Human intronless genes: Functional groups, associated diseases, evolution, and mRNA processing in absence of splicing

Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications

There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.

The spectrum of pre-mRNA splicing in autism

Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.

Splicing targeting drugs highlight intron retention as an actionable vulnerability in advanced prostate cancer

BACKGROUND

Advanced prostate cancer (PC) is characterized by insensitivity to androgen deprivation therapy and chemotherapy, resulting in poor outcome for most patients. Thus, advanced PC urgently needs novel therapeutic strategies. Mounting evidence points to splicing dysregulation as a hallmark of advanced PC. Moreover, pharmacologic inhibition of the splicing process is emerging as a promising option for this disease.

METHOD

By using a representative androgen-insensitive PC cell line (22Rv1), we have investigated the genome-wide transcriptomic effects underlying the cytotoxic effects exerted by three splicing-targeting drugs: Pladienolide B, indisulam and THZ531. Bioinformatic analyses were performed to uncover the gene structural features underlying sensitivity to transcriptional and splicing regulation by these treatments. Biological pathways altered by these treatments were annotated by gene ontology analyses and validated by functional experiments in cell models.

RESULTS

Although eliciting similar cytotoxic effects on advanced PC cells, Pladienolide B, indisulam and THZ531 modulate specific transcriptional and splicing signatures. Drug sensitivity is associated with distinct gene structural features, expression levels and cis-acting sequence elements in the regulated exons and introns. Importantly, we identified PC-relevant genes (i.e. EZH2, MDM4) whose drug-induced splicing alteration exerts an impact on cell survival. Moreover, computational analyses uncovered a widespread impact of splicing-targeting drugs on intron retention, with enrichment in genes implicated in pre-mRNA 3'-end processing (i.e. CSTF3, PCF11). Coherently, advanced PC cells displayed high sensitivity to a specific inhibitor of the cleavage and polyadenylation complex, which enhances the effects of chemotherapeutic drugs that are already in use for this cancer.

CONCLUSIONS

Our study uncovers intron retention as an actionable vulnerability for advanced PC, which may be exploited to improve therapeutic management of this currently incurable disease.

Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome

Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WW domain-binding protein 4 (WBP4) is part of the early spliceosomal complex and has not been previously associated with human pathologies in the Online Mendelian Inheritance in Man (OMIM) database. Through GeneMatcher, we identified ten individuals from eight families with a severe neurodevelopmental syndrome featuring variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal, and gastrointestinal abnormalities. Genetic analysis revealed five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated a complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including in genes associated with abnormalities of the nervous system, potentially underlying the phenotypes of the probands. We conclude that bi-allelic variants in WBP4 cause a developmental disorder with variable presentations, adding to the growing list of human spliceosomopathies.

Dissecting multifunctional roles of forkhead box transcription factor D1 in cancers

As a member of the forkhead box (FOX) family of transcription factors (TF), FOXD1 has recently been implicated as a crucial regulator in a variety of human cancers. Accumulating evidence has established dysregulated and aberrant FOXD1 signaling as a prominent feature in cancer development and progression. However, there is a lack of systematic review on this topic. Here, we summarized the present understanding of FOXD1 functions in cancer biology and reviewed the downstream targets and upstream regulatory mechanisms of FOXD1 as well as the related signaling pathways within the context of current reports. We highlighted the functional features of FOXD1 in cancers to identify the future research consideration of this multifunctional transcription factor and potential therapeutic strategies targeting its oncogenic activity.

Genetic polymorphisms of GGT1 gene (rs8135987, rs5751901 and rs2017869) are associated with neoadjuvant chemotherapy efficacy and toxicities in breast cancer patients

BACKGROUND

Our previous study illustrated the predictive value of serum gamma-glutamyl transpeptidase (GGT) for neoadjuvant chemotherapy (NAC) sensitivity in breast cancer patients. In this study we aim to determine whether single nucleotide polymorphisms (SNPs) in the gamma-glutamyltransferase 1 (GGT1) gene are related to the NAC response and adverse events and to find out a genetic marker in predicting NAC sensitivity.

METHODS

Three SNP loci (rs8135987, rs5751901, rs2017869) of GGT1 gene were selected and tested among breast cancer patients reciving NAC. Four genotype models were used in SNP analysis: co-dominant model compared AA vs. Aa vs. aa; dominant model compared AA vs. Aa + aa; recessive model compared AA + Aa vs. aa; over-dominant model compared AA + aa vs. Aa. Chi-squared test and multivariable logistic regression analysis were performed between SNP genotypes, haplotypes and pathological complete response(pCR), adverse events as well as serum GGT level.

RESULTS

A total of 143 patients were included in the study. For SNP rs8135987 (T > C), the TC genotype in over-dominant model was inversely related with pCR (adjusted OR = 0.30, 95% CI 0.10-0.88, p = 0.029) as well as the risk of peripheral neuropathy (adjusted OR = 0.39, 95% CI 0.15-0.96, p = 0.042). The TC genotype in dominant model was significantly associated with elevated serum GGT level (OR = 3.11, 95% CI 1.07-9.02, p = 0.036). For rs2017869 (G > C), the occurrence of grade 2 or greater neutropenia (OR = 0.39, 95% CI 0.08-0.84, p = 0.025) and leukopenia (OR = 0.24, 95% CI 0.08-0.78, p = 0.017) were both significantly reduced in patients with CC genotypes. For rs5751901(T > C), the CC genotype could significantly reduce the risk of grade 2 or greater neutropenia (OR = 0.29, 95% CI 0.09-0.96, p = 0.036) and leukopenia (OR = 0.27, 95% CI 0.09-0.84, p = 0.024) in recessive model.

