ARID1 is required to regulate and reinforce H3K9me2 in sperm cells in Arabidopsis.

Heterochromatin de-condensation in companion gametic cells is conserved in both plants and animals. In plants, microspore undergoes asymmetric pollen mitosis (PMI) to produce a vegetative cell (VC) and a generative cell (GC). Subsequently, the GC undergoes pollen mitosis (PMII) to produce two sperm cells (SC).

A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants.

Lariat RNA is concomitantly produced by excised intron during RNA splicing, which is usually debranched by DBR1, an RNA debranching enzyme. However, increasing evidence showed that some lariat RNA could escape debranching. Little is known about how and why these lariat RNAs could be retained.

Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells.

Background: Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey.

The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis.

Plant reproduction requires the coordinated development of both male and female reproductive organs. Jasmonic acid (JA) plays an essential role in stamen filament elongation. However, the mechanism by which the JA biosynthesis genes are regulated to promote stamen elongation remains unclear.

Identifying microRNAs and Their Editing Sites in .

MicroRNAs (miRNAs) are small non-coding RNAs that are critical in post-transcriptional regulation. is an important nonhuman primate that is often used in basic and translational researches. However, the annotation of miRNAs in is far from complete, and there are no reports of miRNA editing events in , although editing may affect the biogenesis or functions of the miRNAs.

A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants.

Lariats are formed by excised introns, when the 5' splice site joins with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by RNA debranching enzyme 1, recent findings in animals detected many lariat RNAs under physiological conditions. By contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants.

Anaphase-promoting complex/cyclosome regulates RdDM activity by degrading DMS3 in .

During RNA-directed DNA methylation (RdDM), the DDR complex, composed of DRD1, DMS3, and RDM1, is responsible for recruiting DNA polymerase V (Pol V) to silence transposable elements (TEs) in plants. However, how the DDR complex is regulated remains unexplored. Here, we show that the anaphase-promoting complex/cyclosome (APC/C) regulates the assembly of the DDR complex by targeting DMS3 for degradation.

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon.

Background: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide.

Phased secondary small interfering RNAs in Panaxnotoginseng.

Background: Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.

A lariat-derived circular RNA is required for plant development in Arabidopsis.

Lariat RNA is produced during pre-mRNA splicing, and it is traditionally thought as by-products, due to the quick turnover by debranching followed by degradation. However, recent findings identified many lariat RNAs accumulate with a circular form in higher eukaryotes. Although the remarkable accumulation, biological consequence of lariat-derived circular RNAs (here we name laciRNAs) remains largely unknown.

Small RNA profiles from Panax notoginseng roots differing in sizes reveal correlation between miR156 abundances and root biomass levels.

Plant genomes encode several classes of small regulatory RNAs (sRNAs) that play critical roles in both development and stress responses. Panax notoginseng (Burk.) F.

Small RNA profiles in soybean primary root tips under water deficit.

Background: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling.

Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles.

Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required.