RNA m 6 A modification, signals for degradation or stabilisation?

The RNA modification N6-methyladenosine (m6A) is conserved across eukaryotes, and profoundly influences RNA metabolism, including regulating RNA stability. METTL3 and METTL14, together with several accessory components, form a ‘writer’ complex catalysing m6A modification. Conversely, FTO and ALKBH5 function as demethylases, rendering m6A dynamic. Key to understanding the functional significance of m6A is its ‘reader' proteins, exemplified by YTH-domain-containing proteins (YTHDFs) canonical reader and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) non-canonical reader. These proteins play a crucial role in determining RNA stability: YTHDFs mainly promote mRNA degradation through different cytoplasmic pathways, whereas IGF2BPs function to maintain mRNA stability. Additionally, YTHDC1 functions within the nucleus to degrade or protect certain m6A-containing RNAs, and other non-canonical readers also contribute to RNA stability regulation. Notably, m6A regulates retrotransposon LINE1 RNA stability and/or transcription via multiple mechanisms. However, conflicting observations underscore the complexities underlying m6A's regulation of RNA stability depending upon the RNA sequence/structure context, developmental stage, and/or cellular environment. Understanding the interplay between m6A and other RNA regulatory elements is pivotal in deciphering the multifaceted roles m6A plays in RNA stability regulation and broader cellular biology

A systems biology approach identifies a regulator, BplERF1, of cold tolerance in Betula platyphylla

Cold is an abiotic stress that can greatly affect the growth and survival of plants. Here, we reported that an AP2/ERF family gene, BplERF1, isolated from Betula platyphylla played a contributing role in cold stress tolerance. Overexpression of BplERF1 in B. platyphylla transgenic lines enhanced cold stress tolerance by increasing the scavenging capability and reducing H2O2 and malondialdehyde (MDA) content in transgenic plants. Construction of BplERF-mediated multilayered hierarchical gene regulatory network (ML-hGRN), using Top-down GGM algorithm and the transcriptomic data of BplERF1 overexpression lines, led to the identification of five candidate target genes of BplERF1 which include MPK20, ERF9, WRKY53, WRKY70, and GIA1. All of them were then verified to be the true target genes of BplERF1 by chromatin-immunoprecipitation PCR (ChIP-PCR) assay. Our results indicate that BplERF1 is a positive regulator of cold tolerance and is capable of exerting regulation on the expression of cold signaling and regulatory genes, causing mitigation of reactive oxygen species

The zinc-finger protein OEF-1 stabilizes histone modification patterns and promotes efficient splicing in the Caenorhabditis elegans germline

To ensure stable transmission of genetic information to the next generation, germ cells frequently silence sex chromosomes, as well as autosomal loci that promote inappropriate differentiation programs. In Caenorhabditis elegans, silenced and active genomic domains are established in germ cells by the histone modification complexes MES-2/3/6 and MES-4, which promote silent and active chromatin states, respectively. These states are generally mutually exclusive and modulation of one state influences the pattern of the other. Here, we identify the zinc-finger protein OEF-1 as a novel modifier of this epigenetic balance in the C. elegans germline. Loss of oef-1 genetically enhances mes mutant phenotypes. Moreover, OEF-1 binding correlates with the active modification H3K36me3 and sustains H3K36me3 levels in the absence of MES-4 activity. OEF-1 also promotes efficient mRNA splicing activity, a process that is influenced by H3K36me3 levels. Finally, OEF-1 limits deposition of the silencing modification H3K27me3 on the X chromosome and at repressed autosomal loci. We propose that OEF-1 might act as an intermediary to mediate the downstream effects of H3K36me3 that promote transcript integrity, and indirectly affect gene silencing as a consequence

Studies on the toxicokinetics of intragastricallyadministered paracetamol, aminophenazone, caffeine and chlorphenamine maleate tablets in rats

Purpose: To study the toxicokinetics of paracetamol (PCT), aminophenazone (ACP), caffeine (CFN) and chlorphenamine maleate (CPM) tablets after a single oral gavage, and after oral gavage for 14 consecutive days in rats. Methods: Eighty Sprague Dawley (SD) rats (half male, half female) were randomly divided into 4 groups with 20 rats in each group. Half of the rats were used for the toxicokinetic test after a single oral gavage of PCT, ACP, CFN and CPM tablets, while rats in the other half were used for the toxicokinetic tests after oral gavage for 14 consecutive days. The doses of the four groups were set as 0, 0.5, 1 and 2 tablets/kg body weight, respectively. Blood was taken from the rats and the plasma concentration of paracetamol was determined. Results: There was a significant difference in AUC0-∞ between male and female rats at single oral gavage of 2 tablets/kg of each of the drugs. The exposure amount of PCT (AUC0~t, AUC0-∞ and Cmax) increased with increase in dose, and showed a good linear relationship after a single intragastric administration of each drug, and after 14 consecutive days of intragastric administration at low, medium and high doses. Conclusion: The amount of PCT to which SD rats are exposed after a single intragastric administration of PCT, ACP, CFN and CPM tablets is lower in male than in female rats. However, no significant gender difference in exposure results when these drugs are given intragastrically for 14 consecutive days

An efficient magnetic carbon-based solid acid treatment for corncob saccharification with high selectivity of xylose and enhanced enzymatic digestibility

