Transcriptome analysis of long non-coding RNA associated with embryonic muscle development in chickens

1. Skeletal muscle is an important component of chicken carcass. In chickens, the number of muscle fibres is fixed during the embryonic period, and muscle development during the embryonic period determines the muscle development potential after hatching.2. Beijing-You (BY) and Cornish (CN) chickens show completely different growth rates and body types, and two breeds were used in this study to explore the role of lncRNAs in muscle development during different chicken embryonic periods. A systematic analysis of lncRNAs and mRNAs were conducted in the pectoral muscle tissues of BY and CN chickens at embryonic days 11 (ED11), 13 (ED13), 15 (ED15), 17 (ED17), and 1-day-old (D1) using RNA-seq. A total of 4,104 differentially expressed transcripts (DETs) were identified among the five stages, including 2,359 lncRNAs and 1,745 mRNAs.3. The number of DETs between the two breeds at ED17 (1,658 lncRNAs and 1,016 mRNAs) was much higher than the total number of DET at all the other stages (692 lncRNAs and 729 mRNAs), indicating that the two breeds show the largest difference in gene regulation at ED17.4. Correlation analysis was performed for all differentially expressed lncRNAs and mRNAs during the five periods. Forty-three, cis interaction pairs of lncRNA-mRNA related to chicken muscle development were predicted. The expression of four pairs was verified, and the results showed MSTRG.12395.2-FGFBP2 and MSTRG.18590.6-FMOD were significantly up-regulated in CN at ED11 compared to BY and might be important candidate genes for embryonic muscle development.

Regulation of CREB Functions by Phosphorylation and Sumoylation in Nervous and Visual Systems

CREB is an ubiquitous transcription factor regulating diverse cellular responses. Its phosphorylation at S133 is an essential event for its activation in both nervous and visual systems. The activated CREB is implicated in the regulation of development, protection, learning, memory and plasticity in the nerve system. Moreover, sumoylation, an important post-translational modification of protein, plays a key role in sustaining CREB activation in the rat hippocampus in order to enhance the long-term memory and other aspects. In the visual system, although the CREB activation by phosphorylation at S133 is similar to that as observed in the nervous system, the role of CREB sumoylation remains to be explored. This review will discuss the aspects of CREB functions and their regulation by phosphorylation and sumoylation in both systems.

Spectacles need and ownership among multiethnic students in rural China

OBJECTIVES

The aim of this study is to describe the prevalence and associated factors of spectacles need and ownership among multiethnic school students in rural China.

STUDY DESIGN

School-based cross-sectional study.

METHODS

This school-based eye study was conducted in Yunnan province located in Southwestern China. Questionnaires were filled out by children with the help of their parents concerning demographic characteristics, spectacles usage, and myopia-related lifestyle exposures. Spectacles need was defined as participants who had an uncorrected visual acuity (VA) of less than 6/12 but could be corrected to more than 6/12 in the better-seeing eye, with myopia of less than -0.5 diopters (D), hyperopia of more than +2.0 D, or astigmatism of more than 0.75 D in both eyes. Definition of spectacles ownership was based on spectacles wearing at school on the examination day.

RESULTS

Among the 7681 students aged 5-16 years participating in this study, 7166 (93.3% of the study participants) successfully completed VA tests and questionnaires. The rate of spectacles need among children with an uncorrected VA of 6/12 or worse in either eye was 68.3% (623/912). Among the students who needed spectacles, only 18.9% owned them. Multivariate analyses revealed that spectacles ownership was significantly associated with increasing age (odds ratio [OR]: 1.30; 95% confidence interval [CI]: 1.08-1.55), more time on reading and writing (OR = 1.66; 95% CI: 1.15-2.40), having myopic friend(s) (OR: 1.90; 95% CI: 1.01-3.56), self-awareness of myopia (OR: 6.67; 95% CI: 2.48-17.92), and poorer uncorrected VA (OR: 4.57; 95% CI: 2.78-7.52).

CONCLUSIONS

We observed a lower rate of spectacles ownership among rural children compared with those of similar ages in urban China. These findings may have important public health implications for China and other countries regarding vision-related health resources allocation.

Role of miR-29 as marker of risk of acute rejection after heart transplant

BACKGROUND

Circulating miRNAs are potential biomarkers of the pathogenesis of certain diseases and in monitoring therapeutic responses. We hypothesized that serum miR-29 can determine risk of acute cardiac allograft rejection.

