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This Voices piece will highlight the impact of artificial intelligence on algorithm development among computational biologists. How has worldwide focus on AI changed the path of research in computational biology? What is the impact on the algorithmic biology research community?
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Algoritmos , Inteligencia Artificial , Biología Computacional , Inteligencia Artificial/tendencias , Biología Computacional/métodos , HumanosRESUMEN
Computational methods are desired for single-cell-resolution spatial transcriptomics (ST) data analysis to uncover spatial organization principles for how individual cells exert tissue-specific functions. Here, we present ST data analysis via interaction-aware cell embedding (SPACE), a deep-learning method for cell-type identification and tissue module discovery from single-cell-resolution ST data by learning a cell representation that captures its gene expression profile and interactions with its spatial neighbors. SPACE identified spatially informed cell subtypes defined by their special spatial distribution patterns and distinct proximal-interacting cell types. SPACE also automatically discovered "cell communities"-tissue modules with discernible boundaries and a uniform spatial distribution of constituent cell types. For each cell community, SPACE outputs a characteristic proximal cell-cell interaction network associated with physiological processes, which can be used to refine ligand-receptor-based intercellular signaling analyses. We envision that SPACE can be used in large-scale ST projects to understand how proximal cell-cell interactions contribute to emergent biological functions within cell communities. A record of this paper's transparent peer review process is included in the supplemental information.
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Comunicación Celular , Análisis de la Célula Individual , Transcriptoma , Análisis de la Célula Individual/métodos , Comunicación Celular/genética , Transcriptoma/genética , Humanos , Biología Computacional/métodos , Perfilación de la Expresión Génica/métodos , Animales , Aprendizaje ProfundoRESUMEN
Li-rich Mn-based layered oxides (LMLOs) are expected to be the most promising high-capacity cathodes for the next generation of lithium-ion batteries (LIBs). However, the poor cycling stability and kinetics performance of polycrystalline LMLOs restrict their practical applications due to the anisotropic lattice stress and crack propagation during cycling. Herein, B-doped micron-sized single-crystal Co-free LMLOs were obtained by molten-salt (LiNO3 and H3BO3)-assisted sintering. The results reveal that the low-melting-point molten salt can serve as liquid-phase media to improve the efficiency of atomic mass transfer and crystal nucleation and growth. The modified single-crystal LMLO cathodes can resist the accumulation of anisotropic stress and strain during the cycling and reduce interface side reactions, thus achieving excellent high-voltage stability and kinetics performance. The reversible specific capacity of the single crystals is 210.8 mAh g-1 at 1C with a voltage decay rate of 1.95 mV/cycle and up to 161.1 mAh g-1 at 10C with a capacity retention of 81.06% after 200 cycles.
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Influenza A virus (IAV) represents a constant public health threat. The single-stranded, segmented RNA genome of IAV is replicated in host cell nuclei as a series of 8 ribonucleoprotein complexes (vRNPs) with RNA structures known to exert essential function to support viral replication. Here, we investigate RNA secondary structures and RNA interactions networks of the IAV genome and construct an in vivo structure model for each of the 8 IAV genome segments. Our analyses reveal an overall in vivo and in virio resemblance of the IAV genome conformation but also wide disparities among long-range and intersegment interactions. Moreover, we identify a long-range RNA interaction that exerts an essential role in genome packaging. Disrupting this structure displays reduced infectivity, attenuating virus pathogenicity in mice. Our findings characterize the in vivo RNA structural landscape of the IAV genome and reveal viral RNA structures that can be targeted to develop antiviral interventions.
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Virus de la Influenza A , Gripe Humana , Animales , Ratones , Humanos , Replicación Viral , Genoma , ARN Viral/genética , Virus de la Influenza A/genética , Interacciones Huésped-Patógeno , Genoma Viral , Gripe Humana/genéticaRESUMEN
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5.
