[Cross-Sectional Study of Nutritional Status and Dietary Nutrient Intake in Children with Duchenne Muscular Dystrophy (DMD) in China].

Objective: To investigate the dietary nutrient intake and the nutritional status of children with Duchenne muscular dystrophy (DMD), and to explore the correlation between them, so as to provide theoretical basis for the formulation of proper nutritional treatment for children with DMD. Methods: A total of 223 children aged 2 to 14 years who came to West China Second University Hospital, Sichuan University from July 2017 to April 2021, and who were diagnosed with DMD by genetic testing were enrolled as the subjects of the study. Dietary assessment was conducted with a 3-day 24-hour dietary recall, and serum vitamin D level was measured by chemiluminescence method. Results: Only 33.2% of the children with DMD were found to be of normal nutritional status. The incidences of stunted growth, underweight, overweight and obesity were 13.5%, 14.4%, 14.3% and 8.1%, respectively. Among the children with DMD, those with serum vitamin D deficiency and insufficiency accounted for 9.0% and 89.7%, respectively. According to the dietary recall of the children with MDM, the daily energy ratio of carbohydrate, protein and fat were (47.40±6.64)%, (14.46±2.22)%, and (38.17±5.30)%, respectively. The daily intake of dietary calcium and vitamin D were (433.32±164.39) mg per day and (155.73±89.30) IU per day, respectively. The ratio of daily protein intake to the estimated average requirement for protein ( P=0.003) and ratio of daily energy intake to the estimated energy requirement ( P=0.007) were lower in children with stunted growth than those of DMD children of normal nutritional status. Conclusion: The dietary structure of children with DMD is obviously not suited to their condition and nutritional deficiency coexists with overnutrition among them. Further research needs to be done for developing appropriate nutritional guidance programs and standardized nutritional management measures for children with DMD.

FoxO3 restricts liver regeneration by suppressing the proliferation of hepatocytes.

Upon injury, the liver is capable of substantial regeneration from the original tissue until an appropriate functional size. The underlying mechanisms controlling the liver regeneration processes are not well elucidated. Previous studies have proposed that the transcription factor FoxO3 is involved in various liver diseases, but its exact role in the regulation of liver regeneration remains largely unclear. To directly test the detailed role of FoxO3 in liver regeneration, both a constitutive Albumin-Cre driver line and adeno-associated virus serotype 8 (AAV8)-Tbg-Cre (AAV-Cre)-injected adult FoxO3fl/fl mice were subjected to 70% partial hepatectomy (PH). Our data demonstrate that FoxO3 deletion accelerates liver regeneration primarily by limiting polyploidization and promoting the proliferation of hepatocytes during liver regeneration. RNA-seq analysis indicates that FoxO3 deficiency greatly alters the expression of gene sets associated with cell proliferation and apoptosis during liver regeneration. Chromatin immunoprecipitation-PCR (ChIP-PCR) and luciferase reporter assays reveal that FoxO3 promotes the expression of Nox4 but suppresses the expression of Nr4a1 in hepatocytes. AAV8 virus-mediated overexpression of Nox4 and knockdown of Nr4a1 significantly suppressed hepatocyte proliferation and liver regeneration in FoxO3-deficient mice. We demonstrate that FoxO3 negatively controls hepatocyte proliferation through Nox4 upregulation and Nr4a1 downregulation, thereby ensuring appropriate functional regeneration of the liver. Our findings provide novel mechanistic insight into the therapeutic mechanisms of FoxO3 in liver damage and repair.

Case Report: Cystinosis in a Chinese Child With a Novel CTNS Pathogenic Variant.