METHODS

Peripheral vein blood was collected from 50 healthy volunteers and 506 patients during post-transplant surveillance. Serum cardiac troponin I (cTnI) and miR-29 was detected by ELISA and qRT-PCR assay respectively. Rejection risk was defined as International Society of Heart and Lung Transplant score from leukocyte infiltration of an endomyocardial biopsy. No evidence of rejection was defined as grade R0, mild as R1, moderate as 2R and severe as 3R. Specificity and sensitivity of miR-29 to discriminate rejection was determined by the area under the curve (AUC) of receiver operating characteristic curve analysis. Correlations between miR29 and rejection grade were compared.

RESULTS

Serum miR-29 was 100.8 ± 42.4 copies/μl in R0 groups (P = 0.164 versus controls), 537.5 ± 84.3 copies/μl in R1 groups (P = 0.024) and 1478.4 ± 198.7 copies/μl in the joint R2/R3 groups (P = 0.001). MiR-29 was 1963.5 ± 214.7 six months after transplantation, 1242.5 ± 103.8 after a year, 825.6 ± 58.2 after 2 years, 413.8 ± 61.9 after 3 years and 270.6 ± 34.6 ng/mL after 4 years (P < 0.001). The level of miR-29 correlated positively with cTnI, NT-proBNP, white blood cell counts, and negatively with lymphocyte counts (all P < 0.001). The AUC values (95% CI) for discriminating R0 and R1 was 0.81 (0.75-0.89), and was 0.79 (0.72-0.86) for R0 and R2/R3 (both P < 0.01).

CONCLUSION

miR-29 is a promising predictor of the risk of heart transplant rejection.

Quantitative Contribution of rs75017182 to Dihydropyrimidine Dehydrogenase mRNA Splicing and Enzyme Activity

Dihydropyrimidine dehydrogenase (DPD; DPYD gene) variants have emerged as reliable predictors of adverse toxicity to the chemotherapy agent 5-fluorouracil (5-FU). The intronic DPYD variant rs75017182 has been recently suggested to promote alternative splicing of DPYD. However, both the extent of alternative splicing and the true contribution of rs75017182 to DPD function remain unclear. In the present study we quantified alternative splicing and DPD enzyme activity in rs75017182 carriers utilizing healthy volunteer specimens from the Mayo Clinic Biobank. Although the alternatively spliced transcript was uniquely detected in rs75017182 carriers, canonically spliced DPYD levels were only reduced by 30% (P = 2.8 × 10^-6 ) relative to controls. Similarly, DPD enzyme function was reduced by 35% (P = 0.025). Carriers of the well-studied toxicity-associated variant rs67376798 displayed similar reductions in DPD activity (31% reduction). The modest effects on splicing and function suggest that rs75017182 may have clinical utility as a predictor of 5-FU toxicity similar to rs67376798.

Genetic polymorphisms for 19 autosomal STR loci of Chongqing Han ethnicity and phylogenetic structure exploration among 28 Chinese populations

The allele frequencies and forensic statistical parameters of 19 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D6S1043, Penta D, Penta E, and D12S391) included in the Goldeneye™ DNA ID system 20A kit were obtained in 671 Chinese Han individuals residing in Chongqing, Southwest China. All 19 STR loci were identified in agreement with the Hardy-Weinberg equilibrium. A total of 238 alleles were observed with corresponding allele frequencies that varied from 0.0007 to 0.5119. The combined power of discrimination and the combined probability of exclusion for 19 STR loci in the Chongqing Han population were 0.99999999999999999999998954 and 0.99999998387, respectively. The findings indicated that the 19 autosomal STR loci were highly polymorphic in the Chongqing Han population and can be used as a powerful tool in personal identification and parentage testing. Our genetic study enriched the Chinese local forensic reference database. Population comparisons and phylogenetic analyses revealed that genetic heterogeneity widely existed among the Chongqing Han, Xinjiang Uyghur, and Kazakh populations as well as demonstrated that genetic similarity was tightly associated with those of close geographic origin or of the same ethnic origin.

Molecular Cloning and Developmental Expression Patterns of the Striatin Gene Encoding A Member of the Regulatory Subunits for the Protein Serine/Threonine Phosphatase-2A in Fish

PURPOSE

The protein phosphatase-2A (PP-2A) is one of the most important serine/threonine phosphatases in eukaryotes. The holoenzyme of PP-2A consists of three subunits: a scaffold A subunit, a catalytic C subunit and a regulatory B subunit. While both A and C subunits are coded by two different genes, the B subunits exist in 26 or more isoforms which are encoded by at least 15 different genes. Previous studies have shown that besides regulating specific PP-2A activity, various B subunits may have other functions. To explore the possible roles of the regulatory subunits of PP-2A in vertebrate development, we have cloned the gene encoding goldfish striatin, a member of the B'" family regulatory subunits for PP-2A, and determined their tissue-specific and temporal expression patterns.

