Characterization of exon skipping mutants of the COP1 gene from Arabidopsis

The removal of introns from pre-mRNA requires accurate recognition and selection of the intron splice sites. Mutations which alter splice site selection and which lead to skipping of specific exons are indicative of intron/exon recognition mechanisms involving an exon definition process. In this paper, three independent mutants to the COP1 gene in Arabidopsis which show exon skipping were identified and the mutations which alter the normal splicing pattern were characterized. The mutation in cop1–1 was a G→A change 4 nt upstream from the 3′ splice site of intron 5, while the mutation in cop1–2 was a G→A at the first nucleotide of intron 6, abolishing the conserved G within the 5′ splice site consensus. The effect of these mutations was skipping of exon 6. The mutation in cop1–8 was G→A in the final nucleotide of intron 10 abolishing the conserved G within the 3′ splice site consensus and leading to skipping of exon 11. The splicing patterns surrounding exons 6 and 11 of COP1 in these three mutant lines of Arabidopsis provide evidence for exon definition mechanisms operating in plant splicing.     

In vivo comparison of 2′‐O‐methyl phosphorothioate and morpholino antisense oligonucleotides for Duchenne muscular dystrophy exon skipping

Background

Antisense‐mediated exon skipping is a putative treatment for Duchenne muscular dystrophy (DMD). Using antisense oligonucleotides (AONs), the disrupted DMD reading frame is restored, allowing generation of partially functional dystrophin and conversion of a severe Duchenne into a milder Becker muscular dystrophy phenotype. In vivo studies are mainly performed using 2′‐O‐methyl phosphorothioate (2OMePS) or morpholino (PMO) AONs. These compounds were never directly compared.

Methods

mdx and humanized (h)DMD mice were injected intramuscularly and intravenously with short versus long 2OMePS and PMO for mouse exon 23 and human exons 44, 45, 46 and 51.

Results

Intramuscular injection showed that increasing the length of 2OMePS AONs enhanced skipping efficiencies of human exon 45, but decreased efficiency for mouse exon 23. Although PMO induced more mouse exon 23 skipping, PMO and 2OMePS were more comparable for human exons. After intravenous administration, exon skipping and novel protein was shown in the heart with both chemistries. Furthermore, PMO showed lower intramuscular concentrations with higher exon 23 skipping levels compared to 2OMePS, which may be due to sequestration in the extracellular matrix. Finally, two mismatches rendered 2OMePS but not PMO AONs nearly ineffective.

Conclusions

The results obtained in the present study indicate that increasing AON length improves skipping efficiency in some but not all cases. It is feasible to induce exon skipping and dystrophin restoration in the heart after injection of 2OMePS and unconjugated PMO. Furthermore, differences in efficiency between PMO and 2OMePS appear to be sequence and not chemistry dependent. Finally, the results indicate that PMOs may be less sequence specific than 2OMePS. Copyright © 2009 John Wiley & Sons, Ltd.     

The splicing regulator Sam68 binds to a novel exonic splicing silencer and functions in SMN2 alternative splicing in spinal muscular atrophy

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. An almost identical SMN2 gene is unable to compensate for this deficiency because a single C‐to‐T transition at position +6 in exon‐7 causes skipping of the exon by a mechanism not yet fully elucidated. We observed that the C‐to‐T transition in SMN2 creates a putative binding site for the RNA‐binding protein Sam68. RNA pull‐down assays and UV‐crosslink experiments showed that Sam68 binds to this sequence. In vivo splicing assays showed that Sam68 triggers SMN2 exon‐7 skipping. Moreover, mutations in the Sam68‐binding site of SMN2 or in the RNA‐binding domain of Sam68 completely abrogated its effect on exon‐7 skipping. Retroviral infection of dominant‐negative mutants of Sam68 that interfere with its RNA‐binding activity, or with its binding to the splicing repressor hnRNP A1, enhanced exon‐7 inclusion in endogenous SMN2 and rescued SMN protein expression in fibroblasts of SMA patients. Our results thus indicate that Sam68 is a novel crucial regulator of SMN2 splicing.     

