Cotranscriptional RNA processing and modification in plants

The activities of RNA polymerases shape the epigenetic landscape of genomes with profound consequences for genome integrity and gene expression. A fundamental event during the regulation of eukaryotic gene expression is the coordination between transcription and RNA processing. Most primary RNAs mature through various RNA processing and modification events to become fully functional. While pioneering results positioned RNA maturation steps after transcription ends, the coupling between the maturation of diverse RNA species and their transcription is becoming increasingly evident in plants. In this review, we discuss recent advances in our understanding of the crosstalk between RNA Polymerase II, IV, and V transcription and nascent RNA processing of both coding and noncoding RNAs.

LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering-associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand-specific RNA knockdown characterized FLAIL as a trans-acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA-DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL-mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.

Functional variation in the non-coding genome: molecular implications for food security

The growing world population, in combination with the anticipated effects of climate change, is pressuring food security. Plants display an impressive arsenal of cellular mechanisms conferring resilience to adverse environmental conditions, and humans rely on these mechanisms for stable food production. The elucidation of the molecular basis of the mechanisms used by plants to achieve resilience promises knowledge-based approaches to enhance food security. DNA sequence polymorphisms can reveal genomic regions that are linked to beneficial traits of plants. However, our ability to interpret how a given DNA sequence polymorphism confers a fitness advantage at the molecular level often remains poor. A key factor is that these polymorphisms largely localize to the enigmatic non-coding genome. Here, we review the functional impact of sequence variations in the non-coding genome on plant biology in the context of crop breeding and agricultural traits. We focus on examples of non-coding with particularly convincing functional support. Our survey combines findings that are consistent with the view that the non-coding genome contributes to cellular mechanisms assisting many plant traits. Understanding how DNA sequence polymorphisms in the non-coding genome shape plant traits at the molecular level offers a largely unexplored reservoir of solutions to address future challenges in plant growth and resilience.

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency

Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA and a divergent non-coding (DNC) transcript of unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. Using high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements, we identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC transcription. Nascent transcription profiling showed a genome-wide role of Hda1C in repression of DNC transcription. Live-cell imaging of transcription revealed that mutations in the Hda3 subunit increased the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC transcription regions, supporting DNC transcription repression by histone deacetylation. Our data support the interpretation that DNC transcription results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.

Maternal and direct dietary polyphenol supplementation affect growth, carcass and meat quality of sheep and goats

The beneficial effects of polyphenol intake such as improved nitrogen retention make them interesting feed supplements for ruminants. In contrast, dietary polyphenols may have adverse effects on the bioavailability of nutrients and palatability of the feed which might impair growth performance. The beneficial and adverse effects might differ between different ruminant species as well as between direct intake and intake of polyphenol metabolites via suckling when supplemented to lactating dams. This study investigated the effects of maternal and direct polyphenol supplementation via grape seed extract in sheep and goats on growth, slaughter performance, meat quality and fatty acid profile. The diet of lactating East Friesian Dairy sheep (n = 11) and Saanen goats (n = 9) and of their lambs (n = 16) and kids (n = 13), respectively, was supplemented either with grape seed extract (dams: 7.4% and offspring: 5.6%, P) or without (C). This resulted in four groups per species, namely maternalC/offspringC, maternalC/offspringP, maternalP/offspringC, and maternalP/offspringP. In lambs but not in goats, maternalP increased average daily gain and improved slaughter performance whereas offspringP had no effect. Maternal and offspring diet did not affect physicochemical meat quality in lambs, but direct intake of grape seed extract increased rancid aroma of burger patties. In goat kids, both maternal and offspring diets slightly affected meat colour. While groups of meat fatty acids (FAs) were not affected by diet in both species, maternalP in lambs as well as maternalP and offspringP in goat kids increased the meat n-6 to n-3 FA ratio compared to the respective control groups. In goat kid but not in lamb meat, direct intake of polyphenols affected the proportions of several rumen biohydrogenation intermediates. In conclusion, grape seed extract can be applied in both the maternal and offspring diets in sheep and goats while maintaining or even improving offspring growth performance and carcass quality. Only few species-specific effects of grape seed extract supplementation were observed, and additive effects were scarce. Larger studies are required to confirm the observed species-specific growth response to maternalP during lactation. The underlying reasons for this differential response need to be further evaluated.