METHODS

The cDNA cloning was conducted with RT-PCR-based RACE. The mRNA expression levels for the goldfish striatin were analyzed with RT-PCR. The expression levels of the striatin protein from goldfish were determined with Western blot analysis. The semi-quantitation of the mRNA and protein expression levels was conducted with the software of U-scanning.

RESULTS

Our study revealed that the full length cDNA for striatin consists of 2965 bp coding for a deduced protein of 769 amino acids, which bears a very high level of amino acid sequence identity with the homolog protein from other species. The striatin mRNA is highly expressed in the kidney, to a less degree in brain, fin, muscle, liver, ovary and gill, and the lowest in testis and heart. Similar pattern of protein expression is detected in the above 9 tissues. During the development of goldfish, the striatin mRNA maintains a relatively high level at the 2-cell, multiple cell and blastula stages. Then, it drops down substantially at gastrula stage and fluctuates around this level in the next 8 different stages. At the protein level, the striatin maintained higher level from 2-cell to gastrula stages, then decreased at neurula and optic vesicle stages, and gradually increased again to peak at eye pigmentation stage, then slightly decreased in the next few stages of development.

CONCLUSIONS

Our results suggest that the striatin may play an important role in regulating goldfish development and adult tissue homeostasis. While the former function may or may not occur through PP- 2A functions, the later function appears to occur via PP-2A activity.

Contrast Functions of αA- and αB-Crystallins in Cancer Development

α-Crystallins, initially identified as the structural proteins of the ocular lens, belong to the small heat shock protein family. They play significant roles in maintaining the lens transparency and preventing protein aggregation. α-Crystallins exist in two isoforms: αA and αB, and they display differential tissue distribution. Their mutations are implicated in several human diseases including cardiac myopathies, neurodegenerative diseases, cataracts and various types of cancers. Increased αB expression was detected in retinoblastoma, breast cancer, glioblastoma, prostate and renal cell carcinomas, indicating its role in promoting tumor growth. A complex picture emerges for αA. Although earlier studies suggest that αA may promote cancer development, recent studies from our laboratory demonstrate that αA can act as a tumor suppressor inhibiting cell transformation and retarding cell migration through modulating MAP kinase activity. In this review, we summarize the recent progress about the functions of αA and αB in cancer development.

Novel Deleterious Dihydropyrimidine Dehydrogenase Variants May Contribute to 5-Fluorouracil Sensitivity in an East African Population

Clinical studies have identified specific genetic variants in dihydropyrimidine dehydrogenase (DPD; DPYD gene) as predictors of severe adverse toxicity to the commonly used chemotherapeutic 5-fluorouracil (5-FU); however, these studies have focused on European and European-American populations. Our laboratory recently demonstrated that additional variants in non-European haplotypes are predictive of 5-FU toxicity. The objective of this study was to identify potential risk variants in an understudied East African population relevant to our institution's catchment area. The DPYD protein-coding region was sequenced in 588 individuals of Somali or Kenyan ancestry living in central/southeast Minnesota. Twelve novel nonsynonymous variants were identified, seven of which significantly decreased DPD activity in vitro. The commonly reported toxicity-associated variants, *2A, D949V, and I560S, were not detected in any individuals. Overall, this study demonstrates a critical limitation in our knowledge of pharmacogenetic predictors of 5-FU toxicity, which has been based on clinical studies conducted in populations of limited diversity.

Visualizing retinoic acid morphogen gradients

Morphogens were originally defined as secreted signaling molecules that diffuse from local sources to form concentration gradients, which specify multiple cell fates. More recently morphogen gradients have been shown to incorporate a range of mechanisms including short-range signal activation, transcriptional/translational feedback, and temporal windows of target gene induction. Many critical cell-cell signals implicated in both embryonic development and disease, such as Wnt, fibroblast growth factor (Fgf), hedgehog (Hh), transforming growth factor beta (TGFb), and retinoic acid (RA), are thought to act as morphogens, but key information on signal propagation and ligand distribution has been lacking for most. The zebrafish provides unique advantages for genetics and imaging to address gradients during early embryonic stages when morphogens help establish major body axes. This has been particularly informative for RA, where RA response elements (RAREs) driving fluorescent reporters as well as Fluorescence Resonance Energy Transfer (FRET) reporters of receptor binding have provided evidence for gradients, as well as regulatory mechanisms that attenuate noise and enhance gradient robustness in vivo. Here we summarize available tools in zebrafish and discuss their utility for studying dynamic regulation of RA morphogen gradients, through combined experimental and computational approaches.