The Relationship Between Breakfast Skipping,Chronotype, and Glycemic Control in Type 2 Diabetes

Breakfast skipping is associated with obesity and an increased risk of type 2 diabetes. Later chronotypes, individuals who have a preference for later bed and wake times, often skip breakfast. The aim of the study was to explore the relationships among breakfast skipping, chronotype, and glycemic control in type 2 diabetes patients. We collected sleep timing and 24-h dietary recall from 194 non-shift-working type 2 diabetes patients who were being followed in outpatient clinics. Mid-sleep time on free days (MSF) was used as an indicator of chronotype. Hemoglobin A1C (HbA_1C) values were obtained from medical records. Hierarchical linear regression analyses controlling for demographic, sleep, and dietary variables were computed to determine whether breakfast skipping was associated with HbA_1C. Additional regression analyses were performed to test if this association was mediated by chronotype. There were 22 participants (11.3%) who self-reported missing breakfast. Breakfast skippers had significantly higher HbA_1C levels, higher body mass indices (BMI), and later MSF than breakfast eaters. Breakfast skipping was significantly associated with higher HbA_1C values (B?=?0.108, p?=?0.01), even after adjusting for age, sex, race, BMI, number of diabetes complications, insulin use, depressive symptoms, perceived sleep debt, and percentage of daily caloric intake at dinner. The relationship between breakfast skipping and HbA_1C was partially mediated by chronotype. In summary, breakfast skipping is associated with a later chronotype. Later chronotype and breakfast skipping both contribute to poorer glycemic control, as indicated by higher HbA_1C levels. Future studies are needed to confirm these findings and determine whether behavioral interventions targeting breakfast eating or sleep timing may improve glycemic control in patients with type 2 diabetes.     

By‐passing the nonsense mutation in the 4CV mouse model of muscular dystrophy by induced exon skipping

Background

Duchenne muscular dystrophy (DMD), a severe neuromuscular disorder, is caused by protein‐truncating mutations in the dystrophin gene. Absence of functional dystrophin renders muscle fibres more vulnerable to damage and necrosis. We report antisense oligomer (AO) induced exon skipping in the B6Ros.Cg‐Dmd^mdx–4Cv/J (4^CV) mouse, a muscular dystrophy model arising from a nonsense mutation in dystrophin exon 53. Both exons 52 and 53 must be excised to remove the mutation and maintain the reading frame.

Methods

A series of 2′‐O‐methyl modified oligomers on a phosphorothioate backbone (2OMeAOs) were designed and evaluated for the removal of each exon, and the most effective compounds were then combined to induce dual exon skipping in both myoblast cultures and in vivo. Exon skipping efficiency of 2OMeAOs and phosphorodiamidate morpholino oligomers (PMOs) was evaluated both in vitro and in vivo at the RNA and protein levels.

Results

Compared to the original mdx mouse studies, induction of exon skipping from the 4^CV dystrophin mRNA was far more challenging. PMO cocktails could restore synthesis of near‐full length dystrophin protein in cultured 4^CV myogenic cells and in vivo, after a single intramuscular injection.

Conclusions

By‐passing the protein‐truncating mutation in the 4^CV mouse model of muscular dystrophy could not be achieved with single oligomers targeting both exons and was only achieved after the application of AO cocktails to remove exons 52 and 53. As in previous studies, the stability and efficiency of PMOs proved superior to 2OMeAOs for consistent and sustained protein induction in vivo. Copyright © 2008 John Wiley & Sons, Ltd.     

基于第三代长读段测序数据解析蜜蜂球囊菌基因的可变剪切与可变腺苷酸化

[目的]蜜蜂球囊菌(Ascosphaeraapis,简称球囊菌)是一种专性侵染蜜蜂幼虫的真菌病原,导致的白垩病是严重影响养蜂生产的顽疾,每年给养蜂业造成较大损失.本研究旨在基于已获得的第三代长读段测序数据对球囊菌菌丝(Aam)和孢子(Aas)中基因的可变剪切(alternative splicing,AS)和可变多聚腺...     

Aberrant splicing in MLH1 and MSH2 due to exonic and intronic variants

Single base substitutions in DNA mismatch repair genes which are predicted to lead either to missense or silent mutations, or to intronic variants outside the highly conserved splicing region are often found in hereditary nonpolyposis colorectal cancer (HNPCC) families. In order to use the variants for predictive testing in persons at risk, their pathogenicity has to be evaluated. There is growing evidence that some substitutions have a detrimental influence on splicing. We examined 19 unclassified variants (UVs) detected in MSH2 or MLH1 genes in patients suspected of HNPCC for expression at RNA level. We demonstrate that 10 of the 19 UVs analyzed affect splicing. For example, the substitution MLH1,c.2103G>C in the last position of exon 18 does not result in a missense mutation as theoretically predicted (p.Gln701His), but leads to a complete loss of exon 18. The substitution MLH1,c.1038G>C (predicted effect p.Gln346His) leads to complete inactivation of the mutant allele by skipping of exons 10 and 11, and by activation of a cryptic intronic splice site. Similarly, the intronic variant MLH1,c.306+2dupT results in loss of exon 3 and a frameshift mutation due to a new splice donor site 5 bp upstream. Furthermore, we confirmed complete exon skipping for the mutations MLH1,c.1731G>A and MLH1,c.677G>A. Partial exon skipping was demonstrated for the mutations MSH2,c.1275A>G, MLH1,c.588+5G>A, MLH1,c.790+4A>G and MLH1,c.1984A>C. In contrast, five missense mutations (MSH2,c.4G>A, MSH2,c.2123T>A, MLH1,c.464T>G, MLH1,c.875T>C and MLH1,c.2210A>T) were found in similar proportions in the mRNA as in the genomic DNA. We conclude that the mRNA examination should precede functional tests at protein level. Databases: HNPCC – OMIM 114500, MSH2 – OMIM: 120435; GenBank: NM_000251.1, MLH1 – OMIM: 120436; GenBank: NM_000249.2, InSiGHT mutation database: , Programs: BDGP: , ESEfinder program:     