Winter fields antisense RNAs to kick off flowering

This Outlook discusses the finding by Zhao et al. demonstrating that COOLAIR-mediated FLC silencing is induced by the first seasonal frost in the field, and this acts as a key molecular indicator during autumn for winter arrival.

FLOWERING LOCUS C (FLC), a MADS-box transcription factor, plays a major role in determining flowering time in Arabidopsis. In this issue of Genes & Development, Zhao and colleagues (pp. 888–898) elucidate the role of COOLAIR antisense noncoding RNAs in FLC regulation through field trials and laboratory experiments. COOLAIR-mediated FLC silencing is induced by the first seasonal frost in the field and thus acts as a key molecular indicator during autumn for winter arrival.

TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes

BACKGROUND

The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data.

RESULTS

We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: (i) full-length RNA-seq for detection of splicing patterns and (ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts. We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings and Saccharomyces cerevisiae cells as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the most commonly used community gene models, TAIR10 and Araport11 for A.thaliana and SacCer3 for S.cerevisiae. In particular, we identify multiple transient transcripts missing from the existing annotations. Our new annotations promise to improve the quality of A.thaliana and S.cerevisiae genome research.

CONCLUSIONS

Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region

mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5' UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes.

Dual sgRNA-based Targeted Deletion of Large Genomic Regions and Isolation of Heritable Cas9-free Mutants in Arabidopsis

CRISPR/Cas9 system directed by a gene-specific single guide RNA (sgRNA) is an effective tool for genome editing such as deletions of few bases in coding genes. However, targeted deletion of larger regions generate loss-of-function alleles that offer a straightforward starting point for functional dissections of genomic loci. We present an easy-to-use strategy including a fast cloning dual-sgRNA vector linked to efficient isolation of heritable Cas9-free genomic deletions to rapidly and cost-effectively generate a targeted heritable genome deletion. This step-by-step protocol includes gRNA design, cloning strategy and mutation detection for Arabidopsis and may be adapted for other plant species.

A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.

Organismal benefits of transcription speed control at gene boundaries

RNA polymerase II (RNAPII) transcription is crucial for gene expression. RNAPII density peaks at gene boundaries, associating these key regions for gene expression control with limited RNAPII movement. The connections between RNAPII transcription speed and gene regulation in multicellular organisms are poorly understood. Here, we directly modulate RNAPII transcription speed by point mutations in the second largest subunit of RNAPII in Arabidopsis thaliana. A RNAPII mutation predicted to decelerate transcription is inviable, while accelerating RNAPII transcription confers phenotypes resembling auto-immunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in read-through transcription. The accelerated transcription mutant NRPB2-Y732F exhibits increased association with 5' splice site (5'SS) intermediates and enhanced splicing efficiency. Our findings highlight potential advantages of RNAPII stalling through local reduction in transcription speed to optimize gene expression for the development of multicellular organisms.

Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions.

The function of most lncRNA is unknown. Here, the authors show that transcriptional read-through at the Arabidopsis SVALKA locus produces a cryptic lncRNA that overlaps with the neighboring cold-responsive CBF1 gene and limits CBF1 expression via an RNA polymerase II collision-based mechanism.

Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance

Most DNA in the genomes of higher organisms does not code for proteins. RNA Polymerase II (Pol II) transcribes non-coding DNA into long non-coding RNAs (lncRNAs), but biological roles of lncRNA are unclear. We find that mutations in the yeast lncRNA CUT60 result in poor growth. Defective termination of CUT60 transcription causes read-through transcription across the ATP16 gene promoter. Read-through transcription localizes chromatin signatures associated with Pol II elongation to the ATP16 promoter. The act of Pol II elongation across this promoter represses functional ATP16 expression by a Transcriptional Interference (TI) mechanism. Atp16p function in the mitochondrial ATP-synthase complex promotes mitochondrial DNA stability. ATP16 repression by TI through inefficient termination of CUT60 therefore triggers mitochondrial genome loss. Our results expand the functional and mechanistic implications of non-coding DNA in eukaryotes by highlighting termination of nuclear lncRNA transcription as mechanism to stabilize an organellar genome.