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Modelos Moleculares , Factores de Empalme de ARN , Empalmosomas , Humanos , Empalmosomas/metabolismo , Empalmosomas/química , Factores de Empalme de ARN/metabolismo , Factores de Empalme de ARN/química , Ribonucleoproteína Nuclear Pequeña U2/metabolismo , Ribonucleoproteína Nuclear Pequeña U2/química , Ribonucleoproteína Nuclear Pequeña U2/genética , Microscopía por Crioelectrón , Empalme del ARN , Precursores del ARN/metabolismo , Conformación de Ácido Nucleico , ARN Nuclear Pequeño/metabolismo , ARN Nuclear Pequeño/química , FosfoproteínasRESUMEN
This study aimed to investigate the effectiveness of cellulose nanocrystals (CNC) isolated from cotton in augmenting pectin (PEC)/konjac glucomannan (KGM) composite films containing clove essential oil (CEO) for food packaging application. The effects of CNC dosage on film properties were examined by analyzing the rheology of film-forming solutions and the mechanical, barrier, antimicrobial, and CEO-release properties of the films. Rheological and FTIR analysis revealed the enhanced interactions among the film components after CNC incorporation due to its high aspect ratio and abundant hydroxyl groups, which can also prevent CEO droplet aggregation, contributing to form a compact microstructure as confirmed by SEM and 3D surface topography observations. Consequently, the addition of CNC reinforced the polysaccharide matrix, increasing the tensile strength of the films and improving their barrier properties to water vapor. More importantly, antibacterial, controlled release and kinetic simulation experiments proved that the addition of CNC could further slow down the release rate of CEO, prolonging the antimicrobial properties of the films. PEC/KGM/CEO composite films with 15 wt% CNC was found to have relatively best comprehensive properties, which was also most effective in delaying deterioration of grape quality during the storage of 9 days at 25 °C.
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Antiinfecciosos , Mananos , Nanopartículas , Aceites Volátiles , Syzygium , Celulosa/química , Aceites Volátiles/farmacología , Aceite de Clavo/farmacología , Pectinas , Antiinfecciosos/farmacología , Nanopartículas/químicaRESUMEN
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.
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ARN Largo no Codificante , Humanos , Animales , Ratones , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Pez Cebra/genética , Genómica , GenomaRESUMEN
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
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Codón Iniciador , Conformación de Ácido Nucleico , ARN Bicatenario , ARN Mensajero , Humanos , Arabidopsis/genética , Arabidopsis/inmunología , Codón Iniciador/genética , Reconocimiento de Inmunidad Innata , Sistemas de Lectura Abierta/genética , Biosíntesis de Proteínas/genética , Biosíntesis de Proteínas/inmunología , Ribosomas/metabolismo , ARN Bicatenario/química , ARN Bicatenario/genética , ARN Bicatenario/metabolismo , ARN Mensajero/genética , Transcriptoma , ARN Helicasas DEAD-box/química , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/metabolismo , Aprendizaje ProfundoRESUMEN
Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determine the cryo-EM structures of eukaryotic R2 retrotransposon with ribosomal DNA target and regulatory RNAs. Combined with biochemical and sequencing analysis, we reveal two essential DNA regions, Drr and Dcr, required for recognition and cleavage. The association of 3' regulatory RNA with R2 protein accelerates the first-strand cleavage, blocks the second-strand cleavage, and initiates the reverse transcription starting from the 3'-tail. Removing 3' regulatory RNA by reverse transcription allows the association of 5' regulatory RNA and initiates the second-strand cleavage. Taken together, our work explains the DNA recognition and RNA supervised sequential retrotransposition mechanisms by R2 machinery, providing insights into the retrotransposon and application reprogramming.
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ARN , Retroelementos , ARN/metabolismo , División del ADN , ADN Polimerasa Dirigida por ARN/metabolismo , Transcripción ReversaRESUMEN
Fundamental to post-transcriptional regulation, the in vivo binding of RNA binding proteins (RBPs) on their RNA targets heavily depends on RNA structures. To date, most methods for RBP-RNA interaction prediction are based on RNA structures predicted from sequences, which do not consider the various intracellular environments and thus cannot predict cell type-specific RBP-RNA interactions. Here, we present a web server PrismNet that uses a deep learning tool to integrate in vivo RNA secondary structures measured by icSHAPE experiments with RBP binding site information from UV cross-linking and immunoprecipitation in the same cell lines to predict cell type-specific RBP-RNA interactions. Taking an RBP and an RNA region with sequential and structural information as input ('Sequence & Structure' mode), PrismNet outputs the binding probability of the RBP and this RNA region, together with a saliency map and a sequence-structure integrative motif. The web server is freely available at http://prismnetweb.zhanglab.net.