Regulation of Eye Development by Protein Serine/Threonine Phosphatases-1 and -2A

The protein serine/threonine phosphatases-1 and -2A are major cellular phosphatases, playing a fundamental role in organisms from prokaryotes to eukaryotes. They contribute to 90% dephosphorylation in eukaryote proteins. In the eye, both phosphatases are highly expressed and display important functions in regulating normal eye development. Moreover, they are implicated in pathogenesis through modulation of stress-induced apoptosis. Here we review the recent progresses on these aspects.

The transient expression of miR-203 and its inhibiting effects on skeletal muscle cell proliferation and differentiation

Previous studies have shown that miR-203 is a skin-specific microRNA (miRNA) with a profound role in skin cell differentiation. However, emerging microarray and deep sequencing data revealed that miR-203 is also expressed in embryonic skeletal muscle and myoblasts. In this study, we found that miR-203 was transiently upregulated in chicken embryos on days 10 to 16 (E10-E16) and was sharply downregulated and even not expressed after E16 in chicken embryonic skeletal muscle. Histological profiles and weight variations of embryo skeletal muscle revealed that miR-203 expression is correlated with muscle development. In vitro experiments showed that miR-203 exhibited downregulated expression during myoblast differentiation into myotubes. miR-203 overexpression inhibited myoblast proliferation and differentiation, whereas its loss-of-function increased myoblast proliferation and differentiation. During myogenesis, miR-203 can target and inhibit the expression of c-JUN and MEF2C, which were important for cell proliferation and muscle development, respectively. The overexpression of c-JUN significantly promoted myoblast proliferation. Conversely, knockdown of c-JUN by siRNA suppressed myoblast proliferation. In addition, the knockdown of MEF2C by siRNA significantly inhibited myoblast differentiation. Altogether, these data not only suggested that the expression of miR-203 is transitory during chicken skeletal muscle development but also showed a novel role of miR-203 in inhibiting skeletal muscle cell proliferation and differentiation by repressing c-JUN and MEF2C, respectively.

Variation in sequence and expression of the avian FTO, and association with glucose metabolism, body weight, fatness and body composition in chickens

OBJECTIVE

The fat mass and obesity-associated gene (FTO), a crucial gene that affects human obesity and metabolism, has been widely studied in mammals but remains poorly characterized in birds. We aimed to identify variant FTO transcripts in domestic avian species, and to characterize the expression and biological functions of FTO in chickens.

METHODS

Variant FTO transcripts and their expression in birds were investigated using RACE and real-time quantitative reverse transcriptase-PCR technology. The effects of FTO on glucose metabolism, growth and body composition were determined by fasting and various diet treatments, as well as association analysis in a F₂ resource population. The function of cFTO1 was further studied by overexpression in chick embryo fibroblast (CEF) cells.

RESULTS

Variant FTO transcripts were identified in chicken (cFTO1 to cFTO4), duck (dFTO1, dFTO2 and dFTO4) and goose (gFTO1, gFTO2 and gFTO5). In the chicken, the complete transcript (cFTO1) was predominantly expressed in the leg muscle, pituitary, hypothalamus and cerebellum. Fasting increased both cFTO1 and PGC1α gene expression in the cerebrum, liver, breast muscle and subcutaneous fat, but decreased expression in the pituitary and anterior hypothalamus. In all tested tissues in chickens, a high-glucose diet markedly increased cFTO1 and PGC1α expression. Feeding a high-fat diet increased both cFTO1 and PGC1α expression, except in the pituitary. Overexpression of cFTO1 in CEF cells significantly increased the expression of PGC1α (2.5-fold), STAT3 (2.2-fold) and HL (1.5-fold), a cluster of genes related to energy metabolism. A total of 65 single nucleotide polymorphisms (SNPs) were identified in chicken FTO, and 18 tested SNPs were significantly associated with traits of body weight, body composition and fatness.

CONCLUSIONS

These data collectively indicate that FTO is related to glucose metabolism, body weight, fatness and body composition in birds, thus expanding knowledge of FTO function to non-mammalian species.