Post-encounter vulnerability of some rotifer prey types to predation by the copepod Acanthocyclops robustus

Prey characteristics affecting vulnerability of a number of rotifer species to the predator Acanthocyclops robustus were investigated. Body volume was the main feature affecting the probability of attack after encounter and, with the exception of Polyarthra major, capture after attack. The lorica provided protection against predation in some species and a skipping escape response reduced the likelihood of capture in Polyarthra major.     

Activation of cryptic splice sites is a frequent splicing defect mechanism caused by mutations in exon and intron sequences of the OPA1 gene

Mutations in OPA1 are the most frequent cause underlying autosomal dominant optic atrophy (adOA). Until now only few putative splicing mutations in the OPA1 gene have been investigated at the mRNA level and all these result in exon skipping. Here, we report the identification and cDNA analysis of four intronic and three exonic OPA1 gene mutations that cause a variety of splicing defects including activation of cryptic splice sites in either flanking exon or intron sequences, and a leaky splicing mutation. Our results show that cDNA analysis is of prime importance for the full evaluation of the effect of putative splicing mutations in the OPA1 gene.     

Reln,an Allele ofReelerIsolated from a Chlorambucil Screen, Is Due to an IAP Insertion with Exon Skipping

Thereeler Albany2mutation (Reln^rl-Alb2) in the mouse is an allele ofreelerisolated during a chlorambucil mutagenesis screen. Homozygous animals had drastically reduced concentrations ofreelinmRNA, in which an 85-nt exon was absent. At the genomic level, the mutation was shown to be due to an intracisternal A-particle insertion leading to exon skipping. This appears to be the first observation of retrotransposon insertion during chlorambucil mutagenesis.     

Skipping flights in Ypthima butterflies (Lepidoptera: Nymphalidae)

The skipping flight patterns of three species of Ypthima (Lepidoptera: Nymphalidae) were analyzed using high‐speed video recordings to clarify how wings move and how driving forces are produced. All three species showed a flight pattern that includes a pause that accounts for about 50% of a flap cycle when their wings completely close after each upstroke. The observed pause causes the “skipping” flight trajectory based on the clap–fling mechanism. Pause duration was correlated with upstroke wing motion, suggesting the contribution of the latter to a long pause duration. This is also supported by the temporal relationship between the wing and body motions. The aerodynamic power necessary for the pause flight was calculated for the three species.     

A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model

Exposure to specific doses of hypoxia can trigger endogenous neuroprotective and neuroplastic mechanisms of the central nervous system. These molecular mechanisms, together referred to as hypoxic preconditioning (HPC), remain poorly understood. In the present study, we applied RNA sequencing and bioinformatics analyses to study HPC in a whole-body HPC mouse model. The preconditioned (H4) and control (H0) groups showed 605 differentially expressed genes (DEGs), of which 263 were upregulated and 342 were downregulated. Gene Ontology enrichment analysis indicated that these DEGs were enriched in several biological processes, including metabolic stress and angiogenesis. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that the FOXO and Notch signaling pathways were involved in hypoxic tolerance and protection during HPC. Furthermore, 117 differential alternative splicing events (DASEs) were identified, with exon skipping being the dominant one (48.51%). Repeated exposure to systemic hypoxia promoted skipping of exon 7 in Edrf1 and exon 9 or 13 in Lrrc45. This study expands the understanding of the endogenous protective mechanisms of HPC and the DASEs that occur during HPC.