Objective: To report a rare case of cystinosis with a novel CTNS pathogenic variant in the Chinese population. Methods: Retrospective analysis of the clinical manifestations, laboratory results, and gene detection data of a child with cystinosis. Results: A Chinese Zang ethnic girl could not stand or walk until 3 years old, with additional symptoms including a loss of appetite. Since then, the girl gradually exhibited "X" leg, double wrist joints, a bilateral ankle deformity, and rickets. At the age of 9 years, the girl was hospitalized. Laboratory testing showed that her blood phosphorus, blood calcium and blood potassium levels were significantly decreased. At the same time, the girl's urine glucose and urine protein were positive, although her fasting blood glucose, glycosylated hemoglobin, and 75 g glucose tolerance were not significantly abnormal. Further, blood gas analysis showed metabolic acidosis. These symptoms corresponded to Fanconi syndrome. Gene analysis showed that there was a homozygous pathogenic variant c.140 ≤ 5G > A (p.?) in the CTNS gene, which was a small variation in the intron region. To our knowledge, this is the first report of the rare variant. Conclusion: Attention should be paid to the differential diagnosis of cystinosis by gene analysis in children whose clinical manifestations include exercise dysplasia, renal damage, or multiple organ damage (including bone, thyroid, etc) and who cannot be firmly diagnosed for the time being.

Informal caregiver burden and influencing factors in gynaecological oncology patients hospitalized for chemotherapy: a cross-sectional study.

OBJECTIVE: To determine the level and influencing factors of informal caregiver burden in gynaecological oncology inpatients receiving chemotherapy. METHODS: This cross-sectional study enrolled gynaecological oncology patients and their informal caregivers between May 2018 and November 2018 and measured the caregivers' burden using the Caregiver Burden Inventory. The influencing factors were evaluated with univariate regression analysis and multivariate linear stepwise regression analysis. RESULTS: A total of 138 patients and their informal caregivers completed the questionnaire. The mean ± SD total informal caregiver burden score was 53.18 ± 10.97. The highest mean ± SD score was recorded in the dimension of time-dependent burden (14.28 ± 2.74), followed by developmental burden (13.65 ± 2.15), physical burden (10.52 ± 2.07), social burden (7.61 ± 2.58) and emotional burden (7.12 ± 1.43). Multivariate analysis showed that the informal caregiver's sex, relationship to the patient, daily duration of care, presence of chronic health problems and the duration of the patient's disease were factors influencing the level of caregiver burden. CONCLUSIONS: The informal caregivers of gynaecological cancer patients hospitalized for chemotherapy experience a moderate level of burden. Nursing measures should be considered to reduce informal caregiver burden and improve the quality of lives of both patients and their caregivers.

Forkhead box O3 protects the heart against paraquat-induced aging-associated phenotypes by upregulating the expression of antioxidant enzymes.

Paraquat (PQ) promotes cell senescence in brain tissue, which contributes to Parkinson's disease. Furthermore, PQ induces heart failure and oxidative damage, but it remains unknown whether and how PQ induces cardiac aging. Here, we demonstrate that PQ induces phenotypes associated with senescence of cardiomyocyte cell lines and results in cardiac aging-associated phenotypes including cardiac remodeling and dysfunction in vivo. Moreover, PQ inhibits the activation of Forkhead box O3 (FoxO3), an important longevity factor, both in vitro and in vivo. We found that PQ-induced senescence phenotypes, including proliferation inhibition, apoptosis, senescence-associated ß-galactosidase activity, and p16INK4a expression, were significantly enhanced by FoxO3 deficiency in cardiomyocytes. Notably, PQ-induced cardiac remolding, apoptosis, oxidative damage, and p16INK4a expression in hearts were exacerbated by FoxO3 deficiency. In addition, both in vitro deficiency and in vivo deficiency of FoxO3 greatly suppressed the activation of antioxidant enzymes including catalase (CAT) and superoxide dismutase 2 (SOD2) in the presence of PQ, which was accompanied by attenuation in cardiac function. The direct in vivo binding of FoxO3 to the promoters of the Cat and Sod2 genes in the heart was verified by chromatin immunoprecipitation (ChIP). Functionally, overexpression of Cat or Sod2 alleviated the PQ-induced senescence phenotypes in FoxO3-deficient cardiomyocyte cell lines. Overexpression of FoxO3 and CAT in hearts greatly suppressed the PQ-induced heart injury and phenotypes associated with aging. Collectively, these results suggest that FoxO3 protects the heart against an aging-associated decline in cardiac function in mice exposed to PQ, at least in part by upregulating the expression of antioxidant enzymes and suppressing oxidative stress.