Fatty acid profile of ghee derived from two genotypes (cattle–yak vs yak) grazing different alpine Himalayan pasture sites

The fatty acid (FA) profile of ghee produced from milk of cattle–yak hybrids grazing five mountain pasture sites along a high-alpine transhumance route in Nepal was analysed. Pastures differed in altitude above sea level (2600–4500 m), time period of being grazed and phytochemical composition of the swards. Additionally, a comparison of ghee from purebred yak and hybrid was performed, with samples produced at two of the sites. Pasture site had a strong effect on almost all FAs. Proportions of oleic, linoleic and α-linolenic acid in ghee were smallest on the highest pasture at 4500 m where the largest condensed tannin concentrations in the forages were found. No systematic site effects were found for c9,t11 conjugated linoleic acid and total polyunsaturated FAs. Ghee produced from the hybrids’ milk was richer in major functional FAs such as α-linolenic and linoleic acid, while yak ghee contained more saturated FAs and eicosapentaenoic, docosapentaenoic and docosahexaenoic acids.

Effect of individual Ayurveda plants and mixtures thereof on in vitro ruminal fermentation, methane production and nutrient degradability

In order to identify new ways to mitigate methane emissions from ruminants, six medicinal plants, Achyranthes aspera, Azadirachta indica, Andrographis paniculata, Helicteres isora, Tinospora cordifolia and Piper longum, were evaluated in vitro with respect to ruminal fermentation and methanogenesis. A three-stage approach with n = 6 per treatment was applied. Two 24-h Hohenheim gas test experiments were performed by incubating the plants first as sole substrate and then added to a basal diet (10 g/kg diet DM). Finally, in a 10-day Rusitec experiment, A. paniculata, P. longum and T. cordifolia were supplemented individually and in all binary combinations to a basal diet (25 g/kg DM). Provided as sole substrate, all plants, except P. longum, decreased methane and carbon dioxide production (P < 0.05), and reduced the methane : short-chain fatty acid ratio (P < 0.05) in the Hohenheim gas test. In Rusitec, none of the individual supplements decreased methane production. The combination of A. paniculata with P. longum as a supplement was effective in mitigating the methane : carbon dioxide ratio and simultaneously maintaining feeding value. In conclusion, all medicinal plants incubated as sole substrate, except P. longum, possess anti-methanogenic properties, especially T. cordifolia, A. indica and H. isora. When supplemented at the levels investigated, they were mostly neutral with respect to rumen fermentation and nutrient digestion. Combining A. paniculata with P. longum mitigated methane without side effects on general ruminal fermentation. Further investigations, carried out in vivo, will demonstrate how useful this plant combination is in ruminant nutrition.

Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species

Non-coding transcripts originating from bidirectional promoters have been reported in a wide range of organisms. In yeast, these divergent transcripts can be subdivided into two classes. Some are designated Cryptic Unstable Transcripts (CUTs) because they are terminated by the Nrd1-Nab3-Sen1 pathway and then rapidly degraded by the nuclear exosome. This is the same processing pathway used by yeast snoRNAs. Whereas CUTs are only easily observed in cells lacking the Rrp6 or Rrp47 subunits of the nuclear exosome, Stable Uncharacterized Transcripts (SUTs) are present even in wild-type cells. Here we show that SUTs are partially susceptible to the nuclear exosome, but are primarily degraded by cytoplasmic 5' to 3' degradation and nonsense-mediated decay (NMD). Therefore, SUTs may be processed similarly to mRNAs. Surprisingly, both CUTs and SUTs were found to produce 3' extended species that were also subject to cytoplasmic degradation. The functions, if any, of these extended CUTs and SUTs are unknown, but their discovery suggests that yeasts generate transcripts reminiscent of long non-coding RNAs found in higher eukaryotes.

