BackgroundComputational analysis of cDNA sequences from multiple organisms suggests that a large portion of transcribed DNA does not code for a functional protein. In mammals, noncoding transcription is abundant, and often results in functional RNA molecules that do not appear to encode proteins. Many long noncoding RNAs (lncRNAs) appear to have epigenetic regulatory function in humans, including HOTAIR and XIST. While epigenetic gene regulation is clearly an essential mechanism in plants, relatively little is known about the presence or function of lncRNAs in plants.Methodology/Principal FindingsTo explore the connection between lncRNA and epigenetic regulation of gene expression in plants, a computational pipeline using the programming language Python has been developed and applied to maize full length cDNA sequences to identify, classify, and localize potential lncRNAs. The pipeline was used in parallel with an SVM tool for identifying ncRNAs to identify the maximal number of ncRNAs in the dataset. Although the available library of sequences was small and potentially biased toward protein coding transcripts, 15% of the sequences were predicted to be noncoding. Approximately 60% of these sequences appear to act as precursors for small RNA molecules and may function to regulate gene expression via a small RNA dependent mechanism. ncRNAs were predicted to originate from both genic and intergenic loci. Of the lncRNAs that originated from genic loci, ∼20% were antisense to the host gene loci.Conclusions/SignificanceConsistent with similar studies in other organisms, noncoding transcription appears to be widespread in the maize genome. Computational predictions indicate that maize lncRNAs may function to regulate expression of other genes through multiple RNA mediated mechanisms.

RNA-binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome-wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis. Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3’ untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co-localising RBPs on individual cargo mRNAs.

The nuclear mitotic apparatus (NuMA) protein is well conserved in vertebrates, and dynamically changes its subcellular localization from the interphase nucleus to the mitotic/meiotic spindle poles and the mitotic cell cortex. At these locations, NuMA acts as a key structural hub in nuclear formation, spindle assembly, and mitotic spindle positioning, respectively. To achieve its variable functions, NuMA interacts with multiple factors, including DNA, microtubules, the plasma membrane, importins, and cytoplasmic dynein. The binding of NuMA to dynein via its N-terminal domain drives spindle pole focusing and spindle positioning, while multiple interactions through its C-terminal region define its subcellular localizations and functions. In addition, NuMA can self-assemble into high-ordered structures which likely contribute to spindle positioning and nuclear formation. In this review, we summarize recent advances in NuMA’s domains, functions and regulations, with a focus on human NuMA, to understand how and why vertebrate NuMA participates in these functions in comparison with invertebrate NuMA-related proteins.

BackgroundCells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control.ResultsHere, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1.ConclusionsWe propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.

RNA‐binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome‐wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis. Using individual‐nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3′ untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co‐localising RBPs on individual cargo mRNAs.

The international effort to reduce the environmental impact of electricity generation, especially CO2-emissions requires considerations about alternative energy supply systems. An effective step towards low pollution power generation is the application of hydrogen as a possible alternative gas turbine fuel, if the hydrogen is produced by renewable energy sources, such as wind energy or biomass. The use of hydrogen and hydrogen rich gases as a fuel for industrial applications and power generation combined with the control of polluted emissions, especially NOx, is a major key driver in the design of future gas turbine combustors. The micromix combustion principle allows a secure and low NOx combustion of hydrogen and air and achieves a significant reduction of NOx-emissions. The combustion principle is based on cross-flow mixing of air and gaseous pure hydrogen and burns in multiple miniaturized diffusion-type flames. For the characterization of the jet in cross-flow mixing process, the momentum flux ratio is used. The paper presents an experimental analysis of the momentum flux ratio’s impact on flame anchoring and on the resultant formation of the NOx-emissions. Therefore several prototype test burner with different momentum flux ratios are tested under preheated atmospheric conditions. The investigation shows that the resultant positioning and anchoring of the micro flames highly influences the NOx-formation. Besides the experimental investigations, numerical simulations have been performed by the application of a commercial CFD code. The cold flow simulation results show the mixing of the air and hydrogen after the injection, in particular in the Counter Rotating Vortices (CRV). Furthermore, the hydrogen jet interacts also with another vortex system resulting from a wake flow area behind the combustor geometry. Furthermore, reacting flow simulations have been performed by the application of a Hybrid Eddy Break-Up (EBU) combustion model. The combustion pressure has been varied from atmospheric conditions up to a pressure of 16 bar. The experimental and numerical results highlight further potential of the micromix combustion principle for low NOx-combustion of hydrogen in industrial gas turbine applications.

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1Cells have evolved quality control mechanisms to ensure protein homeostasis by 2 detecting and degrading aberrant mRNAs and proteins. A common source of aberrant 3 mRNAs is premature polyadenylation, which can result in non-functional protein 4 products. Translating ribosomes encountering poly(A) sequences are terminally 5 stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide 6 via the ribosome-associated quality control (RQC). Here, we demonstrate that the 7 conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) 8 promotes ribosome stalling at poly(A) sequences during RQC. We show that MKRN1 9 is positioned upstream of A-rich stretches and poly(A) tails in mRNAs through an 10 interaction with the cytoplasmic poly(A)-binding protein (PABP). We uncover PABP, 11 ribosomal protein RPS10, and additional translational regulators as main ubiquitylation 12 substrates of MKRN1. Consequently, we propose that MKRN1 serves as a first line of 13 poly(A) recognition at the mRNA level to prevent production of erroneous proteins, thus 14 maintaining proteome integrity. 15 Keywords 16 MKRN1, ubiquitylation, RNA binding, ribosome-associated quality control, RQC, 17 poly(A), iCLIP, ubiquitin remnant profiling, translation 18 PABP-interacting motif 2 (PAM2 motif) in rat neurons (Miroci et al. 2012). 61 Nevertheless, the RNA binding specificity and functional role of MKRN1 in human cells 62 remained largely elusive. 63Here, we introduce MKRN1 as a novel factor in RQC. MKRN1 is recruited to A-rich 64 sequences in mRNAs in a PABP-dependent manner, where it acts as a first line of 65 defence against poly(A) translation. MKRN1 depletion abrogates ribosome stalling in 66 reporter assays, accompanied by reduced ubiquitylation of RQC-related proteins. We 67