CONCLUSIONS

The GGT1 gene SNPs might be an independent risk factor for poor response of NAC in breast cancer patients, providng theoretical basis for further precision therapy.

Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome

Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WBP4 (WW Domain Binding Protein 4) is part of the early spliceosomal complex, and was not described before in the context of human pathologies. Ascertained through GeneMatcher we identified eleven patients from eight families, with a severe neurodevelopmental syndrome with variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal and gastrointestinal abnormalities. Genetic analysis revealed overall five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including enrichment for abnormalities of the nervous system and musculoskeletal system genes, suggesting that the overlapping differentially spliced genes are related to the common phenotypes of the probands. We conclude that biallelic variants in WBP4 cause a spliceosomopathy. Further functional studies are called for better understanding of the mechanism of pathogenicity.

Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.)

The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.

The position of the longest intron is related to biological functions in some human genes

The evidence that introns can influence different levels of transfer of genetic information between DNA and the final product is increasing. Longer first introns were found to be a general property of eukaryotic gene structure and shown to contain a higher fraction of conserved sequence and different functional elements. Our work brings more precise information about the position of the longest introns in human protein-coding genes and possible connection with biological function and gene expression. According to our results, the position of the longest intron can be localized to the first third of introns in 64%, the second third in 19%, and the third in 17%, with notable peaks at the middle and last introns of approximately 5% and 6%, respectively. The median lengths of the longest introns decrease with increasing distance from the start of the gene from approximately 15,000 to 5,000 bp. We have shown that the position of the longest intron is in some cases linked to the biological function of the given gene. For example, DNA repair genes have the longest intron more often in the second or third. In the distribution of gene expression according to the position of the longest intron, tissue-specific profiles can be traced with the highest expression usually at the absolute positions of intron 1 and 2. In this work, we present arguments supporting the hypothesis that the position of the longest intron in a gene is another biological factor modulating the transmission of genetic information. The position of the longest intron is related to biological functions in some human genes.

SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection

The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables the rapid generation of conditional alleles via one-step zygote injection. In this study, a total of 13 SCON mouse lines were successfully generated by 2 different laboratories. SCON has conditional intronic functions in various vertebrate species, and its target insertion is as simple as CRISPR/Cas9-mediated gene tagging.

A Truncated Form of the p27 Cyclin-Dependent Kinase Inhibitor Translated from Pre-mRNA Causes G2-Phase Arrest

Pre-mRNA splicing is an indispensable mechanism for eukaryotic gene expression. Splicing inhibition causes cell cycle arrest at the G₁ and G₂/M phases, and this is thought to be one of the reasons for the potent antitumor activity of splicing inhibitors. However, the molecular mechanisms underlying the cell cycle arrest have many unknown aspects. In particular, the mechanism of G₂/M-phase arrest caused by splicing inhibition is completely unknown. Here, we found that lower and higher concentrations of pladienolide B caused M-phase and G₂-phase arrest, respectively. We analyzed protein levels of cell cycle regulators and found that a truncated form of the p27 cyclin-dependent kinase inhibitor, named p27*, accumulated in G₂-arrested cells. Overexpression of p27* caused partial G₂-phase arrest. Conversely, knockdown of p27* accelerated exit from G₂/M phase after washout of splicing inhibitor. These results suggest that p27* contributes to G₂/M-phase arrest caused by splicing inhibition. We also found that p27* bound to and inhibited M-phase cyclins, although it is well known that p27 regulates the G₁/S transition. Intriguingly, p27*, but not full-length p27, was resistant to proteasomal degradation and remained in G₂/M phase. These results suggest that p27*, which is a very stable truncated protein in G₂/M phase, contributes to G₂-phase arrest caused by splicing inhibition.

The Angiotensin AT2 Receptor: From a Binding Site to a Novel Therapeutic Target

Discovered more than 30 years ago, the angiotensin AT2 receptor (AT2R) has evolved from a binding site with unknown function to a firmly established major effector within the protective arm of the renin-angiotensin system (RAS) and a target for new drugs in development. The AT2R represents an endogenous protective mechanism that can be manipulated in the majority of preclinical models to alleviate lung, renal, cardiovascular, metabolic, cutaneous, and neural diseases as well as cancer. This article is a comprehensive review summarizing our current knowledge of the AT2R, from its discovery to its position within the RAS and its overall functions. This is followed by an in-depth look at the characteristics of the AT2R, including its structure, intracellular signaling, homo- and heterodimerization, and expression. AT2R-selective ligands, from endogenous peptides to synthetic peptides and nonpeptide molecules that are used as research tools, are discussed. Finally, we summarize the known physiological roles of the AT2R and its abundant protective effects in multiple experimental disease models and expound on AT2R ligands that are undergoing development for clinical use. The present review highlights the controversial aspects and gaps in our knowledge of this receptor and illuminates future perspectives for AT2R research. SIGNIFICANCE STATEMENT: The angiotensin AT2 receptor (AT2R) is now regarded as a fully functional and important component of the renin-angiotensin system, with the potential of exerting protective actions in a variety of diseases. This review provides an in-depth view of the AT2R, which has progressed from being an enigma to becoming a therapeutic target.

