How introns enhance gene expression

A naturally occurring SNP modulates thermotolerance divergence among grapevines

With the increasing challenges posed by global warming and climate change, heat stress has become a significant threat to the sustainable production of grapevines. However, the genetic basis of grapevine thermotolerance remains poorly understood. Here, we combine genome-wide association study with transcriptomic profiling to identify TTC4 (thermotolerance on chromosome 4), a gene encoding a WRKY transcription factor, as a key determinant of thermotolerance in grapevine. TTC4 directly activates two thermotolerance-related genes, HSP18.1 and APX3. We also identify a heat-suppressed repressor SPL13 (SQUAMOSA-promoter binding protein-like 13) that cannot bind to the GTAT element (TTC4T(7631)) in intron 2 of TTC4, but can bind to the natural variant, GTAC (TTC4C(7631)). Grapevine accessions with TTC4C/C(7631) genotype exhibit significantly lower thermotolerance compared to those with the TTC4T/T(7631) and TTC4C/T(7631) genotypes. This fine-tuned regulation contributes to thermotolerance divergence among grapevine populations. The TTC4T(7631) haplotype holds significant potential as a genetic resource for breeding thermotolerant grapevine varieties.

Design of a GFP reporter for splicing analysis in mammalian cells

Eukaryotic genes are formed by exons and introns. Pre-mRNA splicing promotes exon ligation and intron removal and is performed by a specialized macromolecular machinery named spliceosome, composed of five small ribonucleoprotein particles (snRNPs) and more than one hundred proteins. The activity of this complex is highly accurate due to the coordinated activity of its components. Altered splicing has been related to the development of several diseases, including neurodegenerative disorders, such as amyotrophic lateral sclerosis, and different types of cancer. Detailed understanding of splicing regulation in eukaryotic cells can be achieved using splicing reporter systems. We designed a reporter plasmid suitable for splicing analysis in cultured mammalian cells. Our reporter is based on GFP expression, and the splicing outcome can be easily visualized by fluorescence microscopy. We quantified splicing activity in two human cell lines, HEK-293T and MDA-MB-231, confirming its suitability for use in live cells in culture.

Genome-wide screening reveals repression by nuclear exosome as a prerequisite for intron-mediated enhancement in Saccharomyces cerevisiae

Introns can enhance gene expression, a phenomenon called intron-mediated enhancement (IME). Previously proposed IME mechanisms do not sufficiently explain the variability in enhancement levels, suggesting that IME mechanism has not been fully understood. A comprehensive screening of genes involved in IME can provide valuable insights. Recently, using a luciferase coding sequence (yCLuc), we showed that IME functions by relieving repression rather than simply enhancing expression. The expression of yCLuc is repressed by the specific nucleotide sequence UCUU, and adding an intron relieves this repression in the yeast Saccharomyces cerevisiae. Herein, genome-wide screenings were conducted using S. cerevisiae knockout strain libraries to identify genes involved in IME. For screening, yCLuc was expressed with and without an intron in knockout strains. Consequently, CDC73, a regulator of RNA polymerase II (RNAPII), was identified as essential for enhancement. Additionally, 23 genes specifically involved in the repression were identified. These 23 genes are related to nuclear exosomes, RNA modification, RNAPII regulation, the nuclear pore complex, ribosomes, and chromatin modification. Among these, genes associated with nuclear exosomes, which degrade various RNAs in the nucleus, showed the largest impact on expression. The RNA sequence UCUU has been reported as a target for RNA degradation by nuclear exosomes. These findings suggested that UCUU-containing coding sequences are primarily repressed via RNA degradation by the nuclear exosome through UCUU recognition, with this repression being relieved by the presence of an intron.

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

Emerging evidence indicates that splicing factors mediate the close link between transcription and splicing. However, the mechanisms underlying this coupling remain unclear. U1 small nuclear ribonucleoprotein particle (U1 snRNP) not only initiates splicing but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcriptional elongation. Here, we show that U1 snRNP regulates alternative promoter activity in human cells by inhibiting premature polyadenylation. In genes carrying premature polyadenylation sites between two promoters, U1 snRNP inhibition with antisense oligonucleotides leads to a significant decrease in downstream promoter activity. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility, decreased RNA polymerase II serine 5 phosphorylation, and increased promoter-proximal pause at downstream promoters. Our findings support a model in which U1 snRNP favors productive elongation from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape.

Genome-wide analysis of the KCS gene family in Medicago truncatula and their expression profile under various abiotic stress

Very long-chain fatty acids (VLCFAs) are indispensable constituents of cuticular wax and exert pivotal functions in regulating plant growth, development and response to stress. β-Ketoacyl-CoA synthase (KCS) represents the rate-limiting enzyme for the biosynthesis of VLCFAs. In this study, 25 KCS genes were identified in the M. truncatula genome and were unevenly distributed across seven of the eight chromosomes. The 25 MtKCS genes were clustered into seven groups, each exhibiting conserved gene structure and motif distribution. MtKCS gene promoters contained multiple hormone signaling and stress-responsive elements, indicating that the expression of these genes may be modulated by a range of developmental and environmental stimuli. The expression profiles revealed that the MtKCS genes exhibit diverse expression patterns across various organs/tissues and are differentially expressed under abiotic stress. It is noteworthy that several genes, such as MtKCS2, 10, and 13, exhibited significantly increased expression in leaves under cold, heat, salt, and drought stress. This suggests that MtKCS genes may play an integral role in the abiotic stress resistance of M. truncatula. These findings establish a foundation for understanding the evolution of KCS genes in higher plants and facilitated further functional exploration of MtKCS genes.

Genome-Wide Identification and Characterization of Basic Pentacysteine Transcription Factors in Brassica napus

BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC), a plant-specific transcription factor family, is a group of GAGA_motif binding factors controlling multiple developmental processes of growth and response to abiotic stresses. BPCs recruit histone remodeling factors for transcriptional repression of downstream targets. However, the information about BnaBPCs from Brassica napus remains unclear. Here, we identified 25 BnaBPC genes that were mainly localized in the nucleus, randomly localized on 16 chromosomes, and grouped into three subfamilies based on phylogenetic analysis. Twenty-five BnaBPC genes exhibit syntenic relationships with AtBPC genes, and the polypeptides encoded by BnaBPC genes within the same subfamily share similar conserved motifs and protein domains. The expansion of BnaBPC genes underwent whole-genome duplication events and purifying selection in genomes, and all the BnaBPC genes had the same conserved GAGA binding domains. Additionally, the promoter of each BnaBPC gene consisted of various cis-elements associated with stresses, phytohormones, and growth and development. Notably, the seed-specific regulatory element was found only in the BnaC04.BPC4 promoter. Further expression pattern analysis showed that BnaBPC members are widely expressed in stems, buds, developing seeds and siliques. These findings provide insights into BnaBPC genes and enrich our understanding of their functional characterization in B. napus.

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes

In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.

Investigating the influence of the SIRT6 gene and alternative splicing on canine longevity: an in-depth bioinformatics analysis and experimental confirmation via NGS-based targeted sequencing

Sirtuin 6 (SIRT6) has many functions, but its most notable contribution lies in the intricate regulation of cell senescence and lifespan. The effect of the SIRT6 gene on body size and longevity in dogs has not been extensively studied, particularly with regard to alternative splicing mechanisms. To address this gap, the present study used a comprehensive approach that integrated bioinformatics analysis, DNA sequence analysis, and next-generation sequencing-based targeted sequencing analyses. Our results show that, according to the reference genomes of different dog breeds, the canine SIRT6 gene exhibits different variants according to the dog breed. Except for the exonic variant g.55,146,051C > T (rs851065050) detected in the Boxer breed, all variants obtained from other genomes were determined to be intronic variants. The g.56,075,604 G > T (rs3343377774) intronic variant previously detected in the Labrador Retriever breed was only detected in the small breed group in our study. As a result of in silico analysis, the g.56,075,604 G > T variant has an exonic splicing enhancer (ESE) site; this variant has created the motif of the binding site for the splicing factor ESE_SRp55. The g.55.146,051C > T variant was associated with a change in the ratio of exonic splicing silencer/ESE binding motifs. This change indicates an increased probability of exon skipping for the mutant allele. Thus, as with the intronic variant g.56,075,604 G > T, the mis-splicing induced by the exonic variant g.55,146,051C > T could potentially be associated with an altered distribution of regulatory splicing factors of the canine SIRT6 gene.

