Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency.

Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription-based sequencing method, we study nuclear speckle-associated human transcripts. Our data indicate the existence of three gene groups whose transcripts demonstrate different speckle localization properties: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-messenger RNA stage, and not enriched.

Translational T-box riboswitches bind tRNA by modulating conformational flexibility.

T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box.

Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts.

Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation.

RNA molecules display distinctive organization at nuclear speckles.

RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles.

Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency.

Nuclear speckles, a type of membraneless nuclear organelle in higher eukaryotic cells, play a vital role in gene expression regulation. Using the reverse transcription-based RNA-binding protein binding sites sequencing (ARTR-seq) method, we study human transcripts associated with nuclear speckles. We identify three gene groups whose transcripts demonstrate different speckle localization properties and dynamics: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-mRNA stage, and not enriched in speckles.

KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions.

RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N-kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA-RNA interactions and higher-order RNA structures inside cells, independent of local protein binding to RNA.

Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing.

RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites.

Comparative genetic, biochemical, and biophysical analyses of the four ABCF paralogs support distinct functions related to mRNA translation.

Multiple paralogous ABCF ATPases are encoded in most genomes, but the physiological functions remain unknown for most of them. We herein compare the four K12 ABCFs - EttA, Uup, YbiT, and YheS - using assays previously employed to demonstrate EttA gates the first step of polypeptide elongation on the ribosome dependent on ATP/ADP ratio. A Δ knockout, like Δ , exhibits strongly reduced fitness when growth is restarted from long-term stationary phase, but neither Δ nor Δ exhibits this phenotype.

Entropic control of the free-energy landscape of an archetypal biomolecular machine.

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps.

Non-Destructive Detection of Soybean Pest Based on Hyperspectral Image and Attention-ResNet Meta-Learning Model.

Soybean plays an important role in food, medicine, and industry. The quality inspection of soybean is essential for soybean yield and the agricultural economy. However, soybean pest is an important factor that seriously affects soybean yield, among which leguminivora glycinivorella matsumura is the most frequent pest.

Deep learning modeling mA deposition reveals the importance of downstream cis-element sequences.

The N-methyladenosine (mA) modification is deposited to nascent transcripts on chromatin, but its site-specificity mechanism is mostly unknown. Here we model the mA deposition to pre-mRNA by iM6A (intelligent mA), a deep learning method, demonstrating that the site-specific mA methylation is primarily determined by the flanking nucleotide sequences. iM6A accurately models the mA deposition (AUROC = 0.

Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in .

Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence.

Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators.

Small RNAs (sRNAs) are important gene regulators in bacteria. Many sRNAs act post-transcriptionally by affecting translation and degradation of the target mRNAs upon base-pairing interactions. Here we present a general approach combining imaging and mathematical modeling to determine kinetic parameters at different levels of sRNA-mediated gene regulation that contribute to overall regulation efficacy.

K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.

Protein ubiquitination shows remarkable topological and functional diversity through the polymerization of ubiquitin via different linkages. Deciphering the cellular ubiquitin code is of central importance to understand the physiology of the cell. However, our understanding of its function is rather limited due to the lack of specific binders as tools to detect K29-linked polyubiquitin.

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics.

Mechanical expansion microscopy.

This chapter describes two mechanical expansion microscopy methods with accompanying step-by-step protocols. The first method, mechanically resolved expansion microscopy, uses non-uniform expansion of partially digested samples to provide the imaging contrast that resolves local mechanical properties. Examining bacterial cell wall with this method, we are able to distinguish bacterial species in mixed populations based on their distinct cell wall rigidity and detect cell wall damage caused by various physiological and chemical perturbations.

Deoxyribozyme-based method for absolute quantification of -methyladenosine fractions at specific sites of RNA.

-Methyladenosine (mA) is the most prevalent modified base in eukaryotic mRNA and long noncoding RNA. Although candidate sites for the mA modification are identified at the transcriptomic level, methods for site-specific quantification of absolute mA modification levels are still limited. Herein, we present a facile method implementing a deoxyribozyme, VMC10, which preferentially cleaves the unmodified RNA.

Application of Response Surface Methodology for Improving the Yield of 1,5-bis(ptoluenesulfonyl)- 3,7-Dihydroxyoctahydro-1,5-Diazocine.

Background: 3,3,7,7-tetrakis (difluoramino) octahydro-1,5-dinitro-1,5-diazocine (HNFX), as an important oxidizer in propellants, has received much attention due to its high density and energy. However, there are many difficulties that need to be solved, such as complex synthetic processes, low product yield, high cost of raw materials and complicated purification. In the synthesis of HNFX, the intermediate named 1,5-bis (p-toluenesulfonyl)-3,7-dihydroxyoctahydro-1, 5-diazocine (gem-diol), is difficult to synthesize.

An Improved Method for Bacterial Immunofluorescence Staining To Eliminate Antibody Exclusion from the Fixed Nucleoid.

Immunofluorescence (IF) is widely used to study the cellular localization and organization of proteins. However, steps such as fixation and permeabilization may affect cell morphology and/or introduce artifacts. For bacterial cells, commonly used permeabilization methods for IF include treatment with lysozyme.

Conducting Multiple Imaging Modes with One Fluorescence Microscope.

Fluorescence microscopy is a powerful tool to detect biological molecules in situ and monitor their dynamics and interactions in real-time. In addition to conventional epi-fluorescence microscopy, various imaging techniques have been developed to achieve specific experimental goals. Some of the widely used techniques include single-molecule fluorescence resonance energy transfer (smFRET), which can report conformational changes and molecular interactions with angstrom resolution, and single-molecule detection-based super-resolution (SR) imaging, which can enhance the spatial resolution approximately ten to twentyfold compared to diffraction-limited microscopy.