     

Relevance of chronotype for eating patterns in adolescents

During adolescence, a shift from morningness to eveningness occurs, yet school continues to start early in the morning. Hence, adolescents are at risk for social jetlag, i.e. a discrepancy between biological and social timing. It remains to be determined whether chronotype associates with daily and daytime-specific eating patterns during this potentially critical period. Therefore, the aim of the present study was to investigate whether chronotype is decisive for daily eating patterns [total energy intake (TEI, kcal), total macronutrient intake (% of TEI), eating occasion frequency (n/day), meal frequency (n/day), snack frequency (n/day), duration of nightly fasting], or daytime-specific eating patterns [morning (before 11 am) energy intake (% of TEI), morning macronutrient intake (% of morning energy intake), regular breakfast skipping (no morning energy intake at least on 2 of 3?days, yes/no), evening (after 6 pm) energy intake (% of TEI), evening macronutrient intake (% of evening energy intake), regular dinner skipping (no evening energy intake at least on 2 of 3?days, yes/no)] in German adolescents. Chronotype was assessed by use of the Munich Chronotype Questionnaire and is defined as the midpoint of sleep corrected for sleep-debt accumulated over the workweek (the later the midpoint of sleep, the later the chronotype). A total of 223 participants (10–18?years) provided 346 questionnaires and concurrent 3-day weighed dietary records. Associations between chronotype and eating patterns were analyzed cross-sectionally using multivariable linear and logistic mixed-effects regression models. Adolescents with earlier and later chronotypes did not differ in their daily eating patterns. With respect to daytime-specific eating patterns, 1?h delay in chronotype was associated with 4.0 (95% CI 2.5–6.6) greater odds of regular breakfast skipping (p < 0.0001). In addition, later chronotype was associated with higher evening energy intake (p = 0.0009). In conclusion, our data show that a later chronotype among adolescents is associated with a shift of food consumption toward later times of the day. Hence, adolescents’ eating patterns appear to follow their internal clock rather than socially determined schedules.     

结合三代测序与二代测序技术揭示蜜蜂球囊菌孢子转录组的复杂性

【目的】蜜蜂球囊菌(Ascosphaera apis)是一种专性侵染蜜蜂幼虫的致死性真菌病原。本研究旨在利用PacBio单分子实时(singlemoleculereal-time,SMRT)测序技术对蜜蜂球囊菌孢子(AaS)中基因的可变剪切(alternative splicing,AS)和可变多聚腺苷酸化(alternative polyadenylation,APA)以及长链非编码RNA (long non-coding RNA,lncRNA)进行鉴定和分析,进而揭示蜜蜂球囊菌孢子中转录组的复杂性。【方法】采用Suppa软件对蜜蜂球囊菌孢子中基因的AS事件进行鉴定。通过RT-PCR对不同类型的AS事件进行验证。采用TAPIS pipeline对蜜蜂球囊菌孢子基因的APA位点进行鉴定。利用MEME软件分析孢子全长转录本的poly(A)剪接位点上游50bp的序列特征并鉴定motif。联用CPC和CNCI软件和比对Swiss-prot数据库的方法预测lncRNA,取三者的交集作为高可信度的lncRNA集合。进一步比较lncRNA和mRNA的转录本长度,外显子数量与长度,内含子长度,GC含...     

Eveningness is associated with skipping breakfast and poor nutritional intake in Brazilian undergraduate students

Some studies have proposed that self-reported eveningness, which reflects the preference of performing activities in the evening, may harm nutritional health and influence the eating behavior and nutritional status of individuals. However, the relationship between these variables (eveningness and nutritional status) and the consumption of breakfast, which is currently considered a marker of health, has been insufficiently explored by studies. The aim of this study was to investigate, in undergraduate students, the association between diurnal preference, being overweight, and food consumption (with special focus on breakfast). The study included 721 undergraduate students from a Brazilian public university. Dietary intake was assessed by 24-hour food recall, and the usual time for breakfast was identified. Body weight, height, and waist circumference were measured by trained researchers. Diurnal preference was determined by the Horne and Ostberg questionnaire validated for the Brazilian population, and the participants were classified into three categories: evening (coefficient: 16–41), intermediate type (coefficient: 42–58) or morning type (coefficient: 59–86). The prevalence of skipping breakfast was higher among the evening types (p = 0.02), when compared with morning and intermediate types. A negative association between the diurnal preference coefficient and total caloric (coefficient ?0.25, p = 0.007, r² adjusted = 0.12), carbohydrate (coefficient ?0.19, p = ?0.04, r² adjusted = 0.04) and lipid intake (coefficient ?0.18, p = 0.04, r² adjusted = 0.05) was also found in the breakfast skippers but not in breakfast eaters. In other words, breakfast skippers with diurnal preference values indicative of eveningness consumed more calories, carbohydrates and fats. Evening types presented significant odds of skipping breakfast (OR = 1.7, CI = 1.1–2.9, p = 0.02) when compared with morning and intermediate chronotypes. We conclude that eveningness is associated with skipping breakfast and a higher consumption of calories, carbohydrates and fats in breakfast skippers. These eating behaviors may predispose these individuals to being overweight.