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Proteínas de Unión al ARN , ARN , ARN/química , Proteínas de Unión al ARN/metabolismo , Sitios de Unión , Regulación de la Expresión GénicaRESUMEN
Sperm contributes essential paternal factors, including the paternal genome, centrosome, and oocyte-activation signals, to sexual reproduction. However, it remains unresolved how sperm contributes its RNA molecules to regulate early embryonic development. Here, we show that the Caenorhabditis elegans paternal protein SPE-11 assembles into granules during meiotic divisions of spermatogenesis and later matures into a perinuclear structure where sperm RNAs localize. We reconstitute an SPE-11 liquid-phase scaffold in vitro and find that SPE-11 condensates incorporate the nematode RNA, which, in turn, promotes SPE-11 phase separation. Loss of SPE-11 does not affect sperm motility or fertilization but causes pleiotropic development defects in early embryos, and spe-11 mutant males reduce mRNA levels of genes crucial for an oocyte-to-embryo transition or embryonic development. These results reveal that SPE-11 undergoes phase separation and associates with sperm RNAs that are delivered to oocytes during fertilization, providing insights into how a paternal protein regulates early embryonic development.
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ARN , Semen , Animales , Masculino , ARN/genética , ARN/metabolismo , Motilidad Espermática , Espermatozoides/metabolismo , Espermatogénesis/genética , Caenorhabditis elegans/genética , Oocitos , FertilizaciónRESUMEN
The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the mechanical strength and functions of the membrane, leading to several different types of human diseases. Here, we report the cryo-EM structures of the native spectrin-actin junctional complex (from porcine erythrocytes), which is a specialized short F-actin acting as the central organizational unit of the membrane skeleton. While an α-/ß-adducin hetero-tetramer binds to the barbed end of F-actin as a flexible cap, tropomodulin and SH3BGRL2 together create an absolute cap at the pointed end. The junctional complex is strengthened by ring-like structures of dematin in the middle actin layers and by patterned periodic interactions with tropomyosin over its entire length. This work serves as a structural framework for understanding the assembly and dynamics of membrane skeleton and offers insights into mechanisms of various ubiquitous F-actin-binding factors in other F-actin systems.
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Citoesqueleto , Eritrocitos , Animales , Humanos , Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Citoesqueleto/metabolismo , Eritrocitos/citología , Eritrocitos/metabolismo , Espectrina/análisis , Espectrina/metabolismo , PorcinosRESUMEN
Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called "half maps". Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres, yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net.
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Aprendizaje Profundo , Microscopía por Crioelectrón/métodos , Modelos Moleculares , Algoritmos , Sustancias Macromoleculares , Conformación ProteicaRESUMEN
TRIM33 is a chromatin reader required for mammalian mesendoderm differentiation after activation of Nodal signaling, while its role in mESCs is still elusive. Here, we report that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML-NBs) specifically in mESCs, to mediate Nodal signaling-directed transcription of Lefty1/2. We show that TRIM33 puncta formation in mESCs depends on PML and on specific assembly of PML-NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs, with both PML protein and formation of mESCs-specific PML-NBs being required for TRIM33 recruitment to these loci, and PML-NBs directly associating with the Lefty1/2 loci. Finally, a TurboID proximity-labeling experiment confirmed that TRIM33 is highly enriched only in mESCs-specific PML-NBs. Thus, our study supports a model in which TRIM33 condensates regulate Nodal signaling-directed transcription in mESCs and shows that PML-NBs can recruit distinct sets of client proteins in a cell-context-dependent manner.
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Células Madre Embrionarias de Ratones , Cuerpos Nucleares de la Leucemia Promielocítica , Animales , Humanos , Proteína de la Leucemia Promielocítica/genética , Proteína de la Leucemia Promielocítica/metabolismo , Células Madre Embrionarias de Ratones/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Transducción de Señal , Núcleo Celular/metabolismo , Mamíferos , Factores de Transcripción/genéticaRESUMEN
A capacity to detect the binding profiles of RNA targets for an RNA-binding protein (RBP) under different cellular conditions is essential to understand the functions of the RBP in posttranscriptional regulation. However, the prediction of RBP binding sites in vivo remains challenging. Tools that predict RBP-RNA interactions using sequence and/or predicted structures cannot reflect the exact state of RNA in vivo. PrismNet, which uses both sequences and in vivo RNA structure information from probing experiments, can accurately predict RBP binding under different cellular conditions by deep learning, and can be applied for functional studies of RBPs. Here, we provide a detailed protocol showing how to train a PrismNet model of RBP-RNA interactions for an RBP, and how to apply the model for predictions of the RBP binding under different conditions.