[Effect of golden-hour body temperature bundle management on admission temperature and clinical outcome in preterm infants after birth].

OBJECTIVE: To study the effect of golden-hour body temperature bundle management strategy on admission temperature and clinical outcome in preterm infants with a gestational age of <34 weeks after birth. METHODS: The preterm infants who were born in the delivery room of the West China Second University Hospital of Sichuan University and admitted to the department of neonatology of this hospital within 1 hour after birth from December 2015 to June 2016 and from January to May, 2017 were enrolled. The 173 preterm infants who were admitted from January to May, 2017 were enrolled as the intervention group and were given golden-hour body temperature bundle management. The 164 preterm infants who were admitted from December 2015 to June 2016 were enrolled as the control group and were given conventional body temperature management. RESULTS: The intervention group had a significantly higher mean admission temperature than the control group (36.4±0.4°C vs 35.3±0.6°C; P<0.001). The incidence rate of hypothermia on admission in the intervention group was significantly lower than that in the control group (56.6% vs 97.6%; P<0.001). The intervention group had a significantly lower incidence rate of intracranial hemorrhage within one week after admission than the control group (15.0% vs 31.7%; P<0.05). CONCLUSIONS: Golden-hour body temperature bundle management for preterm infants within one hour after birth can reduce the incidence of hypothermia on admission and improve clinical outcome.

CRISPR/Cas9-mediated efficient and precise targeted integration of donor DNA harboring double cleavage sites in Xenopus tropicalis.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system has emerged as a powerful tool for knock-in of DNA fragments via donor plasmid and homology-independent DNA repair mechanism; however, conventional integration includes unnecessary plasmid backbone and may result in the unfaithful expression of the modified endogenous genes. Here, we report an efficient and precise CRISPR/Cas9-mediated integration strategy using a donor plasmid that harbors 2 of the same cleavage sites that flank the cassette at both sides. After the delivery of donor plasmid, together with Cas9 mRNA and guide RNA, into cells or fertilized eggs, concurrent cleavages at both sides of the exogenous cassette and the desired chromosomal site result in precise targeted integration without plasmid backbone. We successfully used this approach to precisely integrate the EGFP reporter gene into the myh6 locus or the GAPDH locus in Xenopus tropicalis or human cells, respectively. Furthermore, we demonstrate that replacing conventional terminators with the endogenous 3UTR of target genes in the cassette greatly improves the expression of reporter gene after integration. Our efficient and precise method will be useful for a variety of targeted genome modifications, not only in X. tropicalis, but also in mammalian cells, and can be readily adapted to many other organisms.-Mao, C.-Z., Zheng, L., Zhou, Y.-M., Wu, H.-Y., Xia, J.-B., Liang, C.-Q., Guo, X.-F., Peng, W.-T., Zhao, H., Cai, W.-B., Kim, S.-K., Park, K.-S., Cai, D.-Q., Qi, X.-F. CRISPR/Cas9-mediated efficient and precise targeted integration of donor DNA harboring double cleavage sites in Xenopus tropicalis.

CpG oligodeoxynucleotide preconditioning improves cardiac function after myocardial infarction via modulation of energy metabolism and angiogenesis.