Genetics and clinical implications of SPINK1 in the pancreatitis continuum and pancreatic cancer

Serine peptidase inhibitor, Kazal type 1 (SPINK1), a 56-amino-acid protein in its mature form, was among the first pancreatic enzymes to be extensively characterized biochemically and functionally. Synthesized primarily in pancreatic acinar cells and traditionally known as pancreatic secretory trypsin inhibitor, SPINK1 protects the pancreas by inhibiting prematurely activated trypsin. Since 2000, interest in SPINK1 has resurged following the discovery of genetic variants linked to chronic pancreatitis (CP). This review provides a historical overview of SPINK1's discovery, function, and gene structure before examining key genetic findings. We highlight three variants with well-characterized pathogenic mechanisms: c.-4141G > T, a causative enhancer variant linked to the extensively studied p.Asn34Ser (c.101A > G), which disrupts a PTF1L-binding site within an evolutionarily conserved HNF1A-PTF1L cis-regulatory module; c.194 + 2T > C, a canonical 5' splice site GT > GC variant that retains 10% of wild-type transcript production; and an Alu insertion in the 3'-untranslated region, which causes complete loss of function by forming extended double-stranded RNA structures with pre-existing Alu elements in deep intronic regions. We emphasize the integration of a full-length gene splicing assay (FLGSA) with SpliceAI's predictive capabilities, establishing SPINK1 the first disease gene for which the splicing impact of all possible coding variants was prospectively determined. Findings from both mouse models and genetic association studies support the sentinel acute pancreatitis event (SAPE) model, which explains the progression from acute pancreatitis to CP. Additionally, SPINK1 variants may contribute to an increased risk of pancreatic ductal adenocarcinoma (PDAC). Finally, we discuss the therapeutic potential of SPINK1, particularly through adeno-associated virus type 8 (AAV8)-mediated overexpression of SPINK1 as a strategy for treating and preventing pancreatitis, and highlight key areas for future research.

Developmental air pollution exposure augments airway hyperreactivity, alters transcriptome, and DNA methylation in female adult progeny

Maternal exposure to particulate air pollution increases the incidence and severity of asthma in offspring, yet the mechanisms for this are unclear. Known susceptibility loci are a minor component of this effect. We interrogate a mouse allergic airway disease model to assess epigenetic associations between maternal air pollution exposure and asthma responses in offspring. Maternal air pollution exposure increased allergic airway disease severity in adult offspring associated with a suppressed transcriptomic response. Control progeny showed differential expression of 2842 genes across several important pathways, whilst air pollutant progeny showed an 80% reduction in differentially expressed genes and abrogation of many pathway associations. Whole genome CpG methylome analysis following allergen challenge detected differential methylation regions across the genome. Differentially methylated regions were markedly reduced in air pollutant offspring, and this was most evident in intronic regions and some transposable element classes. This study shows that asthma in adult offspring of PM2.5 exposed mothers had a markedly repressed transcriptomic response, a proportion of which was associated with identifiable changes in the lung's methylome. The results point to an epigenetic contribution to the severity of asthma in offspring of mothers exposed to particulate air pollution.

A novel MoClo-mediated intron insertion system facilitates enhanced transgene expression in Chlamydomonas reinhardtii

The Chlamydomonas Modular Cloning (MoClo) toolkit allows for straightforward and flexible construction of genetic modules for gene expression in the microalgal model species, fostering developments in algal biotechnology. Efficiently expressing transgenes from the nuclear genome of C. reinhardtii requires the proper insertion of introns throughout the respective gene, as it can substantially enhance the gene expression. To facilitate synthetic biology approaches in this microalga, we developed a novel strategy for intron insertion into synthetic DNA fragments. Our method aligns with current MoClo standards, and its feasibility is demonstrated by assembling genes of various lengths and successfully expressing them in C. reinhardtii. Examples include enhanced NanoLuc expression with increased intron numbers, a fungal luciferase enabling bioluminescence in C. reinhardtii, and a fungal tryptophan decarboxylase.

Fat-1 Ameliorates Metabolic Dysfunction-Associated Fatty Liver Disease and Atherosclerosis through Promoting the Nuclear Localization of PPARα in Hamsters

Fat-1, an enzyme encoded by the fat-1 gene, is responsible for the conversion of endogenous omega-6 polyunsaturated fatty acids into omega-3 polyunsaturated fatty acids in Caenorhabditis elegans. To better investigate whether the expression of Fat-1 will exert a beneficial function in dyslipidemia and metabolic dysfunction-associated fatty liver disease (MAFLD), we established an adeno-associated virus 9 expressing Fat-1. We found that adeno-associated-virus-mediated expression of Fat-1 markedly reduced the levels of plasma triglycerides and total cholesterol but increased high-density lipoprotein levels in male wild-type hamsters on both chow diet and high-fat diet as well as in chow-diet-fed male LDLR-/- hamsters. Fat-1 ameliorated diet-induced MAFLD in wild-type hamsters by enhancing fatty acid oxidation through the hepatic peroxisome proliferator-activated receptor α (PPARα)-dependent pathway. Mechanistically, Fat-1 increased the levels of multiple lipid derivatives as ligands for PPARα and simultaneously facilitated the nuclear localization of PPARα. Our results provide new insights into the multiple therapeutic potentials of Fat-1 to treat dyslipidemia, MAFLD, and atherosclerosis.

Genome-wide identification and characterization of FORMIN gene family in cotton (Gossypium hirsutum L.) and their expression profiles in response to multiple abiotic stress treatments

FORMIN proteins distinguished by FH2 domain, are conserved throughout evolution and widely distributed in eukaryotic organisms. These proteins interact with various signaling molecules and cytoskeletal proteins, playing crucial roles in both biotic and abiotic stress responses. However, the functions of FORMINs in cotton (Gossypium hirsutum L.) remain uncovered. In this study, 46 FORMIN genes in G. hirsutum (referred to as GhFH) were systematically identified. The gene structures, conserved domains, and motifs of these GhFH genes were thoroughly explored. Phylogenetic and structural analysis classified these 46 GhFH genes into five distinct groups. In silico subcellular localization, prediction suggested that GhFH genes are distributed across various cellular compartments, including the nucleus, extracellular space, cytoplasm, mitochondria, cytoskeleton, plasma membrane, endoplasmic reticulum, and chloroplasts. Evolutionary and functional diversification analyses, based on on-synonymous (Ka) and synonymous (Ks) ratios and gene duplication events, indicated that GhFH genes have evolved under purifying selection. The analysis of cis-acting elements suggested that GhFH genes may be involved in plant growth, hormone regulation, light response, and stress response. Results from transcriptional factors TFs and gene ontology analysis indicate that FORMIN proteins regulate cell wall structure and cytoskeleton dynamics by reacting to hormone signals associated with environmental stress. Additionally, 45 putative ghr-miRNAs were identified from 32 families targeting 33 GhFH genes. Expression analysis revealed that GhFH1, GhFH10, GhFH20, GhFH24, and GhFH30 exhibited the highest levels of expression under red, blue, and white light conditions. Further, GhFH9, GhFH20, and GhFH30 displayed higher expression levels under heat stress, while GhFH20 and GhFH30 showed increased expression under salt stress compared to controls. The result suggests that GhFH20 and GhFH30 genes could play significant roles in the development of G. hirsutum under heat and salt stresses. Overall these findings enhance our understanding of the biological functions of the cotton FORMIN family, offering prospects for developing stress-resistant cotton varieties through manipulation of GhFH gene expression.

STAT4 gene polymorphism may be associated with microscopic polyangiitis susceptibility in a Chinese Guangxi population: A case-control analysis based on propensity score matching

BACKGROUND

Microscopic polyangiitis (MPA) is a severe multisystem autoimmune disease featured by small-vessel vasculitis with few or no immune complex, also has a significant genetic predisposition. Growing evidence has confirmed that STAT4 gene is tightly associated with multiple autoimmune diseases, but its contribution to MPA onset is still elusive.

OBJECTIVE

The aim was to investigated the association between STAT4 gene polymorphisms (rs7572482, rs7574865 and rs12991409) and MPA susceptibility in a Guangxi population of China.

METHODS

260 MPA patients and 295 healthy adult volunteers were selected, 1:1 propensity score matching (PSM) was performed to control potential confounding variables, then 199 MPA patients and 199 healthy adult volunteers matched in gender, ethnicity and age were included in this study. High-throughput sequencing and multiplex PCR were applied to detect the target STAT4 SNPs. SHEsis and SNPstats were used to evaluated the allele frequency, genotype frequency, linkage disequilibrium (LD), haplotype, and the association between SNPs and the MPA susceptibility in multiple genetic models. SNP-SNP interactions were explored based on generalized multifactor dimensionality reduction (GMDR) algorithm. Some clinical indicators, such as renal pathology and therapeutic effects, were collected and compared.

RESULTS

The allele and genotype frequencies of rs7574865 displayed significant diversities between case group and control group (p < 0.05). Strong LD was found between rs7572482 and rs12991409 (D'=0.9). The haplotype GGT was related to a reduced risk of MPA (OR = 0.661, 95 %CI: 0.469-0.931, p = 0.017), and haplotype GTT might perform an increased risk of MPA (OR = 1.922, 95 %CI: 1.225-3.015, p = 0.004). Rs7574865 polymorphism was associated with an increased risk of MPA in codominant model (OR:2.03; p = 0.0093), dominant model (OR: 1.88p = 0.0023), and overdominant model (OR:1.57; p = 0.027). In Han and male subgroups, rs7574865 polymorphism dramatically increased the MPA risk. GMDR suggested that STAT4 rs7574865 and PTPN22 rs3811021 composed the most risk combinations (p = 0.0010). Moreover, renal pathology, Birmingham vasculitis activity score (BVAS), and alanine aminotransferase (ALT) might be linked with STAT4 gene polymorphisms (p < 0.05).

CONCLUSIONS

The genetic polymorphism of STAT4 may be associated with MPA susceptibility and renal pathological classification in Chinese Guangxi population; the T allele of rs7574865 may be an important risk factor for MPA.

Identification of cis-sQTL demonstrates genetic associations and functional implications of inflammatory processes in Nelore cattle muscle tissue

This study aimed to identify splicing quantitative trait loci (cis-sQTL) in Nelore cattle muscle tissue and explore the involvement of spliced genes (sGenes) in immune system-related biological processes. Genotypic data from 80 intact male Nelore cattle were obtained using SNP-Chip technology, while RNA-Seq analysis was performed to measure gene expression levels, enabling the integration of genomic and transcriptomic datasets. The normalized expression levels of spliced transcripts were associated with single nucleotide polymorphisms (SNPs) through an analysis of variance using an additive linear model with the MatrixEQTL package. A permutation analysis then assessed the significance of the best SNPs for each spliced transcript. Functional enrichment analysis was performed on the sGenes to investigate their roles in the immune system. In total, 3,187 variants were linked to 3,202 spliced transcripts, with 83 sGenes involved in immune system processes. Of these, 31 sGenes were enriched for five transcription factors. Most cis-sQTL effects were found in intronic regions, with 27 sQTL variants associated with disease susceptibility and resistance in cattle. Key sGenes identified, such as GSDMA, NLRP6, CASP6, GZMA, CASP4, CASP1, TREM2, NLRP1, and NAIP, were related to inflammasome formation and pyroptosis. Additionally, genes like PIDD1, OPTN, NFKBIB, STAT1, TNIP3, and TREM2 were involved in regulating the NF-kB pathway. These findings lay the groundwork for breeding disease-resistant cattle and enhance our understanding of genetic mechanisms in immune responses.

Decoupling the pleiotropic effects of VRT-A2 during reproductive development enhances wheat grain length and weight

VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT-A2) is a subspecies-forming gene that confers the long-glume and large-grain traits of tetraploid Polish wheat (Triticum polonicum; AABB) and hexaploid Xinjiang rice wheat (T. petropavlovskyi; AABBDD). Transcriptional activation of VRT-A2 due to a natural sequence variation in its Intron-1 region significantly enhances grain weight but also causes some basal spikelets to fail to completely develop, thus decreasing grain number per spike and yield. This yield penalty has presented a challenge for the use of VRT-A2 in breeding high-yield wheat. Here, we report the characterization of 2 regulatory modules that fine-tune VRT-A2 expression in bread wheat (T. aestivum): (i) the APETALA2/Ethylene Responsive Factor (AP2/ERF)-type transcription factor MULTI-FLORET SPIKELET1 (TaMFS1) represses VRT-A2 expression by recruiting a transcriptional corepressor and a histone deacetylase and (ii) the STRUCTURE-SPECIFIC RECOGNITION PROTEIN 1 (TaSSRP1) facilitates VRT-A2 activation by assembling Mediator and further RNA polymerase II. Deleting TaMFS1 triggered moderate upregulation of VRT-A2 results in significantly increased grain weight without the yield penalty. Our study thus provides a feasible strategy for overcoming the tradeoffs of pleotropic genes by editing their upstream transcriptional regulators.

Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns

Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon known as intron-mediated enhancement (IME). IME has been noted across diverse genes and organisms but remains mysterious in many respects. For example, how does intron sequence affect the magnitude of IME? In this study, we performed a massively parallel reporter assay (MPRA) to assess the effect of varying intron sequence on gene expression in a high-throughput manner, in human cells, using tens of thousands of synthetic introns with natural splice sites and randomized internal sequence. We observe that most random introns splice efficiently and enhance gene expression as well as or better than fully natural introns. Nearly all introns stimulate gene expression ∼eight-fold above an intronless control, at both mRNA and protein levels, suggesting that the primary mechanism acts to increase mRNA levels. IME strength is positively associated with splicing efficiency and with the intronic content of poly-uridine stretches, which we confirm using reporter experiments. In sum, this work assesses the IME of a diverse library of introns and uncovers sequence-dependent aspects, but suggests that enhancement of gene expression is a general property of splicing, largely independent of intron sequence.

Interactions Between BMP2/BMP4 Gene Polymorphisms and Fluoride Exposure on Essential Hypertension: A Cross-Sectional Study in China

(1) Objective: To evaluate the relationship between fluoride exposure, interactions of BMP2/BMP4 gene polymorphisms, and fluoride exposure on essential hypertension. (2) Methods: A cross-sectional study was conducted among 725 participants in a high-fluoride region of Shanxi Province, China. Urinary fluoride concentrations were measured as indicators of fluoride exposure. Hypertension was diagnosed based on standard guidelines. BMP2 (rs1005464) and BMP4 (rs17563) polymorphisms were genotyped. Logistic regression and interaction models were performed to evaluate associations and interactions between fluoride exposure, gene polymorphisms, and hypertension. (3) Results: Higher urinary fluoride concentrations were significantly associated with an increased risk of hypertension, exhibiting a dose-dependent relationship. The rs1005464 (G > A) polymorphism of BMP2 was identified as a protective factor against hypertension in individuals with the AG + AA genotype. Significant interactions were observed between the BMP2 rs1005464 and BMP4 rs17563 polymorphisms, influencing hypertension risk. Additionally, both multiplicative and additive interactions between high fluoride exposure and the BMP4 rs17563 polymorphism were identified, highlighting the combined impact of environmental and genetic factors on hypertension. (4) Conclusions: Fluoride exposure is positively associated with hypertension. BMP2 gene polymorphisms affect the risk of hypertension, and BMP4 gene polymorphisms may modify the impact of fluoride on hypertension.

Identification and functional analysis of Wall-Associated Kinase genes in Nicotiana tabacum

Introduction

Wall-associated kinases (WAKs) are pivotal in linking plant cell walls to intracellular signaling networks, thereby playing essential roles in plant growth, development, and stress responses.

Methods

The bioinformatics analysis was employed to identify WAK genes in tobacco. The expression levels of NtWAK genes were assessed by qRT-PCR. The subcellular localization of WAK proteins was observed in tobacco cells and Arabidopsis protoplasts. Kinase activity of the WAK proteins was evaluated through in vitro assays.

Results

We conducted a comprehensive genome-wide identification and analysis of the WAK gene family in tobacco (Nicotiana tabacum). A total of 44 WAK genes were identified in the tobacco genome, which were further classified into three distinct groups. Phylogenetic analysis comparing tobacco WAKs (NtWAKs) with Arabidopsis WAKs (AtWAKs) revealed species-specific expansion of these genes. The WAK proteins within each group displayed similar gene structures and conserved motif distributions. Promoter region analysis indicated that cis-elements of NtWAK genes are primarily involved in regulating plant growth and development, phytohormone signaling, and stress responses. Expression profiling under NaCl, PEG, and ABA treatments suggested that certain NtWAK genes may play key roles in modulating responses to abiotic stress. Three-dimensional structural predictions and subcellular localization analysis showed that NtWAK proteins from the three subgroups exhibit high cytoplasmic similarity and are primarily located to the plasma membrane. Kinase activity assay confirmed that they possess phosphorylation activity.

Discussion

This study represents the first genome-wide analysis of the WAK gene family in N. tabacum, laying the groundwork for future functional investigations.

Unveiling the camelina MBOAT gene family: Phylogenetic insights and regulatory landscape

The membrane-bound O-acyltransferase (MBOAT) gene family comprises enzymes responsible for transferring acyl groups to various lipid molecules. Some members of the MBOAT gene family and their functions have been extensively studied in the model plant Arabidopsis. However, research on the MBOAT gene family in camelina is still limited. In this study, 54 MBOATs were identified on 17 chromosomes and one unidentified scaffold in camelina, including seven newly identified genes. A total of 149 MBOATs were identified in 10 other species. Six subgroups of these MBOATs with different conservation were classified by phylogenetic analysis, showing diversification between monocots and dicots. Detailed analysis of the motif composition, evolutionary relationships, and gene structures of CsaMBOATs are presented. The results of the syntenic analysis suggest that the evolution of CsaMBOAT gene family is primarily driven by segmental and tandem duplications, and that there is a stronger collinearity within dicots. In addition, analysis of CsaMBOAT gene promoter cis-elements reveals a possible transcriptional regulation and tissue-specific expression, highlighting potential role in plant stress responses and hormone signaling. Furthermore, both the transcriptome and RT-qPCR data revealed the changes in the expression levels of DGAT1 during salt stress treatment. Subsequent analyses indicated that DGAT1 influenced the ratio of fatty acid fractions in the plants. Importantly, a large number of transcription factors involved in the regulation of CsaMBOAT gene expression were identified by WGCNA analysis, and the transcriptional data confirmed that the NAC032 and CAMMTA6 genes play a role upstream of DGAT1. This study not only identified the members of the MBOAT in camelina, but also provided insights and clues into its regulatory mechanisms.

Optimization of the intron sequences combined with the CMV promoter increases recombinant protein expression in CHO cells

To meet the requirements of the biopharmaceutical industry, improving the yield of recombination therapeutic protein (RTP) from Chinese hamster ovary (CHO) cells is necessary. The human cytomegalovirus (CMV) promoter is widely used for RTP expression in CHO cells. To further improve RTP production, we truncated the human CMV intron and further evaluated the effect of four synthetic introns, including ctEF-1α first, EF-1α first, chimeric, and β-globin introns combined with the CMV promoter on recombinant expression levels in transient and stably recombinant CHO cells. The results showed that the truncated, EF-1α first, chimeric, and β-globin introns can significantly improve stable transgene expression in CHO cells. The qPCR results indicated that the mRNA level of transgene increased through optimizing intron sequences combined with the CMV promoter. Transcriptomics analysis was performed and found that differential expression of genes involved in mRNA processing, RNA export from nucleus, cytoplasmic translation, transcriptional activation and cell cycle regulation. In conclusion, optimization of the intron sequences combined with the CMV promoter can achieve a higher yield of recombinant proteins in CHO cells. This will be valuable for generating CHO cell lines with high productivity for industrial applications.

Detection of Insertion/Deletions (InDel) Within Five Clock Genes and Their Associations with Growth Traits in Four Chinese Sheep Breeds

Organisms have the capacity to detect day-night fluctuations through oscillators regulated by circadian clock genes, which are crucial for regulating various biological processes. Numerous studies have demonstrated a marked association between these genes and various growth traits of sheep. This study identified polymorphisms at 23 potential loci within five clock genes in four Chinese sheep breeds. Only two polymorphic insertion/deletions (InDels) were detected in CLOCK and PER3 genes, respectively. The distribution of these two loci in four Chinese sheep breeds and their association with growth traits were further explored. A 12 bp deletion was found in the intron of the CLOCK gene (rs604230640), which was significantly associated with body height (p < 0.05), body oblique length (p < 0.05) and cannon girth (p < 0.05) in Hu sheep (HS). A 22 bp insertion in the intron of the PER3 gene (rs600537720) with a dominant genotype of insertion/insertion (II) was found to have a significant association with chest depth (p < 0.05) in Small-Tail Han sheep (STHS), tail width (p < 0.05) in Tong Sheep (TS), and in Lanzhou fat-tailed sheep (LFTS). In conclusion, this study has elucidated the polymorphisms of CLOCK and PER3 genes and has examined the influence of these two genes on the growth traits of sheep. Concurrently, the two molecular markers identified in CLOCK and PER3 could potentially serve in the marker-assisted selection of growing-related traits in local Chinese sheep breeds.

Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon

Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.

IMPORTANCE

This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.

A DAT1 gene and APOE ε4 interaction is associated with apathy and structural brain changes in mild cognitive impairment and Alzheimer's disease

BACKGROUND

Apathy in patients with Alzheimer's disease (AD) is associated with significant morbidity and is often one of the first neuropsychiatric symptoms to present in mild cognitive impairment (MCI). Apathy is associated with accelerated cognitive decline and atrophy in fronto-striatal regions of the brain. Previous work has shown a link between apathy and the APOE gene in the context of AD, as the APOE ε4 allele is already known to be associated with the onset of AD. However, other genetic associations with apathy are largely unexplored.

OBJECTIVE

To examine whether interactions between genetic variants related to neurotransmitter systems and regional brain atrophy are associated with apathy in patients with MCI and AD.

METHODS

In a sample of individuals with AD (n = 266), MCI (n = 518), and cognitively normal controls (n = 378), a partial least squares correspondence analysis modeled interactions between single nucleotide polymorphisms, structural whole-brain imaging variables, and apathy.

RESULTS

An interaction was found between apathy, the possession of an APOE ε4 allele combined with minor homozygosity for the DAT1 (dopamine transporter 1) gene, and regional brain atrophy. This interaction was closely linked to the MCI and AD groups.

CONCLUSIONS

The results point to an association of a dopaminergic genetic marker and apathy in the AD continuum and may inform future design of clinical trials of apathy, as well as new treatment targets.

The Impact of Obesity on Autophagy in Human Adipose-Derived Mesenchymal Stromal Cells

Mesenchymal stromal cells (MSCs) possess therapeutic properties, which can be blunted by obesity. Autophagy, a cellular recycling process, is essential for MSC function. We investigated the mechanisms by which obesity affects the properties of MSCs, with a focus on autophagy. Adipose tissue was obtained from kidney donors [body mass index (BMI) <30 kg/m2, non-obese] or individuals undergoing weight loss surgery (BMI ≥30 kg/m2, obese) for MSC harvesting (n = 11 each); samples were randomized to sequencing (seq; n = 5 each) or functional studies (n = 6 each). MSCs were sequenced to determine their epigenetic (5-hydroxymethylcytosine) and transcriptomic profiles across autophagy-related genes using hydroxymethylated DNA immunoprecipitation sequencing and mRNA-seq, respectively. Genes with shared trends in both datasets underwent Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) validation. During functional studies, 2-h starvation was used to induce autophagy in vitro, enabling detection of changes in the protein expression of microtubule-associated protein 1A/1B-light chain-3 and in autophagic flux. Obesity amplified a starvation-induced reduction in autophagic flux in MSCs while promoting earlier generation of new autophagosomes during autophagy initiation. Integrated analysis of the two sequencing datasets revealed 124 differentially hydroxymethylated genes and 30 differentially expressed mRNAs. Among six overlapping autophagy-related genes, three exhibited same-direction trends. Of these, STX12 and SLC25A4 may be implicated in the impact of obesity on autophagic changes in MSCs. Therefore, human obesity may alter autophagy in adipose tissue-derived MSC, and thereby their metabolism and function.

Comparative analysis of the JRL gene family in the whole-genome of five gramineous plants

The Jacalin-related lectins (JRLs) gene family play a crucial role in regulating plant development and responding to environmental stress. However, a systematic bioinformatics analysis of the JRL gene family in Gramineae plants has been lacking. In this study, we identified 101 JRL proteins from five Gramineae species and classified them into eight distinct clades. Most of the AtJRL proteins clustered in the same group and were differentiated from the Gramineae JRL proteins. The analysis of protein motifs, gene structures and protein domain revealed that the JRL genes play diverse functions in Gramineae plants. Duplication events indicated that tandem duplication significantly contributed to the expansion of the JRL family, with most JRL members underwent purifying selection. Tissue expression profile analysis showed that most OsJRL genes were highly expressed in the roots, while ZmJRL genes exhibited high expression in inflorescences. Furthermore, the expression level of OsJRL and ZmJRL genes were influenced by drought, cold, heat and salt stresses, respectively, implying that these genes play important roles in response to various abiotic stresses. RT-qPCR results demonstrated that OsJRL4 was up-regulated under PEG6000 and NaCl stresses, while OsJRL12 and OsJRL26 were down-regulated under PEG6000. These findings provide comprehensive insights into the JRL gene family in Gramineae plants and will facilitate further functional characterization of JRLs.

Construction of Promoter Elements for Strong, Moderate, and Weak Gene Expression in Drosophila melanogaster

BACKGROUND/OBJECTIVES

Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, as many regulatory proteins need to be expressed in small quantities, and excessive expression can have harmful effects on cells and organisms. Therefore, it is important to select the right promoter when creating transgenic organisms for research and practical applications.

METHODS

In this study, we used the Drosophila melanogaster genome as a source of natural promoter sequences for RNA polymerase II. These sequences were extracted and used to create a set of promoters that are suitable for practical application. The promoters were tested in a model system using fluorescent reporter genes in S2 cells and transgenic lines of Drosophila.

RESULTS

We assessed the expression levels of fluorescent reporter genes to rank the tested promoters from strongest to weakest. Six individual promoters of different sizes were established and compared. Additionally, we designed and tested three pairs of bidirectional promoters that could be used to simultaneously express two proteins.

CONCLUSIONS

Based on our findings, we grouped the tested promoters into three categories: strong, moderate, and weak. These promoters can be utilized in transgenic model systems for protein production at different levels, from high to low. Bidirectional promoters, constructed "head-to-head", meaning oppositely directed with the minimum distance between them, represent a novel tool for the co-expression of proteins.

The Identification of AMT Family Genes and Their Expression, Function, and Regulation in Chenopodium quinoa

Quinoa (Chenopodium quinoa) is an Andean allotetraploid pseudocereal crop with higher protein content and balanced amino acid composition in the seeds. Ammonium (NH4+), a direct source of organic nitrogen assimilation, mainly transported by specific transmembrane ammonium transporters (AMTs), plays important roles in the development, yield, and quality of crops. Many AMTs and their functions have been identified in major crops; however, no systematic analyses of AMTs and their regulatory networks, which is important to increase the yield and protein accumulation in the seeds of quinoa, have been performed to date. In this study, the CqAMTs were identified, followed by the quantification of the gene expression, while the regulatory networks were predicted based on weighted gene co-expression network analysis (WGCNA), with the putative transcriptional factors (TFs) having binding sites on the promoters of CqAMTs, nitrate transporters (CqNRTs), and glutamine-synthases (CqGSs), as well as the putative TF expression being correlated with the phenotypes and activities of GSs, glutamate synthase (GOGAT), nitrite reductase (NiR), and nitrate reductase (NR) of quinoa roots. The results showed a total of 12 members of the CqAMT family with varying expressions in different organs and in the same organs at different developmental stages. Complementation expression analyses in the triple mep1/2/3 mutant of yeast showed that except for CqAMT2.2b, 11/12 CqAMTs restored the uptake of NH4+ in the host yeast. CqAMT1.2a was found to mainly locate on the cell membrane, while TFs (e.g., CqNLPs, CqG2Ls, B3 TFs, CqbHLHs, CqZFs, CqMYBs, CqNF-YA/YB/YC, CqNACs, and CqWRKY) were predicted to be predominantly involved in the regulation, transportation, and assimilation of nitrogen. These results provide the functions of CqAMTs and their possible regulatory networks, which will lead to improved nitrogen use efficiency (NUE) in quinoa as well as other major crops.

Comprehensive method for producing high-affinity mouse monoclonal antibodies of various isotypes against (4-hydroxy-3-nitrophenyl)acetyl (NP) hapten

Monoclonal antibody (mAb) technology has significantly contributed to basic research and clinical settings for various purposes, including protective and therapeutic drugs. However, a rapid and convenient method to generate high-affinity antigen-specific mAbs has not yet been reported. Here, we developed a rapid, easy, and low-cost protocol for antigen-specific mAb production from single memory B cells. Using this method, high-affinity IgG1 mAbs specific to the hapten 4-hydroxy-3-nitrophenylacetyl (NP) were established from NP-CGG immunized C57BL/6 mice within 6 days. Our mAb production system allows flexible switching of IgG1 to any other isotype with the same paratope, enabling the absolute quantification of antigen-specific serum antibody titers and affinity maturation. Additionally, we established a protocol for the production of IgM and IgA, retaining their functional pentamer and dimer structures. This method is also effective against human antigens and pathogens, making it a powerful tool for mAb development in both research and clinical settings.

Rapid Detection of PML::RARA Fusions in Acute Promyelocytic Leukemia: CRISPR/Cas9 Nanopore Sequencing with Adaptive Sampling

Acute promyelocytic leukemia (APL) accounts for approximately 10-15% of newly diagnosed acute myeloid leukemia cases and presents with coagulopathy and bleeding. Prompt diagnosis and treatment are required to minimize early mortality in APL as initiation of all-trans retinoic acid therapy rapidly reverses coagulopathy. The PML::RARA fusion is a hallmark of APL and its rapid identification is essential for rapid initiation of specific treatment to prevent early deaths from coagulopathy and bleeding and optimize patient outcomes. Given limitations and long turnaround time of current gene fusion diagnostic strategies, we have developed a novel amplification-free nanopore sequencing-based approach with low cost, easy setup, and fast turnaround time. We termed the approach CRISPR/Cas9-enriched nanopore sequencing with adaptive sampling (CENAS). Using CENAS, we successfully sequenced breakpoints of typical and atypical PML::RARA fusions in APL patients. Compared with the standard-of-care genetic diagnostic tests, CENAS achieved good concordance in detecting PML::RARA fusions in this study. CENAS allowed for the identification of sequence information of fusion breakpoints involved in typical and atypical PML::RARA fusions and identified additional genes (ANKFN1 and JOSD1) and genomic regions (13q14.13) involving the atypical fusions. To the best of our knowledge, involvements of the ANKFN1 gene, the JOSD1 gene, and the 13q14.13 genomic region flanking with the SIAH3 and ZC3H13 genes have not been reported in the atypical PML::RARA fusions. CENAS has great potential to develop as a point-of-care test enabling immediate, low-cost bedside diagnosis of APL patients with a PML::RARA fusion. Given the early death rate in APL patients still reaches 15%, and ~10% of APL patients are resistant to initial therapy or prone to relapse, further sequencing studies of typical and atypical PML::RARA fusion might shed light on the pathophysiology of the disease and its responsiveness to treatment. Understanding the involvement of additional genes and positional effects related to the PML and RARA genes could shed light on their role in APL and may aid in the development of novel targeted therapies.

Whole-Genome Sequence Analysis of Flammulina filiformis and Functional Validation of Gad, a Key Gene for γ-Aminobutyric Acid Synthesis

Flammulina filiformis is one of the widely produced edible fungi worldwide. It is rich in γ-aminobutyric acid (GABA), a non-protein amino acid with important physiological functions in humans. To investigate the functions of key genes in the GABA metabolic pathway of F. filiformis, we isolated the monokaryon Fv-HL23-1 from the factory-cultivated F. filiformis strain Fv-HL23 and then sequenced and assembled the genome using the PacBio Sequel and Illumina NovaSeq sequencing platforms. The results showed that the genome comprised 140 scaffolds with a total length of 40.96 Mb, a GC content of 49.62%, an N50 of 917,125 bp, and 14,256 protein-coding genes. Phylogenetic analysis based on the whole genome revealed a close evolutionary relationship of Fv-HL23-1 with Armillaria mellea, Lentinula edodes, and Schizophyllum commune. A total of 589 carbohydrate-active enzymes were identified in the genome of Fv-HL23-1, suggesting its strong lignocellulose degradation ability, and 108 CYP450 gene family members were identified, suggesting important functions such as resistance to stress, secondary metabolite synthesis, and growth and development. The F. filiformis proteins glutamate decarboxylase 1 (Ff-GAD1) and glutamate decarboxylase 2 (Ff-GAD2), which may be responsible for GABA synthesis, were identified by protein alignment. Molecular docking analysis showed that Ff-GAD2 may have better catalytic activity than Ff-GAD1. To verify the function of Ff-gad2, its heterologous expression in the mycelia of the mononuclear Hypsizigus marmoreus was analyzed. Compared with wild type, the GABA content of mycelia was increased by 85.40-283.90%, the growth rate was increased by 9.39 ± 2.35%, and the fresh weight was increased by 18.44 ± 7.57%. Ff-GAD2 may play a catalytic role in GABA synthesis. In addition, the expression of the full-length Ff-gad2 gene was increased by 7.96 ± 1.39 times compared with the exon expression level in H. marmoreus mycelia, suggesting that the intron may contribute to the heterologous expression of Ff-GAD2. Based on whole-genome sequencing, we analyzed the enzyme system related to the important life activities of F. filiformis, focusing on the function of Ff-GAD, a key enzyme in the GABA synthesis pathway. The results lay a foundation for elucidating the GABA metabolism pathway of edible fungi and developing targeted breeding strategies for GABA-producing edible fungi.

Establishment of an efficient Agrobacterium tumefaciens-mediated transformation system for an Armillaria species, a host of the fully mycoheterotrophic plant Gastrodia elata

The genus Armillaria (Basidiomycota, Agaricales, Physalacriaceae) comprises pathogenic fungi that cause root-rot disease in plants, as well as species with low pathogenicity, some of which are hosts of the fully mycoheterotrophic orchid plant Gastrodia elata (Orchidaceae). To investigate the mechanisms underlying such special interactions between Armillaria fungi and G. elata, it is crucial to establish genetic transformation platforms for the Armillaria fungi and G. elata. In this study, an Armillaria strain Arm37 was isolated from G. elata, which can form symbiosis with G. elata in axenic culture under laboratory conditions. A vector pYT-EV containing a cassette for hygromycin-resistance selection and a cassette for expressing or silencing target genes was constructed. An Agrobacterium tumefaciens-mediated transformation (ATMT) system for Arm37 was successfully developed and optimized to achieve a transformation efficiency of 32%. The ATMT system was successfully used to express the reporter genes eGFP encoding enhanced green fluorescent protein and GUS encoding β-glucuronidase and to effectively silence the endogenous gene URA3 encoding orotidine-5'-phosphate decarboxylase in Arm37. This ATMT system established for Arm37 provides an efficient genetic tool for exploring the Arm37 genes that are involved in the unique interaction between the Armillaria fungi and fully mycoheterotrophic plant G. elata.

The light-harvesting chlorophyll a/b-binding proteins of photosystem II family members are responsible for temperature sensitivity and leaf color phenotype in albino tea plant

INTRODUCTION

Light-harvesting chlorophyll a/b-binding (LHCB) protein complexes of photosystem II are integral to the formation of thylakoid structure and the photosynthetic process. They play an important role in photoprotection, a crucial process in leaf development under low-temperature stress. Nonetheless, potential key genes directly related to low-temperature response and albino phenotype have not been precisely identified in tea plant. Moreover, there are no studies simultaneously investigating multiple albino tea cultivars with different temperature sensitivity.

OBJECTIVES

The study aimed to clarify the basic characteristics of CsLHCB gene family members, and identify critical CsLHCB genes potentially influential in leaf color phenotypic variation and low-temperature stress response by contrasting green and albino tea cultivars. Concurrently, exploring the differential expression of the CsLHCB gene family across diverse temperature-sensitive albino tea cultivars.

METHODS

We identified 20 putative CsLHCB genes according to phylogenetic analysis. Evolutionary relationships, gene duplication, chromosomal localization, and structures were analyzed by TBtools; the physiological and biochemical characteristics were analyzed by protein analysis websites; the differences in coding sequences and protein accumulation in green and albino tea cultivars, gene expression with maturity were tested by molecular biology technology; and protein interaction was analyzed in the STRING database.

RESULTS

All genes were categorized into seven groups, mapping onto 7 chromosomes, including three tandem and one segmental duplications. They all own a conserved chlorophyll A/B binding protein domain. The expression of CsLHCB genes was tissue-specific, predominantly in leaves. CsLHCB5 may play a key role in the process of leaf maturation and senescence. In contrast to CsLHCB5, CsLHCB1.1, CsLHCB2, and CsLHCB3.2 were highly conserved in amino acid sequence between green and albino tea cultivars. In albino tea cultivars, unlike in green cultivars, the expression of CsLHCB1.1, CsLHCB1.2, and CsLHCB2 was down-regulated under low-temperature stress. The accumulation of CsLHCB1 and CsLHCB5 proteins was lower in albino tea cultivars. Greater accumulation of CsLHCB2 protein was detected in RX1 and RX2 compared to other albino cultivars.

CONCLUSIONS

CsLHCB1.1, CsLHCB1.2, and CsLHCB2 played a role in the response to low-temperature stress. The amino acid sequence site mutation of CsLHCB5 would distinguish the green and albino tea cultivars. The less accumulation of CsLHCB1 and CsLHCB5 had a Chl influence on albino leaves. Albino cultivars more sensitive to temperature exhibited lower CsLHCB gene expression. CsLHCB2 may serve as an indicator of temperature sensitivity differences in albino tea cultivars. This study could provide a reference for further studies of the functions of the CsLHCB family and contribute to research on the mechanism of the albino in tea plant.

The Intra-Articular Delivery of a Low-Dose Adeno-Associated Virus-IL-1 Receptor Antagonist Vector Alleviates the Progress of Arthritis in an Osteoarthritis Rat Model

Background/Objectives: Interleukin-1 (IL-1) is a pivotal mediator in the pathological progression of osteoarthritis (OA), playing a central role in disease progression. However, the rapid clearance of IL-1 receptor antagonist (IL-1Ra) from the joints may hinder the efficacy of intra-articular IL-1Ra injections in reducing OA-associated pain or cartilage degradation. Methods: Sustaining sufficient levels of IL-1Ra within the joints via adeno-associated virus (AAV)-mediated gene therapy presents a promising therapeutic strategy for OA. In this study, we constructed an IL-1Ra expression cassette employing intron insertion in the coding sequence (CDS) region to enhance protein expression levels. Furthermore, we incorporated precisely targeted liver-specific microRNA (miRNA) sequences to specifically downregulate transgene expression within hepatic tissues, thereby ensuring more targeted and controlled regulation of gene expression. Results: A rat model of OA was employed to compare the efficacy of AAV5 and AAV9 for IL-1Ra delivery at both high and low doses. It was observed that low-dose, but not high-dose, AAV9-IL-1Ra resulted in a significant reduction in joint swelling, accompanied by a decrease in the diameter of the affected area and the preservation of biomarkers associated with trabecular bone integrity. Conclusions: These results highlight the great potential of AAV9-IL-1Ra in osteoarthritis therapy, with the promise of achieving long-term improvement through a single intra-articular injection.