An effective method for corncob saccharification was investigated over a magnetic carbon-based solid acid (MMCSA) catalyst in the aqueous phase. MMCSA was synthesized through a simple and inexpensive impregnation-carbonization-sulfonation process. Under the optimal reaction conditions (150 °C, 2 h, 0.5 g corncob, 0.5 g catalyst and 50 ml deionized water), 74.9% of xylose yield was directly obtained from corncob, with 91.7% cellulose retention in the residue. After reaction, the MMCSA was easily separated from the residue by an external magnet and reused 4 times showing high stability and catalytic activity. The enzymatic digestibility of the pretreated residue reached 95.2%, with a total sugar yield of 90.4%. The morphologic and structural properties of the natural and treated corncobs were analyzed primarily through 3D X-ray microscopy to characterize the cell wall thickness, porosity, and pore surface area distribution. The increase of macropores (pore surface areas > 200 μm2) was beneficial to the accessibility of cellulose to cellulosic enzymes, so the enzymatic digestibility was enhanced immediately. Compared with other traditional hydrolysis methods, this two-step hydrolysis approach represents an environmentally friendly and sustainable saccharification of lignocellulose to produce xylose and glucose while achieving the same level of reaction efficiency

Cytoplasm affects grain weight and filled-grain ratio in indica rice

<p>Abstract</p> <p>Background</p> <p>Cytoplasmic effects on agronomic traits -involving cytoplasmic and nuclear genomes of either different species or different cultivars - are well documented in wheat but have seldom been demonstrated in rice (<it>Oryza sativa </it>L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three <it>indica </it>cultivars - Guichao 2, Jiangchengkugu, and Dianrui 449 - into the cytoplasms of six <it>indica </it>cultivars - Dijiaowujian, Shenglixian, Zhuzhan, Nantehao, Aizizhan, and Peta. These 18 nuclear substitution lines were evaluated during the winter season of 2005 in Sanya, Hainan, China, and during the summer season of 2006 in Kunming, Yunnan, China. The effects of 6 cytoplasm sources, 3 nucleus sources, 2 locations and their interactions were estimated for plant height, panicle length, panicle number per plant, spikelet number per panicle, grain weight, filled-grain ratio, and yield per plot.</p> <p>Results</p> <p>For five of the seven traits, analysis of variance showed that there were no significant cytoplasmic effects or interactions involving cytoplasmic effects. The effect of cytoplasm on 1000-grain weight was highly significant. Mean 1000-grain weight over the two locations in four of the six cytoplasms clustered close to the overall mean, whereas plants with Nantehao cytoplasm had a high, and those with Peta cytoplasm a low mean grain weight. There was a highly significant three-way interaction affecting filled-grain ratio. At Sanya, cytoplasms varied in very narrow ranges within nuclear backgrounds. Strong cytoplasmic effects were observed only at Kunming and in only two of the three nuclear backgrounds; in the Jianchenkugu nuclear background, there was no evidence of strong cytoplasmic effects at either location. In the Dianrui 449 and Guichao 2 nuclear background evaluated at Kunming, filled-grain ratios of the six cytoplasms showed striking rank shifts</p> <p>Conclusions</p> <p>We detected cytoplasmic variation for two agronomically important traits in <it>indica </it>rice. The cytoplasm source had a significant effect on grain weight across the two experimental locations. There was also a significant cytoplasmic effect on filled-grain ratio, but only in two of three nuclear background and at one of the two locations. The results extend our previous findings with <it>japonica </it>rice, suggesting that the selection of appropriate cytoplasmic germplasm is broadly important in rice breeding, and that cytoplasmic effects on some traits, such as filled-grain ratio, cannot be generalized; effects should be evaluated in the nuclear backgrounds of interest and at multiple locations.</p

A Systematic RNAi Screen Reveals a Novel Role of a Spindle Assembly Checkpoint Protein BuGZ in Synaptic Transmission in C. elegans

Synaptic vesicles (SV) store various neurotransmitters that are released at the synapse. The molecular mechanisms of biogenesis, exocytosis, and endocytosis for SV, however, remain largely elusive. In this study, using Complex Object Parametric Analysis and Sorter (COPAS) to monitor the fluorescence of synapto-pHluorin (SpH), we performed a whole-genome RNAi screen in C. elegans to identify novel genetic modulators in SV cycling. One hundred seventy six genes that up-regulating SpH fluorescence and 96 genes that down-regulating SpH fluorescence were identified after multi-round screen. Among these genes, B0035.1 (bugz-1) encodes ortholog of mammalian C2H2 zinc-finger protein BuGZ/ZNF207, which is a spindle assembly checkpoint protein essential for mitosis in human cells. Combining electrophysiology, imaging and behavioral assays, we reveal that depletion of BuGZ-1 results in defects in locomotion. We further demonstrate that BuGZ-1 promotes SV recycling by regulating the expression levels of endocytosis-related genes such as rab11.1. Therefore, we have identified a bunch of potential genetic modulators in SV cycling, and revealed an unexpected role of BuGZ-1 in regulating synaptic transmission

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. Here, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS), which enables Ψ-to-C transitions, for quantitative profiling of Ψ at single-base resolution. BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS detected all known Ψ sites in human rRNA and spliceosomal small nuclear RNAs and generated the quantitative Ψ map of human small nucleolar RNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine editing sites and N1-methyladenosine. Depletion of pseudouridine synthases TRUB1, PUS7 and PUS1 elucidated their targets and sequence motifs. We further identified a highly abundant Ψ114 site in Epstein–Barr virus-encoded small RNA EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation across virus families