Unmethylated CpG oligodeoxynucleotide (CpG-ODN), a Toll-like receptor 9 (TLR9) ligand, has been shown to protect against myocardial ischemia/reperfusion injury. However, the potential effects of CpG-ODN on myocardial infarction (MI) induced by persistent ischemia remains unclear. Here, we investigated whether and how CpG-ODN preconditioning protects against MI in mice. C57BL/6 mice were treated with CpG-ODN by i.p. injection 2 hr prior to MI induction, and cardiac function, and histology were analyzed 2 weeks after MI. Both 1826-CpG and KSK-CpG preconditioning significantly improved the left ventricular (LV) ejection fraction (LVEF) and LV fractional shortening (LVFS) when compared with non-CpG controls. Histological analysis further confirmed the cardioprotection of CpG-ODN preconditioning. In vitro studies further demonstrated that CpG-ODN preconditioning increases cardiomyocyte survival under hypoxic/ischemic conditions by enhancing stress tolerance through TLR9-mediated inhibition of the SERCA2/ATP and activation of AMPK pathways. Moreover, CpG-ODN preconditioning significantly increased angiogenesis in the infarcted myocardium compared with non-CpG. However, persistent TLR9 activation mediated by lentiviral infection failed to improve cardiac function after MI. Although CpG-ODN preconditioning increased angiogenesis in vitro, both the persistent stimulation of CpG-ODN and stable overexpression of TLR9 suppressed the tube formation of cardiac microvascular endothelial cells. CpG-ODN preconditioning significantly protects cardiac function against MI by suppressing the energy metabolism of cardiomyocytes and promoting angiogenesis. Our data also indicate that CpG-ODN preconditioning may be useful in MI therapy.

[A Survey and Analysis of Exercise Among Pregnant Women Conducted Using the Theory of Reasoned Action].

BACKGROUND: Prior research has highlighted the significant relationship between gestational weight gain and pregnancy outcomes. Exercise is one of the main factors that affects body weight. Therefore, exercising appropriately during pregnancy is an important activity for promoting healthy pregnancy outcomes. PURPOSE: To explore the status and features of maternal exercise during pregnancy and to analyze the related influence factors using the "theory of reasoned action" in order to provide evidence-based guidance on exercise during pregnancy. METHODS: Convenience sampling was used to recruit pregnant women from four hospitals of different administrative levels in Chengdu, China. A self-developed questionnaire was used to collect data. Data were input using Epidata and analyzed using SPSS 21.0. RESULTS: Data provided by 587 pregnant women in their first trimester, 522 in their second trimester, and 522 in their third trimester were used in analysis. Significant differences were found between the three groups in terms of housework loading and lifting. Further, participants in the third trimester were significantly more likely to exercise less than 3 times per week and less than 30 minutes per session than their first and second trimester peers (p < .001). Structural equation modeling identified that: behavior intention had a significant effect on level of physical activity; attitudes and norms affected behavior by affecting intention; monthly income and educational background affected behavior by influencing attitude; and educational background affected behavior by influencing perceived norms. CONCLUSIONS: The findings of the present study support that personal situation, the family, and social norms impact the behavior of women significantly more during pregnancy than before pregnancy.

[Risk Prediction of Feeding Intolerance in Preterm Infants].

OBJECTIVES: To identify risk factors associated with feeding intolerance (FI) in preterm infants. METHODS: Preterm infants treated in the neonatal unit of a hospital from August 2014 to January 2015 were recruited in this study. A clinical observation table was developed based on the reactive scope model. Data in relation to predictive homeostasis, reactive homeostasis, homeostatic overload, homeostatic failure and other aspects were collected and compared between those with and without FI.Alogistic regression model was established to determine predictors of FI. RESULTS: 1.A total of 207 preterm infants were included in the study: 125 male and 82 female. They had an average gestational age of (33.48±1.66) weeks (ranging from 27+2 to 37 weeks) and an average birth body mass of (2 019.55±334.38) g(ranging from 830 g to 3 120 g).2.The incidence of FI was 33.8%. FI in preterm infants often occurred during the period of being fed within 72 h.The main clinical manifestation of FI was gastric retentionin early-preterm infants and emesis in late-preterm infants.3.Gestational age, birth body mass, fetal distress, aminophylline application, intrauterine infection, breast milk feeding and interval between stools were associated with FI. Gestational age and birth body mass were found to be significant protectors of FI in the logistic regression model. FI declined with increased gestational age and birth body mass. Fetal distress, aminophylline application, and >3 d interval between stools were found to be significant risks of FI in the logistic regression model.4.The prediction model had a 92.73% forecast generation rate of return, with 97.14% sensitivity,88.32%specificity, and 91.30% accuracy. CONCLUSIONS: Low gestational age, low birth body mass, fetal distress,aminophylline application, and >3 d interval between stools are independent risk factors associate with FI. The prediction model can identify high risk cases of FI.