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Proteínas de Unión al ARN , ARN , Sitios de Unión/genética , Regulación de la Expresión Génica , Unión Proteica , ARN/química , Proteínas de Unión al ARN/metabolismoRESUMEN
RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.
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Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) positively affect the initial control ratio of non-small cell lung cancer (NSCLC). Rapidly acquired resistance to EGFR-TKI is a major hurdle in successful treatment. However, the mechanisms that control the resistance of EGFR-TKI remain largely unknown. RNA structures have widespread and crucial functions in many biological regulations; however, the functions of RNA structures in regulating cancer drug resistance remain unclear. Here, the psoralen analysis of RNA interactions and structures (PARIS) method is used to establish the higher-order RNA structure maps of EGFR-TKI-resistant and -sensitive cells of NSCLC. Our results show that RNA structural regions are enriched in untranslated regions (UTRs) and correlate with translation efficiency (TE). Moreover, yrdC N6-threonylcarbamoyltransferase domain containing (YRDC) promotes resistance to EGFR-TKI. RNA structure formation in YRDC 3' UTR suppresses embryonic lethal abnormal vision-like 1 (ELAVL1) binding, leading to EGFR-TKI sensitivity by impairing YRDC translation. A potential cancer therapy strategy is provided using antisense oligonucleotide (ASO) to perturb the interaction between RNA and protein. Our study reveals an unprecedented mechanism through which the RNA structure switch modulates EGFR-TKI resistance by controlling YRDC mRNA translation in an ELAVL1-dependent manner.
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BACKGROUND: RNA G-quadruplexes (rG4s) are non-canonical structural motifs that have diverse functional and regulatory roles, for instance in transcription termination, alternative splicing, mRNA localization and stabilization, and translational process. We recently developed the RNA G-quadruplex structure sequencing (rG4-seq) technique and described rG4s in both eukaryotic and prokaryotic transcriptomes. However, rG4-seq suffers from a complicated gel purification step and limited PCR product yield, thus requiring a high amount of RNA input, which limits its applicability in more physiologically or clinically relevant studies often characterized by the limited availability of biological material and low RNA abundance. Here, we redesign and enhance the workflow of rG4-seq to address this issue. RESULTS: We developed rG4-seq 2.0 by introducing a new ssDNA adapter containing deoxyuridine during library preparation to enhance library quality with no gel purification step, less PCR amplification cycles and higher yield of PCR products. We demonstrate that rG4-seq 2.0 produces high-quality cDNA libraries that support reliable and reproducible rG4 identification at varying RNA inputs, including RNA mounts as low as 10 ng. rG4-seq 2.0 also improved the rG4-seq calling outcome and nucleotide bias in rG4 detection persistent in rG4-seq 1.0. We further provide in vitro mapping of rG4 in the HEK293T cell line, and recommendations for assessing RNA input and sequencing depth for individual rG4 studies based on transcript abundance. CONCLUSIONS: rG4-seq 2.0 can improve the identification and study of rG4s in low abundance transcripts, and our findings can provide insights to optimize cDNA library preparation in other related methods.
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G-Cuádruplex , Humanos , ARN/química , Transcriptoma , Células HEK293 , Análisis de Secuencia de ARN/métodosRESUMEN
Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., single-cell RNA sequencing, scRNA-seq, single-cell assay for transposase-accessible chromatin use sequencing, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX's advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build upon previous scientific insights.
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COVID-19 , Análisis de la Célula Individual , Animales , Humanos , Ratones , Cromatina , Análisis de Secuencia de ARN/métodos , Análisis de la Célula Individual/métodos , TransposasasRESUMEN
Beyond transferring genetic information, RNAs are molecules with diverse functions that include catalyzing biochemical reactions and regulating gene expression. Most of these activities depend on RNAs' specific structures. Therefore, accurately determining RNA structure is integral to advancing our understanding of RNA functions. Here, we summarize the state-of-the-art experimental and computational technologies developed to evaluate RNA secondary and tertiary structures. We also highlight how the rapid increase of experimental data facilitates the integrative modeling approaches for better resolving RNA structures. Finally, we provide our thoughts on the latest advances and challenges in RNA structure determination methods, as well as on future directions for both experimental approaches and artificial intelligence-based computational tools to model RNA structure. Ultimately, we hope the technological advances will deepen our understanding of RNA biology and facilitate RNA structure-based biomedical research such as designing specific RNA structures for therapeutics and deploying RNA-targeting small-molecule drugs.