Spotlight on Plant Bromodomain Proteins

Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.

RNA silencing pathways in plant development and defense

RNA silencing refers to a conserved eukaryotic process and is regarded as one of the most important processes in plants, with the ability to regulate gene expression both transcriptionally and post-transcriptionally. Different classes of non-coding RNAs (ncRNAs) constitute key components of the RNA silencing pathways and play pivotal roles in modulating various biological processes as well as host-pathogen interactions. One of the most extensively studied classes of ncRNAs are the 20-24 nucleotide (nt) long microRNAs (miRNAs), which are core components of the endogenous gene silencing pathway. miRNAs act as negative regulators of endogenous gene expression through either mRNA-target cleavage, translational inhibition, or DNA methylation, and are inextricably linked to a plethora of developmental processes, such as leaf pattern formation as well as abiotic and biotic stress responses. In this review, we focus on the role of the RNA silencing pathways in the regulation of developmental processes as well as in the plant responses to biotic stress.

Screening for trisomy at 11-13 weeks' gestation: use of pregnancy-associated plasma protein-A, placental growth factor or both

OBJECTIVE

Serum pregnancy-associated plasma protein-A (PAPP-A) and placental growth factor (PlGF) at 11-13 weeks' gestation are reduced in pregnancies with fetal trisomy and in those that subsequently develop pre-eclampsia (PE). In screening for trisomy, the established biochemical marker is PAPP-A, whereas in screening for PE, the preferred marker is PlGF. The objective of this study was to examine the impact of replacing PAPP-A by PlGF in first-trimester screening for trisomies 21, 18 and 13 by maternal age, fetal nuchal translucency thickness (NT) and free β-human chorionic gonadotropin (β-hCG).

METHODS

This was a prospective screening study in singleton pregnancies for trisomies 21, 18 and 13 by a combination of maternal age, fetal NT and serum PAPP-A and free β-hCG at 11-13 weeks' gestation in which we also measured PlGF. Multiples of the median (MoM) values were calculated for PAPP-A, free β-hCG and PlGF. The dataset was split randomly into training and test datasets of roughly equal size, and the parameters for PlGF obtained from the training dataset were used in risk calculation for the test dataset. Standardized detection rates were computed by obtaining the likelihood ratios for biochemistry and fetal NT for trisomy-21, -18 and -13 pregnancies in the sample and then applying these to each year of maternal age from 12 to 50 to estimate the age-specific detection rates. These were then weighted according to the maternal age distributions of trisomy-21, -18 and -13 pregnancies in England and Wales in 2018. Similarly, standardized false-positive rates (FPR) were computed by obtaining the likelihood ratios for biochemistry and NT, as appropriate, in normal pregnancies in the sample and then applying these to each year of maternal age from 12 to 50 to estimate the age-specific FPRs. A modeling approach was used to assess the performance of screening according to gestational age at biochemical testing.

RESULTS

The study population of 71 266 pregnancies included 70 858 (99.4%) with normal fetal karyotype or birth of a phenotypically normal neonate and 263 with trisomy 21, 109 with trisomy 18 and 36 with trisomy 13. There are five main findings of this study. First, the performance of screening for trisomy by the first-trimester combined test or the combined test in which PAPP-A is replaced by PlGF is substantially better at 11 than at 13 weeks' gestation; for example, the detection rates of trisomy 21 by the combined test were 94%, 90% and 84%, at 5% FPR, when testing was carried out at 11, 12 and 13 weeks, respectively, and the corresponding values in screening by a test in which PAPP-A is replaced by PlGF were 90%, 87% and 86%, respectively. Second, in trisomy-21 pregnancies, the deviation of median PAPP-A MoM from normal decreases with increasing gestational age, whereas the deviation in PlGF does not change with gestational age. Third, the performance of screening for trisomy 21 during the 11^th and 12^th gestational weeks is superior if screening includes PAPP-A rather than PlGF, whereas during the 13^th week the performance is slightly higher with the use of PlGF rather than PAPP-A. Fourth, in our population with mean gestational age at testing of 12.7 weeks, screening by maternal age, fetal NT, serum free β-hCG and serum PAPP-A predicted 88%, 96% and 97% of cases of fetal trisomies 21, 18 and 13, respectively, at a FPR of 5%; the respective values in screening by a test in which PAPP-A is replaced by PlGF were 85%, 96% and 96%. Fifth, addition of serum PlGF does not improve the prediction of trisomy provided by maternal age, fetal NT and serum free β-hCG and PAPP-A.

CONCLUSION

In first-trimester screening for trisomy, the preferred biochemical marker is PAPP-A rather than PlGF, especially when biochemical testing is carried out during the 11^th week of gestation or earlier. However, if PlGF was to be used rather than PAPP-A, the same detection rate can be achieved but at a higher FPR. This may be an acceptable compromise to minimize cost and achieve effective screening for both trisomy and PE. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

Viral Detection: Past, Present, and Future

Viruses are essentially composed of a nucleic acid (segmented or not, DNA, or RNA) and a protein coat. Despite their simplicity, these small pathogens are responsible for significant economic and humanitarian losses that have had dramatic consequences in the course of human history. Since their discovery, scientists have developed different strategies to efficiently detect viruses, using all possible viral features. Viruses shape, proteins, and nucleic acid are used in viral detection. In this review, the development of these techniques, especially for plant and mammalian viruses, their strengths and weaknesses as well as the latest cutting-edge technologies that may be playing important roles in the years to come are described.

DCL-suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology

RNA silencing is a universal mechanism involved in development, epigenetic modifications and responses to biotic and abiotic stresses. The major components of this mechanism are Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) proteins. Understanding the role of each component is of great scientific and agronomic importance. Plants, including Nicotiana benthamiana, an important plant model, usually possess four DCL proteins, each of which has a specific role, namely being responsible for the production of an exclusive small RNA population. Here, we used RNA interference (RNAi) technology to target DCL proteins and produced single and combinatorial mutants for DCL. We analysed the phenotype for each DCL knockdown plant, together with the small RNA profile, by next-generation sequencing (NGS). We also investigated transgene expression, as well as viral infections, and were able to show that DCL suppression results in distinct developmental defects, changes in small RNA populations, increases in transgene expression and, finally, higher susceptibility in certain RNA viruses. Therefore, these plants are excellent tools for the following: (i) to study the role of DCL enzymes; (ii) to overexpress proteins of interest; and (iii) to understand the complex relationship between the plant silencing mechanism and biotic or abiotic stresses.