Complete normalization of hepatic G6PC deficiency in murine glycogen storage disease type Ia using gene therapy.

Glycogen storage disease type Ia (GSD-Ia) patients deficient in glucose-6-phosphatase-alpha (G6Pase-alpha or G6PC) manifest disturbed glucose homeostasis. We examined the efficacy of liver G6Pase-alpha delivery mediated by AAV-GPE, an adeno-associated virus (AAV) serotype 8 vector expressing human G6Pase-alpha directed by the human G6PC promoter/enhancer (GPE), and compared it to AAV-CBA, that directed murine G6Pase-alpha expression using a hybrid chicken beta-actin (CBA) promoter/cytomegalovirus (CMV) enhancer. The AAV-GPE directed hepatic G6Pase-alpha expression in the infused G6pc(-/-) mice declined 12-fold from age 2 to 6 weeks but stabilized at wild-type levels from age 6 to 24 weeks. In contrast, the expression directed by AAV-CBA declined 95-fold over 24 weeks, demonstrating that the GPE is more effective in directing persistent in vivo hepatic transgene expression. We further show that the rapid decline in transgene expression directed by AAV-CBA results from an inflammatory immune response elicited by the AAV-CBA vector. The AAV-GPE-treated G6pc(-/-) mice exhibit normal levels of blood glucose, blood metabolites, hepatic glycogen, and hepatic fat. Moreover, the mice maintained normal blood glucose levels even after 6 hours of fasting. The complete normalization of hepatic G6Pase-alpha deficiency by the G6PC promoter/enhancer holds promise for the future of gene therapy in human GSD-Ia patients.

Generation of mice with a conditional allele for G6pc.

Glucose-6-phosphatase-alpha (G6Pase-alpha or G6PC) catalyzes the hydrolysis of glucose-6-phosphate to glucose and is a key enzyme in interprandial glucose homeostasis. Mutations in the human G6PC gene, expressed primarily in the liver, kidney, and intestine, cause glycogen storage disease Type Ia (GSD-Ia), an autosomal recessive disorder characterized by a disturbed glucose homeostasis. For better understanding of the roles of G6Pase-alpha in different tissues and in pathological conditions, we have generated mice harboring a conditional null allele for G6pc by flanking Exon 3 of the G6pc gene with loxP sites. We confirmed the null phenotype by using the EIIa-Cre transgenic approach to generate mice lacking Exon 3 of the G6pc gene. The resulting homozygous Cre-recombined null mice manifest a phenotype mimicking G6Pase-alpha-deficient mice and human GSD-Ia patients. This G6pc conditional null allele will be valuable to examine the consequence of tissue-specific G6Pase-alpha deficiency and the mechanisms of long-term complications in GSD-Ia.

Identification and characterization of glnA promoter and its corresponding trans-regulatory protein GlnR in the rifamycin SV producing actinomycete, Amycolatopsis mediterranei U32.

The genetic requirements for the transcription of glnA, encoding the major glutamine synthetase in a rifamycin SV-producing Amycolatopsis mediterranei strain, U32, were investigated. Primer extension experiments showed that the promoter of U32 glnA (pglnA) was likely to have two transcription initiation sites: P(1) and P(2), located 157 and 45 nucleotides (nt) upstream of the translational start codon, respectively. Gel mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element located at 45 to 75 nt downstream of P1, or 38 to 68 nt upstream of P(2). The sequence of the cis-element displayed high similarity to the corresponding regions of pglnA from Streptomyces coelicolor and S. roseosporus. With xylE as a reporter gene, the expression levels of U32 pglnA and its deletion derivatives under different nitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in S. lividans TK54, S. coelicolor J508 and S. coelicolor FS10 (glnR mutant). These in vivo studies showed that the activation of U32 pglnA in S. coelicolor required GlnR, and its binding to the U32 pglnA was further confirmed by the gel mobility shift assay. Cloning and heterologous expression of the U32 glnR allowed us to detect the in vitro interaction between the U32 GlnR and the corresponding pglnA cis-element. Further evidence shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for the active transcription of glnA in U32.