Identification, Phylogeny, Divergence, Structure, and Expression Analysis of A20/AN1 Zinc Finger Domain Containing Stress-Associated Proteins (SAPs) Genes in Jatropha curcas L

Jatropha is a small woody perennial biofuel-producing shrub. Stress-associated proteins (SAPs) are novel stress regulatory zinc-finger proteins and are mainly associated with tolerance against various environmental abiotic stresses in Jatropha. In the present study, the JcSAP gene family were analyzed comprehensively in Jatropha curcas and 11 JcSAP genes were identified. Phylogenetic analysis classified the JcSAP genes into four groups based on sequence similarity, similar gene structure features, conserved A20 and/or AN1 domains, and their responsive motifs. Moreover, the divergence analysis further evaluated the evolutionary aspects of the JcSAP genes with the predicted time of divergence from 9.1 to 40 MYA. Furthermore, a diverse range of cis-elements including light-responsive elements, hormone-responsive elements, and stress-responsive elements were detected in the promoter region of JcSAP genes while the miRNA target sites predicted the regulation of JcSAP genes via a candid miRNA mediated post-transcriptional regulatory network. In addition, the expression profiles of JcSAP genes in different tissues under stress treatment indicated that many JcSAP genes play functional developmental roles in different tissues, and exhibit significant differential expression under stress treatment. These results collectively laid a foundation for the functional diversification of JcSAP genes.

Exploring the roles of the Cdc2-like kinases in cancers

The Cdc2-like kinases (CLKs 1-4) are involved in regulating the alternative splicing of a variety of genes. Their activity contributes to important cellular processes such as proliferation, differentiation, apoptosis, migration, and cell cycle regulation. Abnormal expression of CLKs can lead to cancers; therefore, pharmacological inhibition of CLKs may be a useful therapeutic strategy. This review summarises what is known about the roles of each of the CLKs in cancerous cells, as well as the effects of relevant small molecule CLK inhibitors.

Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework

A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA–Phe233del showed that the occurrence of the Phe233del affects between 220–320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein–DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA–Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics–Molecular Mechanics (QM–MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.

Identification and Expression Analysis of Zinc Finger A20/AN1 Stress-Associated Genes SmSAP Responding to Abiotic Stress in Eggplant

Stress-associated proteins (SAP), a class of zinc-finger proteins, have been identified as novel stress regulatory proteins in stress responses. However, SAP genes in eggplant (SmSAP) have been little reported. It has important significance in identifying SAP members, understanding the molecular mechanisms underlying stress responses, and tolerance. We performed a comprehensive study of the A20/AN1 domains, motifs, gene structures, phylogenetic relationships, chromosomal locations, gene replications, collinearity, cis-acting elements, and expression pattern responses to various abiotic stresses. Twenty-one SAP genes were identified in eggplant (SmSAP) and were localized on 10 chromosomes. A phylogenetic analysis revealed that most of the SmSAP proteins showed a high homology with the tomato SAP members, and 21 members were divided into four groups based on the homology of the SAP members in eggplant, tomato, rice, and Arabidopsis. Further analysis revealed that SmSAP proteins contain the characteristic A20/AN1 domains, the A20 domain composed of motif 2 (ILCINNCGFFGSPATMNLCSKCYKDMJLK). Four pairs of tandem duplications were found in eggplant, and 10 SmSAP genes had collinearity with SAP genes from Arabidopsis, potato, or tomato, but only four SmSAP genes were collinear with SAP genes in the three species mentioned above. Moreover, the promoters of SmSAP genes were predicted to contain many cis-acting elements that respond to abiotic stress and hormones. A qRT-PCR analysis of the four selected SmSAP genes exhibited diverse expression levels in response to various environmental stresses. These results provided a comprehensive analysis of the SmSAP genes and lay a solid foundation for improving the understanding of the functional diversification of SAP genes under various environmental stresses in eggplant.

Differential Functions of Pepper Stress-Associated Proteins in Response to Abiotic Stresses

Stress-associated proteins (SAPs), a group of zinc-finger-type proteins, have been identified as novel regulators of plant abiotic and biotic stresses. However, although they have been discovered in different plant species, their precise functional roles remain unclear. Here, we identified 14 SAP subfamily genes in the pepper genome. An investigation of the promoter regions of these genes for cis-regulatory elements associated with abiotic stress responses revealed the presence of multiple stress-related elements. Domain and phylogenetic analyses using the corresponding protein sequences revealed that the CaSAP genes can be classified into six groups (I-VI) and sorted into two broad types. Expression levels of the CaSAP genes were found to be differentially induced by low temperature, the dehydration stress, or exogenous abscisic acid. Group II and IV genes were highly induced by the low temperature and dehydration treatments, respectively. Moreover, subcellular localization analysis indicated that the proteins in these two groups are distributed in the nucleus, cytoplasm, and plasma membrane. Among the pepper plants silenced with the three identified group II CaSAP genes, the CA02g10410-silenced plants showed tolerance to low temperature, whereas the CA03g17080-silenced plants were found to have temperature-sensitive phenotypes. Interestingly, group IV CaSAP-silenced pepper plants showed drought-tolerant phenotypes. These findings contribute to a preliminary characterization of CaSAP genes and provide directions for future research on the biological role of CaSAPs in response to different abiotic stresses.

