Post-transcriptional and translational regulation of plant gene expression by transposons

Transposons are mobile DNA sequences that can move within the genome and integrate in new genomic locations. They are widespread in eukaryotes and prokaryotes and can influence gene expression when landing within or nearby a gene. Although transposon-induced regulation of gene expression at the transcriptional level has been extensively studied, there has been less focus on regulation at the post-transcriptional and translational levels. Recent studies in maize (Zea mays) and other plant species suggest that transposon insertions can affect RNA processing, RNA stability, protein translation and protein stability. We will describe the diverse mechanisms by which transposons can influence gene expression at the post-transcriptional and translational levels, and discuss the interactions between these mechanisms.

A novel active transposon creates allelic variation through altered translation rate to influence protein abundance

Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for 'B73 active transposable element hAT', creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

BACKGROUND

DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize.

RESULTS

We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs.

CONCLUSIONS

These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

Radial free forearm flap versus pectoralis major pedicled flap for reconstruction in patients with tongue cancer: Assessment of quality of life

Background

This study investigated the quality of life of Chinese patients with tongue cancer who had undergone immediate flap reconstruction surgery. In addition, we compared 2 groups of patients: those who had received radial forearm free flap (RFFF) surgery and others who had received pectoralis major myocutaneous flap (PMMF) surgery.

Material and Methods

Patients who received RFFF or PMMF reconstruction after primary tongue cancer treated with total and subtotal tongue resection were eligible for the current study. The patients’ demographic data, medical history, and quality of life scores (14-item Oral Health Impact Profile (OHIP-14) and the University of Washington Quality of Life (UW-QOL) questionnaires) were collected.

Results

A total of 41 of 63 questionnaires were returned (65.08%). There were significant differences between the 2 groups in the gender (p< .05). Patients reconstructed with RFFF performed better in the shoulder domains, in addition to worse appearance domains.

Conclusions

Using either RFFF or PMMF for reconstruction of defects after tongue cancer resection significantly influences a patient’s quality of life. Data from this study provide useful information for physicians and patients during their discussion of reconstruction modalities for tongue cancers.

Key words:Quality of life, radial forearm free flaps, pectoralis major myocutaneous flap, tongue cancer, oral function.

A meta-analysis of probiotics for preventing necrotizing enterocolitis in preterm neonates

Necrotizing enterocolitis (NEC) is one of the most common acquired diseases of the gastrointestinal tract in preterm infants. Some randomized, controlled trials (RCTs) have indicated that probiotics may potentially lower the incidence of NEC and mortality. However, debate still remains about the safety of probiotics and their influence on normal infant growth. We performed this meta-analysis to assess the safety and benefits of probiotic supplementation in preterm infants. We searched in PubMed, Embase, and Cochrane databases for English references, and in Wanfang, VIP, and CNKI databases for Chinese references. Ultimately, 27 RCTs (including 9 Chinese articles) were incorporated into this meta-analysis. Relative risk (RR) and weighted mean difference (WMD) were calculated using a random-effects or fixed-effects model, depending on the data type and heterogeneity. A total of 6655 preterm infants, including the probiotic group (n=3298) and the placebo group (n=3357), were eligible for inclusion in this meta-analysis. For Bell stage ≥I and gestational age <37 weeks, risk of NEC incidence was significantly lower in the probiotic group [RR=0.35, 95% confidence interval (CI)=0.27-0.44, P<0.00001]. For Bell stage ≥II or gestational age <34 weeks, there were likewise significant differences between the probiotic and placebo groups concerning NEC incidence (RR=0.34, 95%CI=0.25-0.48, P<0.00001; and RR=0.39, 95%CI=0.27-0.56, P<0.00001). Risk of death was significantly reduced in the probiotic group (RR=0.58, 95%CI=0.46-0.75, P<0.0001). In contrast, there was no significant difference concerning the risk of sepsis (RR=0.94, 95%CI=0.83-1.06, P=0.31). With respect to weight gain and the age at which infants reached full feeds, no significant differences were found between the probiotic and placebo groups (WMD=1.07, 95%CI=−0.21-2.34, P=0.10; and WMD=−1.66, 95%CI=−3.6-0.27, P=0.09). This meta-analysis has shown that, regardless of gestational age and NEC stage, probiotic supplementation could significantly reduce the risk of NEC in preterm infants. Analysis also indicated that such supplementation did not increase the incidence risk of sepsis or of mortality. Finally, the study showed that probiotic supplementation may have no adverse effect on normal feeding and growth.