Bacterial type I glutamine synthetase of the rifamycin SV producing actinomycete, Amycolatopsis mediterranei U32, is the only enzyme responsible for glutamine synthesis under physiological conditions.

The structural gene for glutamine synthetase, glnA, from Amycolatopsis mediterranei U32 was cloned via screening a genomic library using the analog gene from Streptomyces coelicolor. The clone was functionally verified by complementing for glutamine requirement of an Escherichia coli glnA null mutant under the control of a lac promoter. Sequence analysis showed an open reading frame encoding a protein of 466 amino acid residues. The deduced amino acid sequence bears significant homologies to other bacterial type I glutamine synthetases, specifically, 71% and 72% identical to the enzymes of S. coelicolor and Mycobacterium tuberculosis, respectively. Disruption of this glnA gene in A. mediterranei U32 led to glutamine auxotrophy with no detectable glutamine synthetase activity in vivo. In contrast, the cloned glnA gene can complement for both phenotypes in trans. It thus suggested that in A. mediterranei U32, the glnA gene encoding glutamine synthetase is uniquely responsible for in vivo glutamine synthesis under our laboratory defined physiological conditions.

Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction.

Esf2p is the Saccharomyces cerevisiae homolog of mouse ABT1, a protein previously identified as a putative partner of the TATA-element binding protein. However, large-scale studies have indicated that Esf2p is primarily localized to the nucleolus and that it physically associates with pre-rRNA processing factors. Here, we show that Esf2p-depleted cells are defective for pre-rRNA processing at the early nucleolar cleavage sites A0 through A2 and consequently are inhibited for 18S rRNA synthesis. Esf2p was stably associated with the 5' external transcribed spacer (ETS) and the box C+D snoRNA U3, as well as additional box C+D snoRNAs and proteins enriched within the small-subunit (SSU) processome/90S preribosomes. Esf2p colocalized on glycerol gradients with 90S preribosomes and slower migrating particles containing 5' ETS fragments. Strikingly, upon Esf2p depletion, chromatin spreads revealed that SSU processome assembly and compaction are inhibited and glycerol gradient analysis showed that U3 remains associated within 90S preribosomes. This suggests that in the absence of proper SSU processome assembly, early pre-rRNA processing is inhibited and U3 is not properly released from the 35S pre-rRNAs. The identification of ABT1 in a large-scale analysis of the human nucleolar proteome indicates that its role may also be conserved in mammals.

The functional landscape of mouse gene expression.

BACKGROUND: Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function. RESULTS: We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis. CONCLUSIONS: We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.

Exploration of essential gene functions via titratable promoter alleles.

Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and subjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.

ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.

We report that Esf1p (Ydr365cp), an essential, evolutionarily conserved nucleolar protein, is required for the biogenesis of 18S rRNA in Saccharomyces cerevisiae. Depletion of Esf1p resulted in delayed processing of 35S precursor and a striking loss of 18S rRNA. Esf1p physically associated with ribosomal proteins and proteins involved in 18S rRNA biogenesis. Consistent with its role in 18S rRNA biogenesis, Esf1p also physically associated with U3 and U14 snoRNAs, but did not appear to be a core component of the SSU processome. These data indicate that Esf1p plays a direct role in early pre-rRNA processing.

High-definition macromolecular composition of yeast RNA-processing complexes.

A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete sub-complexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery.

A panoramic view of yeast noncoding RNA processing.

Predictive analysis using publicly available yeast functional genomics and proteomics data suggests that many more proteins may be involved in biogenesis of ribonucleoproteins than are currently known. Using a microarray that monitors abundance and processing of noncoding RNAs, we analyzed 468 yeast strains carrying mutations in protein-coding genes, most of which have not previously been associated with RNA or RNP synthesis. Many strains mutated in uncharacterized genes displayed aberrant noncoding RNA profiles. Ten factors involved in noncoding RNA biogenesis were verified by further experimentation, including a protein required for 20S pre-rRNA processing (Tsr2p), a protein associated with the nuclear exosome (Lrp1p), and a factor required for box C/D snoRNA accumulation (Bcd1p). These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA.