H4ac and H2A.Z deposition with other chromatin remodeling complexes in plants. Although significant progress has been made, a full understanding of the complex functions remains unavailable. Current evidence indicates that NuA4-C in yeast and TIP60 in humans are central regulators of transcription, acting not only through histone acetylation but also by influencing transcription elongation and RNA splicing, although direct evidence for similar functions in plant NuA4-C still remains limited. This regulatory role might be critical for integrating developmental programs with environmental signalling pathways. While initial insights into the recruitment of NuA4-C to target genes have emerged, further research is needed to clarify how its activity is controlled and modulated in different biological contexts.

Methylosome and SMN complexes are dispensable for plant viability in Arabidopsis thaliana.

The role of RNA splicing as a modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures has only recently started to emerge. Here, we analyzed the role of temperature in regulating the functionality of factors associated with snRNP biogenesis, a key process underlying pre-mRNA splicing. Taking advantage of mutants showing temperature-dependent phenotypes, we conducted a comprehensive study of the role that the methylosome and SMN complexes have in plant development. Genetic, phylogenetic, and confocal analyses, as well as in vivo and in vitro evidence, reveal remarkable differences in the composition and importance of these complexes between plants and vertebrate animals. The SMN complex in Arabidopsis is apparently reduced to a single protein, GEMIN2, that is not essential for plant development, and the existence of a SMN ortholog is uncertain. Similarly, components of the methylosome previously implicated in snRNP biogenesis are not essential for plant viability. Our results suggest that factors considered central to snRNP biogenesis in animals have less crucial roles in plants and highlight how an evolutionarily conserved molecular process like RNA splicing has nevertheless evolved plant specific characteristics.