Variations in HBA gene contribute to high-altitude hypoxia adaptation via affected O2 transfer in Tibetan sheep

Tibetan sheep are indigenous to the Qinghai-Xizang Plateau. Owing to the harsh hypoxic environment in this plateau, the hemoglobin (Hb) protein in Tibetan sheep has undergone adaptive changes over time. Hb is primarily responsible for transporting O2 and CO2 between the lungs and other tissues of the body. The α subunit of Hb, encoded by the HBA gene, is a crucial component of the protein. However, whether variations in the HBA gene sequence affect the adaptation of Tibetan sheep to high-altitude hypoxia remains unclear. In this study, we sequenced the HBA gene and identified three single nucleotide polymorphisms (SNPs). These SNPs were genotyped in Tibetan and Hu sheep using Kompetitive Allele-Specific PCR (KASP). The results showed that the frequencies of the AT genotype and H1H2 haplotype were higher in Tibetan sheep than in Hu sheep. Individuals with the AT genotype exhibited higher P50 levels, whereas those with the H1H2 haplotype exhibited lower PO2 and SaO2 levels. The higher P50 levels indicated that O2 was more readily released from oxygenated Hb into the tissues, with the lower PO2 and SaO2 levels facilitating this process. These findings indicate that variations in the HBA gene sequence contribute to enhancing O2 transfer efficiency in Tibetan sheep.

The FSCN1 gene rs2966447 variant is associated with increased serum fascin-1 levels and breast cancer susceptibility

Fascin-1 (FSCN1) is recognized as an actin-binding protein, commonly exhibits up-regulation in breast cancer (BC) and is crucial for tumor invasion and metastasis. The existence of FSCN1 gene polymorphisms may raise the potential for developing BC, and there are still no studies focusing on the relationship between the FSCN1 rs2966447 variant and BC risk in Egyptian females. Thus, we investigated the serum fascin-1 levels in BC patients and the association between the FSCN1 rs2966447 variant with its serum levels and BC susceptibility. Genotyping was conducted in 153 treatment-naïve BC females with different stages and 144 apparent healthy females by TaqMan® allelic discrimination assay, whereas serum fascin-1 level quantification was employed by ELISA. The FSCN1 rs2966447 variant demonstrated a significant association with BC susceptibility under all utilized genetic models, cancer stages and estrogen receptor negativity. Also, BC females with AT and TT genotypes had higher serum fascin-1 levels and tumor size than those with the AA genotype. Moreover, serum fascin-1 levels were significantly elevated in the BC females, notably in those with advanced-stages. Furthermore, serum fascin-1 levels were markedly positively correlated with number of positive lymph nodes as well as tumor size. Collectively, these findings revealed that the FSCN1 rs2966447 variant may be regarded as a strong candidate for BC susceptibility. Also, this intronic variant is associated with increased serum fascin-1 levels and tumor size.

High temperature-induced Cscaspase-8 disrupts the developmental relationship between Chilo suppressalis and its endoparasitoid

Host hemolymph is an important place of growth and development for most endoparasitoids. Immunofluorescence assay showed that parasitism induced Chilo suppressalis larvae to produce large numbers of granulocytes, but high temperatures led to granulocytes apoptosis and loss of phagocytosis. In addition, high temperatures activated the endoplasmic reticulum apoptotic pathway, leading to apoptosis of prohemocytes. In the present study, the initiator Cscaspase-8 was obtained from the rice pest C. suppressalis. The results of real-time PCR showed that Cscaspase-8 expression was highest in hemocytes; furthermore, transcription was most highly in female adults. Cscaspase-8 was significantly induced when larvae were exposed to 39 °C for a 2-h period. Cscaspase-8 expression was significantly elevated after 2 d of parasitism. Results of the interference test showed that the survival rate of C. suppressalis larvae is not affected by Cscaspase-8 gene silencing under high temperature and parasitism stress. However, developmental delays were observed in Cotesia chilonis larvae when the host Cscaspase-8 gene was knocked down. These results contribute to the current knowledge on the regulatory mechanisms of apoptosis in insects subjected to high temperature and parasitism stress.

Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs

Background

Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain poorly understood in Chinese and Western pigs. By comparing the chromatin accessibility profiles of skeletal muscle, liver, and fat between these two pig populations, we aimed to identify key regulatory elements that could explain phenotypic differences observed between the two groups.

Results

Our results revealed that the genome-wide chromatin accessibility profiles were largely similar at a qualitative level within tissues. However, we also identified local regions that exhibited quantitative differences, most of which occurred in liver tissue. Interestingly, we found that most of the increased chromatin accessibility in the livers of Chinese pigs was associated with tissue-specific openness. Furthermore, we observed a positive correlation between the ATAC-seq signal at the transcript start site (TSS) and the expression levels of nearby genes. Motif enrichment analysis revealed NR2F1 as a key regulator in Chinese pigs. Differentially expressed genes (DEGs) in Chinese pigs showed enrichment for NR2F1 response targets. One of the genes regulated by NR2F1 in Chinese pigs, NPC1, harbored a high alternative allelic frequency in the intron region.

Conclusion

Overall, our study provides valuable insights into the regulatory dynamics underlying phenotypic variation in pigs. By elucidating the role of CREs in driving phenotypic variation, we can better understand the genetic basis of complex traits and potentially identify targets for genetic improvement in livestock breeding programs.

Genome-wide identification and expression analysis of CASPL gene family in Zea mays (L.)

Casparian strip membrane domain proteins like (CASPL), exhibit profound associations with root development, stress responsiveness and mineral element uptake in plants. Nonetheless, a comprehensive bioinformatics analysis of the ZmCASPL gene family in maize remains unreported. In the study, we have identified 47 ZmCASPL members at the whole-genome level, systematically classifying them into six distinct groups. Furthermore, our analysis revealed that the same group of ZmCASPL contains similar gene structures and conserved motifs. Duplication events showed whole genome duplication (WGD) and tandem duplication (TD) contribute to the generation of the ZmCASPL gene family together in maize, but the former plays a more prominent role. Furthermore, we observed that most ZmCASPL genes contain MYB-binding sites (CAACCA), which are associated with the Casparian strip. Utilizing RNA-seq data, we found that ZmCASPL21 and ZmCASPL47 are specifically highly expressed only in the roots. This finding implies that ZmCASPL21 and ZmCASPL47 may be involved in the Casparian strip development. Additionally, RNA-seq analysis illuminated that drought, salt, heat, cold stresses, low nitrogen and phosphorus conditions, as well as pathogen infection, significantly impact the expression patterns of ZmCASPL genes. RT-qPCR revealed that ZmCASPL 5/13/25/44 genes showed different expression patterns under PEG and NaCl treatments. Collectively, these findings provide a robust theoretical foundation for further investigations into the functional roles of the ZmCASPL gene family in maize.

Identification of New Cultivar and Different Provenances of Dendrocalamus brandisii (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome

Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for distinguishing them. Although the new cultivar 'Manxie No.1' has significant differences in the branch characteristics and the color of shoot sheaths compared to the D. brandisii, it still lacks precise genetic information at the molecular level. This study identified 231,789 microsatellite markers based on the whole genome of D. brandisii and analyzed their type composition and distribution on chromosomes in detail. Then, using TP-M13-SSR fluorescence-labeling technology, 34 pairs of polymorphic primers were screened to identify the new cultivar 'Manxie No.1' and 11 different geographical provenances of D. brandisii. We also constructed DNA fingerprinting profiles for them. At the same time, we mapped six polymorphic SSRs to the gene of D. brandisii, among which SSR673 was mapped to DhB10G011540, which is related to plant immunity. The specific markers selected in this study can rapidly identify the provenances and the new cultivar of D. brandisii and help explore candidate genes related to some important traits.

Association of Toll-Like Receptor 7 (TLR7) Polymorphisms with Predisposition to Systemic Lupus Erythematosus (SLE): A Meta and Trial Sequential Analysis

Systemic Lupus Erythematosus (SLE) is an autoimmune disorder characterized by autoantibody production and organ involvement. The role of toll-like receptor-7 in SLE is well established. Although genetic variations in the TLR-7 gene have been associated with an increased risk of developing SLE, the findings are not consistent. We performed a meta-analysis of previously published articles on four important single nucleotide polymorphisms in the TLR-7 gene (rs3853839, rs179008, rs179019, and rs179010) to reach a valid conclusion. Various literature databases, including PubMed, Science Direct, and Scopus, were scoured for eligible reports until May 10, 2023. GPower software v.3 was used to assess the power of individual reports included in the meta-analysis. Comprehensive Meta-analysis v3 software was used to perform all statistics. The publication biases in each genetic comparison model were investigated using funnel plots and Egger's regression test. To test heterogeneity, Cochrane Q statistics, probability value and I2 were used. Considering the predefined inclusion and exclusion criteria, the current study included a total of 10 eligible studies that included 15,472 SLE cases and 16,721 healthy controls. The meta-analysis revealed a significant association between TLR7 polymorphisms (rs179019 and rs179010) and susceptibility to SLE development. Other TLR7 polymorphisms (rs3853839 and rs179008), on the other hand, showed no significant association. Furthermore, the trial sequential analysis identified the need for additional case control studies for TLR-7 polymorphisms (rs3853839, rs179008, and rs179019) other than the rs179010 polymorphism. TLR7 variants for rs179010 and rs179019 are risk factor for the development of SLE. Further investigations are required to reach a valid conclusion.