A chromatin-based mechanism for limiting divergent noncoding transcription

In addition to their annotated transcript, many eukaryotic mRNA promoters produce divergent noncoding transcripts. To define determinants of divergent promoter directionality, we used genomic replacement experiments. Sequences within noncoding transcripts specified their degradation pathways, and functional protein-coding transcripts could be produced in the divergent direction. To screen for mutants affecting the ratio of transcription in each direction, a bidirectional fluorescent protein reporter construct was introduced into the yeast nonessential gene deletion collection. We identified chromatin assembly as an important regulator of divergent transcription. Mutations in the CAF-I complex caused genome-wide derepression of nascent divergent noncoding transcription. In opposition to the CAF-I chromatin assembly pathway, H3K56 hyperacetylation, together with the nucleosome remodeler SWI/SNF, facilitated divergent transcription by promoting rapid nucleosome turnover. We propose that these chromatin-mediated effects control divergent transcription initiation, complementing downstream pathways linked to early termination and degradation of the noncoding RNAs.

Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription

Antisense transcription is widespread in many genomes; however, how much is functional is hotly debated. We are investigating functionality of a set of long noncoding antisense transcripts, collectively called COOLAIR, produced at Arabidopsis FLOWERING LOCUS C (FLC). COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either early or extends into the FLC promoter region. We now show that splicing of COOLAIR is functionally important. This was revealed through analysis of a hypomorphic mutation in the core spliceosome component PRP8. The prp8 mutation perturbs a cotranscriptional feedback mechanism linking COOLAIR processing to FLC gene body histone demethylation and reduced FLC transcription. The importance of COOLAIR splicing in this repression mechanism was confirmed by disrupting COOLAIR production and mutating the COOLAIR proximal splice acceptor site. Our findings suggest that altered splicing of a long noncoding transcript can quantitatively modulate gene expression through cotranscriptional coupling mechanisms.

Influence of experience on intake and feeding behavior of dairy sheep when offered forages from woody plants in a multiple-choice situation

A satisfactory intake of novel low-quality forages by ruminants may require previous experience with this feed. Therefore, this study tested in sheep whether experience with forages from woody plants had an influence on feed intake, feeding behavior, and nutrient supply when offered in a multiple-choice arrangement. Two sheep experiments were conducted, 1 in Syria (Mediterranean region; Exp. 1) and the other in Switzerland (Central Europe; Exp. 2), that investigated 5 and 6 woody test plants, respectively. In Exp. 1, the test plants were Artemisia herba-alba, Atriplex leucoclada, Haloxylon articulatum, Noaea mucronata, and Salsola vermiculata. In Exp. 2, Betula pendula, Castanea sativa, and Juglans regia were used in addition to A. leucoclada, H. articulatum, and S. vermiculata (the plants most consumed in Exp. 1). In each experiment, 12 lactating sheep (Awassi sheep in Exp. 1 and East Friesian Milk sheep in Exp. 2) were allocated to 2 groups ("experienced" and "naïve"). Experienced sheep subsequently were familiarized with each test plant during a learning period of binary choices (1 test plant vs. barley straw) for 4 h in the morning for 7 d each. The naïve group received only straw. During the rest of the day, a basal diet composed of barley straw (ad libitum) and concentrate was offered to both groups. For the 2 wk following the learning period, the sheep were subjected to feeding of the basal diet to avoid carryover effects of the last offered test plant. In the following multiple-choice period, both groups were allowed to select from all test plants during 4 h in the morning for 14 d. Forage intake after 4 and 24 h and feeding behavior during the first 30 min of the test feeding were assessed. Milk yield and composition were measured at the end of the multiple-choice period. Nutrient intake was calculated using feed intake measurements and compositional analyses. Only in Exp. 2, group differences (P < 0.05) were found on d 1 of the multiple-choice period. The experienced sheep consumed more total forage, straw, OM, NDF, ADF, and ADL (nutrients without concentrate). However, across the entire multiple-choice period, there were no differences (P ≥ 0.05) in forage and nutrient intake, feeding behavior, and milk yield and composition between the groups in both experiments. This suggests that sheep can quickly adapt to previously unknown woody feeds of varying origin and quality offered as dried supplements.

Evaluation of the use of a tablet computer with a high-resolution display for interpreting emergency CT scans

PURPOSE

Evaluation of the potential usability of an iPad 3 with a high-resolution display in CT emergency diagnosis compared to a 3 D PACS workstation.

MATERIALS AND METHODS

3 readers used a 5-point Likert scale to evaluate 40 CCT scans and 40 CTPA scans to determine the detectability of early signs of infarction in CCT or segmental and subsegmental pulmonary embolisms in CT angiography of the pulmonary arteries (CTPA) on the iPad 3 (Apple Inc., USA) using an application for image viewing (Visage Ease, Visage Imaging GmbH, Berlin) and on a 3 D PACS workstation (Visage 7.1, Visage Imaging, Berlin) using a certified monitor for image viewing. The results were compared using the Wilcoxon rank sum test, Spearman's correlation coefficient, and a kappa statistic.

RESULTS

There was no significant difference in the median evaluations for the readings of both the CCT scans and the CTPA scans on the iPad 3 and on the workstation (p > 0.05) for all three readers. The mean Spearman's correlation coefficient for CCT and CTPA was 0.46 (± 0.2) and 0.69 (± 0.16), respectively, for the comparison iPad/PACS, 0.41 (± 0.16) and 0.68 (± 0.06), respectively, for the interobserver agreement on the iPad, and 0.35 (± 0.05) and 0.68 (± 0.10), respectively, for the interobserver agreement on the PACS. Mean kappa values for CCT of 0.52 (± 0.17) for the comparison iPad/PACS and 0.33 (± 0.16) and 0.32 (± 0.16), respectively, for the interobserver agreement on the iPad and the PACS were achieved. For CTPA average kappa values of 0.67 (± 0.19) were calculated for the comparison iPad/PACS and 0.69 (± 0.08) and 0.60 (± 0.14), respectively, for the interobserver concordance on the iPad 3 and the PACS. All differences were not statistically significant (p > 0.05).

CONCLUSION

The variability of the interpretation of typical emergency scans on an iPad 3 with a high-resolution display and on a 3 D PACS workstation does not differ from the interobserver variability.

Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination

The essential helicase-like protein Sen1 mediates termination of RNA Polymerase II (Pol II) transcription at snoRNAs and other noncoding RNAs in yeast. A mutation in the Pol II subunit Rpb1 that increases the elongation rate increases read-through transcription at Sen1-mediated terminators. Termination and growth defects in sen1 mutant cells are partially suppressed by a slowly transcribing Pol II mutant and are exacerbated by a faster-transcribing Pol II mutant. Deletion of the nuclear exosome subunit Rrp6 allows visualization of noncoding RNA intermediates that are terminated but not yet processed. Sen1 mutants or faster-transcribing Pol II increase the average lengths of preprocessed snoRNA, CUT, and SUT transcripts, while slowed Pol II transcription produces shorter transcripts. These connections between transcription rate and Sen1 activity support a model whereby kinetic competition between elongating Pol II and Sen1 helicase establishes the temporal and spatial window for early Pol II termination.

Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing

Noncoding RNA is emerging as an important regulator of gene expression in many organisms. We are characterizing RNA-mediated chromatin silencing of the Arabidopsis major floral repressor gene, FLC. Through suppressor mutagenesis, we identify a requirement for CstF64 and CstF77, two conserved RNA 3'-end-processing factors, in FLC silencing. However, FLC sense transcript 3' processing is not affected in the mutants. Instead, CstF64 and CstF77 are required for 3' processing of FLC antisense transcripts. A specific RNA-binding protein directs their activity to a proximal antisense polyadenylation site. This targeted processing triggers localized histone demethylase activity and results in reduced FLC sense transcription. Targeted 3' processing of antisense transcripts may be a common mechanism triggering transcriptional silencing of the corresponding sense gene.