The rare rs769301934 variant in NHLRC1 is a common cause of Lafora disease in Turkey

Lafora disease (LD) is a severe form of progressive myoclonus epilepsy inherited in an autosomal recessive fashion. It is associated with biallelic pathogenic variations in EPM2A or NHLRC1, which encode laforin and malin, respectively. The disease usually starts with adolescent onset seizures followed by progressive dementia, refractory status epilepticus and eventually death within 10 years of onset. LD is generally accepted as having a homogenous clinical course with no considerable differences between EPM2A or NHLRC1 associated forms. Nevertheless, late-onset and slow progressing forms of the disease have also been reported. Herein, we have performed clinical and genetic analyses of 14 LD patients from 12 different families and identified 8 distinct biallelic variations in these patients. Five of these variations were novel and/or associated with the LD phenotype for the first time. Interestingly, almost half of the cases were homozygous for the rare rs769301934 (NM_198586.3(NHLRC1): c.436 G > A; p.(Asp146Asn)) allele in NHLRC1. A less severe phenotype with an onset at a later age may be the reason for the biased inflation of this variant, which is already present in the human gene pool and can hence arise in the homozygous form in populations with increased parental consanguinity.

HPDL deficiency causes a neuromuscular disease by impairing the mitochondrial respiration

Mitochondrial diseases are caused by variants in both mitochondrial and nuclear genomes. A nuclear gene HPDL (4-hydroxyphenylpyruvate dioxygenase-like), which encodes an intermembrane mitochondrial protein, has been recently implicated in causing a neurodegenerative disease characterized by pediatric-onset spastic movement phenotypes. Here, we report six Chinese patients with bi-allelic HPDL pathogenic variants from four unrelated families showing neuropathic symptoms of variable severity, including developmental delay/intellectual disability, spasm, and hypertonia. Seven different pathogenic variants are identified, of which five are novel. Both fibroblasts and immortalized lymphocytes derived from patients show impaired mitochondrial respiratory function, which is also observed in HPDL-knockdown (KD) HeLa cells. In these HeLa cells, overexpression of a wild-type HPDL gene can rescue the respiratory phenotype of oxygen consumption rate. In addition, a decreased activity of the oxidative phosphorylation (OXPHOS) complex II is observed in patient-derived lymphocytes and HPDL-KD HeLa cells, further supporting an essential role of HPDL in the mitochondrial respiratory chain. Collectively, our data expand the clinical and mutational spectra of this mitochondrial neuropathy and further delineate the possible disease mechanism involving the impairment of the OXPHOS complex II activity due to the bi-allelic inactivations of HPDL.

Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role

The structure of eukaryotic genes is generally a combination of exons interrupted by intragenic non-coding DNA regions (introns) removed by RNA splicing to generate the mature mRNA. A fraction of genes, however, comprise a single coding exon with introns in their untranslated regions or are intronless genes (IGs), lacking introns entirely. The latter code for essential proteins involved in development, growth, and cell proliferation and their expression has been proposed to be highly specialized for neuro-specific functions and linked to cancer, neuropathies, and developmental disorders. The abundant presence of introns in eukaryotic genomes is pivotal for the precise control of gene expression. Notwithstanding, IGs exempting splicing events entail a higher transcriptional fidelity, making them even more valuable for regulatory roles. This work aimed to infer the functional role and evolutionary history of IGs centered on the mouse genome. IGs consist of a subgroup of genes with one exon including coding genes, non-coding genes, and pseudogenes, which conform approximately 6% of a total of 21,527 genes. To understand their prevalence, biological relevance, and evolution, we identified and studied 1,116 IG functional proteins validating their differential expression in transcriptomic data of embryonic mouse telencephalon. Our results showed that overall expression levels of IGs are lower than those of MEGs. However, strongly up-regulated IGs include transcription factors (TFs) such as the class 3 of POU (HMG Box), Neurog1, Olig1, and BHLHe22, BHLHe23, among other essential genes including the β-cluster of protocadherins. Most striking was the finding that IG-encoded BHLH TFs fit the criteria to be classified as microproteins. Finally, predicted protein orthologs in other six genomes confirmed high conservation of IGs associated with regulating neural processes and with chromatin organization and epigenetic regulation in Vertebrata. Moreover, this study highlights that IGs are essential modulators of regulatory processes, such as the Wnt signaling pathway and biological processes as pivotal as sensory organ developing at a transcriptional and post-translational level. Overall, our results suggest that IG proteins have specialized, prevalent, and unique biological roles and that functional divergence between IGs and MEGs is likely to be the result of specific evolutionary constraints.

The evolution of autophagy proteins - diversification in eukaryotes and potential ancestors in prokaryotes

Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.

The master transcription factor SOX2, mutated in anophthalmia/microphthalmia, is post-transcriptionally regulated by the conserved RNA-binding protein RBM24 in vertebrate eye development