Complementary deoxyribonucleic acid cloning of avian G0/G1 switch gene 2, and its expression and association with production traits in chicken

As a member of the G0/G1 switch genes, G0/G1 switch gene 2 (G0S2) is related to many regulatory processes in the human and mouse. For example, it interacts directly with adipose triglyceride lipase to active its triglyceride hydrolysis activities. In this study, G0S2 gene cDNA of the chicken (522 bp), zebra finch (420 bp), sparrow (417 bp), pigeon (417 bp), and Bengalese finch (416 bp) were cloned, and each of them was encoded as a protein of 99 amino acids. The expression of G0S2 mRNA was determined by real-time reverse-transcription PCR analysis in 20 tested tissues of 21- and 91-d-old chickens. The highest mRNA level was found in abdominal fat and subcutaneous fat in both stages. Considerable G0S2 mRNA was also observed in chicken heart and muscle tissues. Expression of the chicken G0S2 gene varied at different stages and sexes. The abundance of G0S2 mRNA on d 21 was far higher than that on d 91. The abundance in female chickens was higher than that in males at both stages. In the coding region, we found 4 SNP, among which only G197A led to a change in the amino acids (Arg66Gln); the rest were synonymous substitutions. Association analysis showed that both G102A and G255A were significantly associated with head width (P < 0.05) and were highly significantly associated with leg muscle color (P < 0.01). The G102A was significantly associated with shank diameter at 63 d (P < 0.05). The SNP G197A was significantly associated with shank diameter at 49 d; CP content of leg muscle; total weights of the heart, liver, gizzard, and glandular stomach; and small intestine length (P < 0.05). In conclusion, much higher G0S2 mRNA was detected in both male and female chickens at 21 d of age than at 91 d of age, and 3 SNP (G102A, G197, and G255A) were associated with chicken production traits.

Size-normalized Robustness of Dpp Gradient in Drosophila Wing Imaginal Disc

Exogenous environmental changes are known to affect the intrinsic characteristics of biological organizms. For instance, the synthesis rate of the morphogen decapentaplegic (Dpp) in a Drosophila wing imaginal disc has been found to double with an increase of 5.9°C in ambient temprerature. If not compensated, such a change would alter the signaling Dpp gradient significantly and thereby the development of thewing imaginal disc. To learn how flies continue to develop "normally" under such an exogenous change, we formulate in this paper a spatially two-dimensional reaction-diffusion system of partial differential equations (PDE) that accounts for the biological processes at work in the Drosophila wing disc essential for the formation of signaling Dpp gradient. By way of this PDE model, we investigate the effect of the apical-basal thickness and antero-posterior span of the wing on the shape of signaling gradients and the robustness of wing development in an altered environment (including an enhanced morphogen synthesis rate). Our principal result is a delineation of the role of wing disc size change in maintaining the magnitude and shape of the signaling Dpp gradient. The result provides a theoretical basis for the observed robustness of wing development, preserving relative but not absolute tissue pattern, when the morphogen synthesis rate is significantly altered. A similar robustness considerqation for simultaneous changes of multiple intrinsic system characteristics is also discussed briefly.

Effects of the thyroid hormone responsive spot 14alpha gene on chicken growth and fat traits

The thyroid hormone responsive spot 14alpha (THRSPalpha) gene plays important roles in chicken growth and fat deposition. The aim of this study was to identify new variations in the gene to determine their effects on growth and fat traits in chicken and to observe the effects of the THRSPalpha gene on chicken lipid profile and lipoprotein and glucose and triiodothyronine effects on the THRSPalpha expression in liver and fat cells. Two new variations, namely A197835978G and G197836086A, and a reported 9-bp insertion-deletion (indel) of the THRSPalpha gene were genotyped by single-stranded conformational polymorphism in a Xinghua x White Recessive Rock F(2) full-sib resource population. The results showed that the A197835978G was significantly associated with hatch weight and BW at 28 d of age and breast muscle weight at 90 d of age in chickens (P < 0.05). The G197836086A was significantly associated with cingular fat width (P = 0.0349) and breast muscle crude fat content (P = 0.0349). The indel was significantly associated with abdominal fat weight (P = 0.0445). The above new THRSPalpha polymorphisms were also significantly associated with the total cholesterol and low-density lipoprotein, in which the THRSPalpha GA/AG genotype was associated with lipid and lipoprotein and the THRSPalpha BB indel genotype was significantly associated with liver weight in chicken breeds. The mRNA expression analysis in vivo and in vitro culture studies suggested that the THRSPalpha gene is more responsive to glucose than triiodothyronine. In conclusion, the 3 variations of the chicken THRSPalpha gene were associated with both growth and fat traits in this study. Such effects of the THRSPalpha gene were further supported from the data of observations in association analysis of the gene with phenotypic records and plasma lipid profiles, in the THRSPalpha gene expression in chicken development, and in vivo and in vitro cell culture observation of liver and abdominal fat tissues.