Genomic insights into cytokinin oxidase/dehydrogenase (CKX) gene family, identification, phylogeny and synteny analysis for its possible role in regulating seed number in Pigeonpea (Cajanus cajan (L.) Millsp.)

Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This comprehensive study provides information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffolds. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their possible role as negative regulators. These genes can be potential targets to undertake seed and biomass improvement in pigeonpea.

Comparative Analysis of Casparian Strip Membrane Domain Protein Family in Oryza sativa (L.) and Arabidopsis thaliana (L.)

The Casparian strip membrane domain proteins (CASPs) are pivotal for the formation of the Casparian strip (CS) in endodermal cells and play a crucial role in a plant's response to environmental stresses. However, existing research on the CASP gene family in rice and Arabidopsis lacks a comprehensive bioinformatics analysis and necessitates further exploration. In this study, we identified 41 OsCASP and 39 AtCASP genes, which were grouped into six distinct subgroups. Collinearity analysis underscored the pivotal roles of WGD and TD events in driving the evolution of CASPs, with WGDs being the dominant force. On the one hand, the analysis of cis-elements indicated that most OsCASP and AtCASP genes contain MYB binding motifs. On the other hand, RNA-seq revealed that the majority of OsCASP and AtCASP genes are highly expressed in roots, particularly in endodermal cells, where OsCASP_like11/9 and AtCASP_like1/31 demonstrated the most pronounced expression. These results suggest that OsCASP_like11/9 and AtCASP_like1/31 might be candidate genes involved in the formation of the endodermis CS. RT-qPCR results demonstrated that OsCASP_like2/3/13/17/21/30 may be candidate genes for the ion defect process. Collectively, this study offers a theoretical foundation for unraveling the biological functions of CASP genes in rice and Arabidopsis.

Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice

Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.

Genome-wide identification and analysis of the EIN3/EIL gene family in broomcorn millet (Panicum miliaceum L.)

The EIN3/EIL gene family holds a pivotal role as it encodes a crucial transcription factor in plants. During the process of polyploidization in broomcorn millet (Panicum miliaceum L.), there is an intriguing above-average amplification observed within the EIN3/EIL gene family. Nonetheless, our current knowledge of this gene family in broomcorn millet remains limited. Hence, in this study, we conducted a comprehensive analysis of the EIN3/EIL gene family in broomcorn millet, aiming to provide a deeper understanding of the potential evolutionary changes. Additionally, we analyzed the EIN3/EIL gene family of Panicum hallii L., a close relative of broomcorn millet, to enhance our characterization efforts. Within this study, we identified a total of 15 EIN3/EIL genes specific to broomcorn millet. Through covariance analysis, it was revealed that all PmEIL genes, except PmEIL1 and PmEIL15, had duplicate copies generated through genome-wide duplication events. Importantly, the Ka/Ks values of all duplicated genes were found to be less than 1, indicating strong purifying selection. Phylogenetic analysis showed that these genes could be categorized into four distinct evolutionary branches, showcasing similar characteristics among members within the same branch. However, there appeared to be an uneven distribution of cis-acting elements amid the EIN3/EIL genes. Further examination of transcriptomic data shed light on the diverse spatiotemporal and stress-related expression patterns exhibited by the EIN3/EIL genes in broomcorn millet. Notably, under cold stress, the expression of PmEIL3/4/8/14 was significantly up-regulated, while under drought stress, PmEIL4/5/6 displayed significant up-regulation. Intriguingly, the expression pattern of PmEIL15 showed an opposite pattern in resistant and sensitive cultivars. The findings of this study augment our understanding of the EIN3/EIL gene family in broomcorn millet and offer a valuable reference for future investigations into polyploid studies. Moreover, this study establishes a theoretical foundation for further exploration of the ethylene signaling pathway in broomcorn millet.

Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions

The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.

Integrated Analysis of the Association Between Variants at PAX7 and NSCL/P in the Han Population

OBJECTIVE

Paired box 7 (PAX7) has been considered as a candidate gene for non-syndromic cleft lip with or without palate (NSCL/P). However, there is no research for the XXX, and previous studies concentrated on limited variants. This study aimed to conduct sufficiently dense and powerful scans of variants at PAX7 and explored the roles of variants at PAX7 in NSCL/P among the XXX.

DESIGN

Targeted region sequencing was performed to thoroughly screen variations, followed by a two-phase association analysis. 159 NSCL/P cases and 542 controls were analyzed in phase 1. Then in phase 2, the validation study was performed using 1626 cases and 2255 controls. We also explored the roles of variants at PAX7 gene in NSCL/P subtypes. Additionally, indirect associations were found by calculating LD and haplotypes.

SETTING

The study was conducted in XXX.

PATIENTS, PARTICIPANTS

159 NSCL/P cases and 542 controls were analyzed in phase 1. Then in phase 2, the validation study was performed using 1626 cases and 2255 controls.

INTERVENTIONS

Blood samples were collected.

MAIN OUTCOME MEASURES

To explore the association analysis between variants at PAX7 and NSCL/P in XXX.

RESULTS

The results showed that rs2236810, rs114882979 and rs2236804 were significantly associated with NSCL/P, which were predicted to have regulatory functions. Besides, variants at PAX7 function differently in the NSCL/P subtypes. We also discovered a PAX7 missense variant, NM_001135254 p.A369 V (NM_002584.2:c.1106C > T).

CONCLUSIONS

In summary, we confirmed 3 SNPs at PAX7 were significantly associated with NSCL/P in XXX and identified a missense variant, NM_001135254 p.A369 V (NM_002584.2:c.1106C > T).

Genome-Wide Identification and Characterization of Ammonium Transporter (AMT) Genes in Chlamydomonas reinhardtii

Ammonium transporters (AMTs) are vital plasma membrane proteins facilitating NH4+ uptake and transport, crucial for plant growth. The identification of favorable AMT genes is the main goal of improving ammonium-tolerant algas. However, there have been no reports on the systematic identification and expression analysis of Chlamydomonas reinhardtii (C. reinhardtii) AMT genes. This study comprehensively identified eight CrAMT genes, distributed across eight chromosomes, all containing more than 10 transmembrane structures. Phylogenetic analysis revealed that all CrAMTs belonged to the AMT1 subfamily. The conserved motifs and domains of CrAMTs were similar to those of the AMT1 members of OsAMTs and AtAMTs. Notably, the gene fragments of CrAMTs are longer and contain more introns compared to those of AtAMTs and OsAMTs. And the promoter regions of CrAMTs are enriched with cis-elements associated with plant hormones and light response. Under NH4+ treatment, CrAMT1;1 and CrAMT1;3 were significantly upregulated, while CrAMT1;2, CrAMT1;4, and CrAMT1;6 saw a notable decrease. CrAMT1;7 and CrAMT1;8 also experienced a decline, albeit less pronounced. Transgenic algas with overexpressed CrAMT1;7 did not show a significant difference in growth compared to CC-125, while transgenic algas with CrAMT1;7 knockdown exhibited growth inhibition. Transgenic algas with overexpressed or knocked-down CrAMT1;8 displayed reduced growth compared to CC-125, which also resulted in the suppression of other CrAMT genes. None of the transgenic algas showed better growth than CC-125 at high ammonium levels. In summary, our study has unveiled the potential role of CrAMT genes in high-ammonium environments and can serve as a foundational research platform for investigating ammonium-tolerant algal species.