Mutations in the key transcription factor, SOX2, alone account for 20% of anophthalmia (no eye) and microphthalmia (small eye) birth defects in humans-yet its regulation is not well understood, especially on the post-transcription level. We report the unprecedented finding that the conserved RNA-binding motif protein, RBM24, positively controls Sox2 mRNA stability and is necessary for optimal SOX2 mRNA and protein levels in development, perturbation of which causes ocular defects, including microphthalmia and anophthalmia. RNA immunoprecipitation assay indicates that RBM24 protein interacts with Sox2 mRNA in mouse embryonic eye tissue. and electrophoretic mobility shift assay shows that RBM24 directly binds to the Sox2 mRNA 3'UTR, which is dependent on AU-rich elements (ARE) present in the Sox2 mRNA 3'UTR. Further, we demonstrate that Sox2 3'UTR AREs are necessary for RBM24-based elevation of Sox2 mRNA half-life. We find that this novel RBM24-Sox2 regulatory module is essential for early eye development in vertebrates. We show that Rbm24-targeted deletion using a constitutive CMV-driven Cre in mouse, and rbm24a-CRISPR/Cas9-targeted mutation or morpholino knockdown in zebrafish, results in Sox2 downregulation and causes the developmental defects anophthalmia or microphthalmia, similar to human SOX2-deficiency defects. We further show that Rbm24 deficiency leads to apoptotic defects in mouse ocular tissue and downregulation of eye development markers Lhx2, Pax6, Jag1, E-cadherin and gamma-crystallins. These data highlight the exquisite specificity that conserved RNA-binding proteins like RBM24 mediate in the post-transcriptional control of key transcription factors, namely, SOX2, associated with organogenesis and human developmental defects.

Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes

Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.

The Molecular Function of PURA and Its Implications in Neurological Diseases

In recent years, genome-wide analyses of patients have resulted in the identification of a number of neurodevelopmental disorders. Several of them are caused by mutations in genes that encode for RNA-binding proteins. One of these genes is PURA, for which in 2014 mutations have been shown to cause the neurodevelopmental disorder PURA syndrome. Besides intellectual disability (ID), patients develop a variety of symptoms, including hypotonia, metabolic abnormalities as well as epileptic seizures. This review aims to provide a comprehensive assessment of research of the last 30 years on PURA and its recently discovered involvement in neuropathological abnormalities. Being a DNA- and RNA-binding protein, PURA has been implicated in transcriptional control as well as in cytoplasmic RNA localization. Molecular interactions are described and rated according to their validation state as physiological targets. This information will be put into perspective with available structural and biophysical insights on PURA’s molecular functions. Two different knock-out mouse models have been reported with partially contradicting observations. They are compared and put into context with cell biological observations and patient-derived information. In addition to PURA syndrome, the PURA protein has been found in pathological, RNA-containing foci of patients with the RNA-repeat expansion diseases such as fragile X-associated tremor ataxia syndrome (FXTAS) and amyotrophic lateral sclerosis (ALS)/fronto-temporal dementia (FTD) spectrum disorder. We discuss the potential role of PURA in these neurodegenerative disorders and existing evidence that PURA might act as a neuroprotective factor. In summary, this review aims at informing researchers as well as clinicians on our current knowledge of PURA’s molecular and cellular functions as well as its implications in very different neuronal disorders.

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences

Single-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases.

Database URL:http://v2.sinex.cl/

Cancer, Retrogenes, and Evolution

This review summarizes the knowledge about retrogenes in the context of cancer and evolution. The retroposition, in which the processed mRNA from parental genes undergoes reverse transcription and the resulting cDNA is integrated back into the genome, results in additional copies of existing genes. Despite the initial misconception, retroposition-derived copies can become functional, and due to their role in the molecular evolution of genomes, they have been named the “seeds of evolution”. It is convincing that retrogenes, as important elements involved in the evolution of species, also take part in the evolution of neoplastic tumors at the cell and species levels. The occurrence of specific “resistance mechanisms” to neoplastic transformation in some species has been noted. This phenomenon has been related to additional gene copies, including retrogenes. In addition, the role of retrogenes in the evolution of tumors has been described. Retrogene expression correlates with the occurrence of specific cancer subtypes, their stages, and their response to therapy. Phylogenetic insights into retrogenes show that most cancer-related retrocopies arose in the lineage of primates, and the number of identified cancer-related retrogenes demonstrates that these duplicates are quite important players in human carcinogenesis.

Obesity induced by high-fat diet is associated with critical changes in biological and molecular functions of mesenchymal stromal cells present in visceral adipose tissue

The mesenchymal stromal cells (MSCs) residing within the stromal component of visceral adipose tissue appear to be greatly affected by obesity, with impairment of their functions and presence of senescence. To gain further insight into these phenomena, we analyzed the changes in total proteome content and secretome of mouse MSCs after a high-fat diet (HFD) treatment compared to a normal diet (ND). In healthy conditions, MSCs are endowed with functions mainly devoted to vesicle trafficking. These cells have an immunoregulatory role, affecting leukocyte activation and migration, acute inflammation phase response, chemokine signaling, and platelet activities. They also present a robust response to stress. We identified four signaling pathways (TGF-β, VEGFR2, HMGB1, and Leptin) that appear to govern the cells' functions. In the obese mice, MSCs showed a change in their functions. The immunoregulation shifted toward pro-inflammatory tasks with the activation of interleukin-1 pathway and of Granzyme A signaling. Moreover, the methionine degradation pathway and the processing of capped intronless pre-mRNAs may be related to the inflammation process. The signaling pathways we identified in ND MSCs were replaced by MET, WNT, and FGFR2 signal transduction, which may play a role in promoting inflammation, cancer, and aging.

Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency

Pre-mRNA splicing is an essential mechanism for ensuring integrity of the transcriptome in eukaryotes. Therefore, splicing deficiency might cause a decrease in functional proteins and the production of nonfunctional, aberrant proteins. To prevent the production of such aberrant proteins, eukaryotic cells have several mRNA quality control mechanisms. In addition to the known mechanisms, we previously found that transcription elongation is attenuated to prevent the accumulation of pre-mRNA under splicing-deficient conditions. However, the detailed molecular mechanism behind the defect in transcription elongation remains unknown. Here, we showed that the RNA binding protein Rbm38 reduced the transcription elongation defect of the SMEK2 gene caused by splicing deficiency. This reduction was shown to require the N- and C-terminal regions of Rbm38, along with an important role being played by the RNA-recognition motif of Rbm38. These findings advance our understanding of the molecular mechanism of the transcription elongation defect caused by splicing deficiency.

Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle

Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the key cell-cycle factors and their known alternative splicing isoforms. We discuss different levels of pre-mRNA splicing regulation such as post-translational modifications and changes in the expression of splicing factors. We describe the effect of chromatin dynamics on pre-mRNA splicing during the cell cycle. In addition, we focus on spliceosome component SF3B1, which is mutated in many types of cancer, and describe the link between SF3B1 and its inhibitors and the cell cycle.

Splicing Factor Transcript Abundance in Saliva as a Diagnostic Tool for Breast Cancer

Breast cancer is the second leading cause of death in women above 60 years in the US. Screening mammography is recommended for women above 50 years; however, 22% of breast cancer cases are diagnosed in women below this age. We set out to develop a test based on the detection of cell-free RNA from saliva. To this end, we sequenced RNA from a pool of ten women. The 1254 transcripts identified were enriched for genes with an annotation of alternative pre-mRNA splicing. Pre-mRNA splicing is a tightly regulated process and its misregulation in cancer cells promotes the formation of cancer-driving isoforms. For these reasons, we chose to focus on splicing factors as biomarkers for the early detection of breast cancer. We found that the level of the splicing factors is unique to each woman and consistent in the same woman at different time points. Next, we extracted RNA from 36 healthy subjects and 31 breast cancer patients. Recording the mRNA level of seven splicing factors in these samples demonstrated that the combination of all these factors is different in the two groups (p value = 0.005). Our results demonstrate a differential abundance of splicing factor mRNA in the saliva of breast cancer patients.

Production of novel pladienolide analogues through native expression of a pathway-specific activator

Aberrant splicing of pre-mRNA is implicated in many human genetic disorders. Small molecules that target the spliceosome are important leads as therapeutics and research tools, and one compound of significant interest is the polyketide natural product pladienolide B. Here, we describe the reactivation of quiescent pladienolide B production in the domesticated lab strain Streptomyces platensis AS6200 by overexpression of the pathway-specific activator PldR. The resulting dysregulation of the biosynthetic genes led to the accumulation and isolation of five additional intermediate or shunt metabolites of pladienolide B biosynthesis, including three previously unreported congeners. These compounds likely comprise the entire pladienolide biosynthetic pathway and demonstrate the link between polyketide tailoring reactions and bioactivity, particularly the importance of the 18,19-epoxide. Each congener demonstrated specific inhibitory activity against mammalian cell lines, with successive modifications leading to increased activity (IC₅₀: 8 mM to 5 μM).

Reactivation of quiescent polyketide production in a domesticated lab strain.

Genomic Indexing by Somatic Gene Recombination of mRNA/ncRNA - Does It Play a Role in Genomic Mosaicism, Memory Formation, and Alzheimer's Disease?

Recent evidence indicates that genomic individuality of neurons, characterized by DNA-content variation, is a common if not universal phenomenon in the human brain that occurs naturally but can also show aberrancies that have been linked to the pathomechanism of Alzheimer’s disease and related neurodegenerative disorders. Etiologically, this genomic mosaic has been suggested to arise from defects of cell cycle regulation that may occur either during brain development or in the mature brain after terminal differentiation of neurons. Here, we aim to draw attention towards another mechanism that can give rise to genomic individuality of neurons, with far-reaching consequences. This mechanism has its origin in the transcriptome rather than in replication defects of the genome, i.e., somatic gene recombination of RNA. We continue to develop the concept that somatic gene recombination of RNA provides a physiological process that, through integration of intronless mRNA/ncRNA into the genome, allows a particular functional state at the level of the individual neuron to be indexed. By insertion of defined RNAs in a somatic recombination process, the presence of specific mRNA transcripts within a definite temporal context can be “frozen” and can serve as an index that can be recalled at any later point in time. This allows information related to a specific neuronal state of differentiation and/or activity relevant to a memory trace to be fixed. We suggest that this process is used throughout the lifetime of each neuron and might have both advantageous and deleterious consequences.

Cadmium Uptake, MT Gene Activation and Structure of Large-Sized Multi-Domain Metallothioneins in the Terrestrial Door Snail Alinda biplicata (Gastropoda, Clausiliidae)

Terrestrial snails (Gastropoda) possess Cd-selective metallothioneins (CdMTs) that inactivate Cd²⁺ with high affinity. Most of these MTs are small Cysteine-rich proteins that bind 6 Cd²⁺ equivalents within two distinct metal-binding domains, with a binding stoichiometry of 3 Cd²⁺ ions per domain. Recently, unusually large, so-called multi-domain MTs (md-MTs) were discovered in the terrestrial door snail Alinda biplicata (A.b.). The aim of this study is to evaluate the ability of A.b. to cope with Cd stress and the potential involvement of md-MTs in its detoxification. Snails were exposed to increasing Cd concentrations, and Cd-tissue concentrations were quantified. The gene structure of two md-MTs (9md-MT and 10md-MT) was characterized, and the impact of Cd exposure on MT gene transcription was quantified via qRT PCR. A.b. efficiently accumulates Cd at moderately elevated concentrations in the feed, but avoids food uptake at excessively high Cd levels. The structure and expression of the long md-MT genes of A.b. were characterized. Although both genes are intronless, they are still transcribed, being significantly upregulated upon Cd exposure. Overall, our results contribute new knowledge regarding the metal handling of Alinda biplicata in particular, and the potential role of md-MTs in Cd detoxification of terrestrial snails, in general.