MicroRNA expression profiling studies on bronchopulmonary dysplasia: a systematic review and meta-analysis

Over the past several years, several microRNA (miRNA) expression profiling studies have been carried out on bronchopulmonary dysplasia (BPD) in mammalian lung tissues. The most effective way to identify these important miRNAs is to systematically search for similar signatures identified in multiple independent studies. Accordingly, a meta-analysis was conducted to review published miRNA expression profiling studies that compared miRNA expression profiles between BPD lung tissues and normal lung tissues. A vote-counting strategy that considered the total number of studies and time points reporting differential expression was applied. Furthermore, cut-off criteria of statistically significant differentially expressed miRNAs as defined by the author and their predicted target genes, if available, as well as the list of up- and down-regulated miRNA features, were collected and recorded. Results of the meta-analysis revealed that four up-regulated miRNAs (miRNA-21, miRNA-34a, miRNA-431, and Let-7f) and one down-regulated miRNA (miRNA-335) were differentially expressed in BPD lung tissues compared with normal groups. In addition, eight miRNAs (miRNA-146b, miRNA-29a, miRNA-503, miRNA-411, miRNA-214, miRNA-130b, miRNA-382, and miRNA-181a-1*) were found to show differential expression not only in the process of normal lung development, but also during the progress of BPD. Finally, several meaningful target genes (such as the HPGD and NTRK genes) of common miRNAs (such as miRNA-21 and miRNA-141) were systematically predicted. These specific miRNAs may provide clues of the potential mechanisms involved in BPD. Further mechanistic and external validation studies are needed to confirm the clinical significance of these miRNAs in the development of BPD.

Effect of neferine on liver ischemia-reperfusion injury in rats

INTRODUCTION

Liver ischemia/reperfusion leads to the formation of reactive oxygen species (ROS) that cause liver injury, a critical clinical problem during liver surgery and transplantation. The aim of the present study was to investigate the hepatoprotective and antioxidant effects of neferine against liver ischemia/reperfusion injury in rats.

MATERIALS AND METHODS

Wistar rats were randomly divided into 4 groups (n = 8): sham group; model group, and neferine high and low groups (50 and 25 mg/kg, respectively). After either saline or neferine was orally administered for 5 days rat livers were subjected to 30 minutes of ischemia followed by 6 hours of reperfusion. Aspartate aminotransferase (AST), alanine aminotransferase (ALT), and hydroxyl radical levels were measured in serum. The liver was removed to assay malondialdehyde (MDA) and carbonyl contents, superoxide dismutase (SOD), and glutathione peroxidase (GPx) activities, as well as to evaluate histopathologic changes.

RESULTS

Neferine significantly prevented AST and ALT elevations, reduced hydroxyl radical release, inhibited SOD and GPx activities, and decreased MDA and carbonyl contents. At the same time, neferine attenuated the histopathologic changes.

CONCLUSION

Neferine protected against liver ischemia/reperfusion in rats through antioxidant mechanisms. However, further studies are needed to verify whether the hepatoprotection of neferine is correlated with anti-inflammatory and anti-apoptotic effects.

Bimetallic chips for a surface plasmon resonance instrument

In this work we have replaced a commonly used Au film with an Au/Ag bimetallic film working as the sensing chip in the commercial surface plasmon resonance (SPR) instrument, Biacore 3000. The bimetallic chip gives out sharper SPR dip than that by the chip made of an Au film. The applicability and stability of the bimetallic chip on the Biacore 3000 are tested by real-time monitoring of biological coupling processes between sulfamethoxazole (SMX) and anti-SMX, which is useful in rapid detection of contaminations in food products. The bimetallic chip performs stably in 6 times' usage and regeneration. Our experiment is helpful to push the bimetallic film into real applications in commercial SPR instruments.