The Melanin-Concentrating Hormone (MCH) System: A Tale of Two Peptides

The melanin-concentrating hormone (MCH) system is a robust integrator of exogenous and endogenous information, modulating arousal and energy balance in mammals. Its predominant function in teleosts, however, is to concentrate melanin in the scales, contributing to the adaptive color change observed in several teleost species. These contrasting functions resulted from a gene duplication that occurred after the teleost divergence, which resulted in the generation of two MCH-coding genes in this clade, which acquired distinctive sequences, distribution, and functions, examined in detail here. We also describe the distribution of MCH immunoreactivity and gene expression in a large number of species, in an attempt to identify its core elements. While initially originated as a periventricular peptide, with an intimate relationship with the third ventricle, multiple events of lateral migration occurred during evolution, making the ventrolateral and dorsolateral hypothalamus the predominant sites of MCH in teleosts and mammals, respectively. Substantial differences between species can be identified, likely reflecting differences in habitat and behavior. This observation aligns well with the idea that MCH is a major integrator of internal and external information, ensuring an appropriate response to ensure the organism’s homeostasis. New studies on the MCH system in species that have not yet been investigated will help us understand more precisely how these habitat changes are connected to the hypothalamic neurochemical circuits, paving the way to new intervention strategies that may be used with pharmacological purposes.

Control of human testis-specific gene expression

Background

As a result of decades of effort by many investigators we now have an advanced level of understanding about several molecular systems involved in the control of gene expression. Examples include CpG islands, promoters, mRNA splicing and epigenetic signals. It is less clear, however, how such systems work together to integrate the functions of a living organism. Here I describe the results of a study to test the idea that a contribution might be made by focusing on genes specifically expressed in a particular tissue, the human testis.

Experimental design

A database of 239 testis-specific genes was accumulated and each was examined for the presence of features relevant to control of gene expression. These include: (1) the presence of a promoter, (2) the presence of a CpG island (CGI) within the promoter, (3) the presence in the promoter of a transcription factor binding site near the transcription start site, (4) the level of gene expression, and (5) the above features in genes of testis-specific cell types such as spermatocyte and spermatid that differ in their extent of differentiation.

Results

Of the 107 database genes with an annotated promoter, 56 were found to have one or more transcription factor binding sites near the transcription start site. Three of the binding sites observed, Pax-5, AP-2αA and GRα, stand out in abundance suggesting they may be involved in testis-specific gene expression. Compared to less differentiated testis-specific cells, genes of more differentiated cells were found to be (1) more likely to lack a CGI, (2) more likely to lack introns and (3) higher in expression level. The results suggest genes of more differentiated cells have a reduced need for CGI-based regulatory repression, reduced usage of gene splicing and a smaller set of expressed proteins.

RNA-protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity

RNA-protein interactions are crucial for most biological processes in all organisms. However, it appears that the complexity of RNA-based regulation increases with the complexity of the organism, creating additional regulatory circuits, the scope of which is only now being revealed. It is becoming apparent that previously unappreciated features, such as disordered structural regions in proteins or non-coding regions in DNA leading to higher plasticity and pliability in RNA-protein complexes, are in fact essential for complex, precise and fine-tuned regulation. This review addresses the issue of the role of RNA-protein interactions in generating eukaryotic complexity, focusing on the newly characterized disordered RNA-binding motifs, moonlighting of metabolic enzymes, RNA-binding proteins interactions with different RNA species and their participation in regulatory networks of higher order.

Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns

We previously showed that the first intron of genes exhibits several interesting characteristics not seen in other introns: 1) it is the longest intron on average in almost all eukaryotes, 2) it presents the highest number of conserved sites, and 3) it exhibits the highest density of regulatory chromatin marks. Here, we expand on our previous study by integrating various multiomics data, leading to further evidence supporting the functionality of sites in the first intron. We first show that trait-associated single-nucleotide polymorphisms (TASs) are significantly enriched in the first intron. We also show that within the first intron, the density of epigenetic chromatin signals is higher near TASs than in distant regions. Furthermore, the distribution of several chromatin regulatory marks is investigated in relation to gene expression specificity (i.e., housekeeping vs. tissue-specific expression), essentiality (essential genes vs. nonessential genes), and levels of gene expression; housekeeping genes or essential genes contain greater proportions of active chromatin marks than tissue-specific genes or nonessential genes, and highly expressed genes exhibit a greater density of chromatin regulatory marks than genes with low expression. Moreover, we observe that genes carrying multiple first-intron TASs interact with each other within a large protein-protein interaction network, ultimately connecting to the UBC protein, a well-established protein involved in ubiquitination. We believe that our results shed light on the functionality of first introns as a genomic entity involved in gene expression regulation.

Genomic Analysis of Stress Associated Proteins in Soybean and the Role of GmSAP16 in Abiotic Stress Responses in Arabidopsis and Soybean

Stress associated proteins (SAPs) containing A20/AN1 zinc finger domains have emerged as novel regulators of stress responses. In this study, 27 SAP genes were identified in soybean. The phylogenetic relationships, exon-intron structure, domain structure, chromosomal localization, putative cis-acting elements, and expression patterns of SAPs in various tissues under abiotic stresses were analyzed. Among the soybean SAP genes, GmSAP16 was significantly induced by water deficit stress, salt, and abscisic acid (ABA) and selected for further analysis. GmSAP16 was located in the nucleus and cytoplasm. The overexpression of GmSAP16 in Arabidopsis improved drought and salt tolerance at different developmental stages and increased ABA sensitivity, as indicated by delayed seed germination and stomatal closure. The GmSAP16 transgenic Arabidopsis plants had a higher proline content and a lower water loss rate and malondialdehyde (MDA) content than wild type (WT) plants in response to stresses. The overexpression of GmSAP16 in soybean hairy roots enhanced drought and salt tolerance of soybean seedlings, with higher proline and chlorophyll contents and a lower MDA content than WT. RNA inference (RNAi) of GmSAP16 increased stress sensitivity. Stress-related genes, including GmDREB1B;1, GmNCED3, GmRD22, GmDREB2, GmNHX1, and GmSOS1, showed significant expression alterations in GmSAP16-overexpressing and RNAi plants under stress treatments. These results indicate that soybean SAP genes play important roles in abiotic stress responses.

Intronless mRNAs transit through nuclear speckles to gain export competence

Nuclear speckles (NSs) store splicing factors. Wang et al. show that many naturally intronless mRNAs associate with NSs and that speckle association enhances their export by facilitating TREX recruitment, suggesting that trafficking to NSs could be an important quality control step in intronless mRNA export.

Nuclear speckles (NSs) serve as splicing factor storage sites. In this study, we unexpectedly found that many endogenous intronless mRNAs, which do not undergo splicing, associate with NSs. These associations do not require transcription, polyadenylation, or the polyA tail. Rather, exonic splicing enhancers present in intronless mRNAs and their binding partners, SR proteins, promote intronless mRNA localization to NSs. Significantly, speckle targeting of mRNAs promotes the recruitment of the TREX export complex and their TREX-dependent nuclear export. Furthermore, TREX, which accumulates in NSs, is required for releasing intronless mRNAs from NSs, whereas NXF1, which is mainly detected at nuclear pores, is not. Upon NXF1 depletion, the TREX protein UAP56 loses speckle concentration but coaccumulates with intronless mRNAs and polyA RNAs in the nucleoplasm, and these RNAs are trapped in NSs upon UAP56 codepletion. We propose that the export-competent messenger RNP assembly mainly occurs in NSs for intronless mRNAs and that entering NSs serves as a quality control step in mRNA export.

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes

Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.

Nucleosome Positioning of Intronless Genes in the Human Genome

Nucleosomes, the basic units of chromatin, are involved in transcription regulation and DNA replication. Intronless genes, which constitute 3 percent of the human genome, differ from intron-containing genes in evolution and function. Our analysis reveals that nucleosome positioning shows a distinct pattern in intronless and intron-containing genes. The nucleosome occupancy upstream of transcription start sites of intronless genes is lower than that of intron-containing genes. In contrast, high occupancy and well positioned nucleosomes are observed along the gene body of intronless genes, which is perfectly consistent with the barrier nucleosome model. Intronless genes have a significantly lower expression level than intron-containing genes and most of them are not expressed in CD4+ T cell lines and GM12878 cell lines, which results from their tissue specificity. However, the highly expressed genes are at the same expression level between the two types of genes. The highly expressed intronless genes require a higher density of RNA Pol II in an elongating state to compensate for the lack of introns. Additionally, 5' and 3' nucleosome depleted regions of highly expressed intronless genes are deeper than those of highly expressed intron-containing genes.

The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties

The reprimo (RPRM) gene family is a group of single exon genes present exclusively within the vertebrate lineage. Two out of three members of this family are present in humans: RPRM and RPRM-Like (RPRML). RPRM induces cell cycle arrest at G2/M in response to p53 expression. Loss-of-expression of RPRM is related to increased cell proliferation and growth in gastric cancer. This evidence suggests that RPRM has tumor suppressive properties. However, the molecular mechanisms and signaling partners by which RPRM exerts its functions remain unknown. Moreover, scarce studies have attempted to characterize RPRML, and its functionality is unclear. Herein, we highlight the role of the RPRM gene family in gastric carcinogenesis, as well as its potential applications in clinical settings. In addition, we summarize the current knowledge on the phylogeny and expression patterns of this family of genes in embryonic zebrafish and adult humans. Strikingly, in both species, RPRM is expressed primarily in the digestive tract, blood vessels and central nervous system, supporting the use of zebrafish for further functional characterization of RPRM. Finally, drawing on embryonic and adult expression patterns, we address the potential relevance of RPRM and RPRML in cancer. Active investigation or analytical research in the coming years should contribute to novel translational applications of this poorly understood gene family as potential biomarkers and development of novel cancer therapies.

Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution

BACKGROUND

Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa.

RESULTS

In this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2.

CONCLUSIONS

Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.

Improved ontology for eukaryotic single-exon coding sequences in biological databases

Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.

Evidence-based gene models for structural and functional annotations of the oil palm genome

Background

Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools.

Results

Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC₃ (fraction of cytosine and guanine in the third position of a codon) with over half the GC₃-rich genes (GC₃ ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures.

Conclusions

We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC₃-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops.

Reviewers

This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.