Complex Regulation Research Articles

Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists

Hyperparasitism is a common pattern in nature that is not limited to cellular organisms. Giant viruses infecting protists can be hyperparasitized by smaller ones named virophages. In addition, both may carry episomal DNA molecules known as transpovirons in their particles. They all share transcriptional regulatory elements that dictate the expression of their genes within viral factories built by giant viruses in the host cytoplasm. This suggests the existence of interactions between their respective transcriptional networks. Here we investigated Acanthamoeba castellanii cells infected by a giant virus (megavirus chilensis), and coinfected with a virophage (zamilon vitis) and/or a transpoviron (megavirus vitis transpoviron). Infectious cycles were monitored through time-course RNA sequencing to decipher the transcriptional program of each partner and its impact on the gene expression of the others. We found highly diverse transcriptional responses. While the giant virus drastically reshaped the host cell transcriptome, the transpoviron had no effect on the gene expression of any of the players. In contrast, the virophage strongly modified the giant virus gene expression, albeit transiently, without altering the protein composition of mature viral particles. The virophage also induced the overexpression of transpoviron genes, likely through the indirect upregulation of giant virus-encoded transcription factors. Together, these analyses document the intricated transcriptionally regulated networks taking place in the infected cell.

Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits

As synthetic biology expands, creating “drag-and-drop” regulatory tools that can achieve diverse regulatory outcomes are paramount. Herein, we develop a approach for engineering complex post-transcriptional control by rewiring the Carbon Storage Regulatory (Csr) Network of Escherichia coli. We co-opt native interactions of the Csr Network to establish post-transcriptional logic gates and achieve complex bacterial regulation. First, we rationally engineer RNA-protein interactions to create a genetic toolbox of 12 BUFFER Gates that achieves a 15-fold range of expression. Subsequently, we develop a Csr-regulated NOT Gate by integrating a cognate 5’ UTR that is natively Csr-activated into our platform. We then deploy the BUFFER and NOT gates to build a bi-directional regulator, two input Boolean Logic gates OR, NOR, AND and NAND and a pulse-generating circuit. Last, we port our Csr-regulated BUFFER Gate into three industrially relevant bacteria simply by leveraging the conserved Csr Network in each species.

Structural basis and molecular mechanisms of Cl- transmembrane transport in cardiomyocytes

The intracellular concentration of chlorine anions ([Cl-]i), the equilibrium potential for chlorine anions (ECl) and transmembrane chloride currents (ICl) are the factors that significantly influence the electrophysiological properties of excitable tissue, including the myocardium. Several types of chloride (anion) conductance have been identified in the heart. In recent years, a number of transmembrane proteins demonstrating chloride conductance have been identified (CFTR, ClC, TMEM16, LRRC8), and the expression of these macromolecules in cardiac tissue has been confirmed. Accumulated data allow for establishing a molecular substrate for some chloride anion currents (ICl,PKA, ICl,ir, ICl,vol, ICl,swell, ICl,Ca, Ito2) detected in the heart. Furthermore, the molecular mechanisms regulating [Cl-]i and ECl through chloride cotransporters (KCC, NKCC1) and chloride-bicarbonate exchangers have been established. The variety of structures determining chloride transmembrane conductivity and the complexity of molecular mechanisms regulating chloride homeostasis underlie the complex effects of activation of chloride transporters in the pacemaker, conduction system and working myocardium of the heart. This review discusses the structural, biophysical properties and molecular regulation of chloride transporter protein complexes identified in the myocardium. The review also covers the mechanisms by which chloride transmembrane transport influences the bioelectrical activity of cardiomyocytes.

Evolution of the lipoxygenase gene family in Pyropia haitanensis and its response to biotic and abiotic stresses

Macroalgae contain a chemically diverse and unique set of oxylipins that derived from lipid peroxidation play pivotal roles in response to various environmental stresses in the intertidal zone. Specific enzymes involved in biosynthesizing these oxylipins remain largely unknown. Lipoxygenase (LOX) is a key enzyme in the oxylipin biosynthetic pathway. Here, six homologous LOX genes were identified in Pyropia haitanensis. To investigate the evolutionary status of the LOX gene family in red algae and its role in the adaptation of P. haitanensis to the intertidal environment, this study analyzed the evolution, structure, and enzymatic activities of these genes. Phylogenetic analysis and homologous sequence alignment indicated that the P. haitanensis LOX genes had two evolutionary origins. PhLOX and PhLOX2 possess an SRPBCC domain at the N-terminus that may have been acquired from marine bacteria through horizontal gene transfer, while PhLOX3–6 may have been acquired from cyanobacteria. Cis-Regulatory analysis revealed numerous elements upstream of the PhLOX genes associated with abiotic stress and hormone regulation, as well as binding sites for defense-related transcription factors. The in-vitro enzymatic activity of PhLOXs was detected, revealing that PhLOX and PhLOX2 exhibited the highest activities. PhLOX3–6 showed a substrate preference for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), but it had lower activity. The transcriptional expression levels of the six PhLOX genes varied under different biotic and abiotic stresses. For example, all PhLOX genes were significantly upregulated after mechanical damage, while PhLOX5 responded to low temperatures. In summary, P. haitanensis acquired a series of LOX genes from marine bacteria and cyanobacteria during its evolutionary history, among which PhLOX and PhLOX2 were selected as the likely primary functional genes. Its functional diversity to cope with various environmental stresses is achieved through the complex transcriptional regulation of PhLOX genes.

Regulatory Mechanisms Governing the Autophagy-Initiating VPS34 Complex and Its inhibitors.

VPS34 is a crucial protein in cells, essential for handling cellular stress through its involvement in autophagy and endocytosis. This protein functions as a Class III phosphatidylinositol 3-kinase, producing phosphatidylinositol 3-phosphate, which is necessary for autophagy and vesicle trafficking. Additionally, VPS34 forms two mutually exclusive complexes, each playing a vital role in autophagy and endocytic sorting. These complexes share common subunits, including VPS15, VPS34, and Beclin 1, with complex I having ATG14 as a specific subunit. Due to its association with various human diseases, regulation of the VPS34 complex I has garnered significant interest, emerging as a potential therapeutic target for drug discovery. Summaries of the structure, function of VPS34 complexes, and developed VPS34 inhibitors have been provided, along with discussions on the regulation mechanism of VPS34, particularly in relation to the initiation complex I of autophagy. This offers valuable insights for treating autophagy-related diseases.

Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions. Specifically, Cu-Zn superoxide dismutase and heat shock proteins were up-regulated to counter oxidative stress and protein misfolding. Proteins involved in intracellular trafficking, secretion, and vesicular transport; RNA processing and modification showed enhanced abundance and regulating stress response pathways. Additionally, haloalkane dehalogenase and homogentisate 1,2-dioxygenase played pivotal roles in lindane mineralization. Bioinformatics analysis highlighted enriched pathways such as Glyoxylate and dicarboxylate metabolism and Purine metabolism, that are crucial for combating adverse environments. We identified the hub protein 26 S proteasome regulatory subunit complex as potential biomarker and remedial targets for mycoremediation of wastewater, suggesting practical applications for environmental remediation.

MENYINGKAP IMPLEMENTASI DAN DAMPAK MODEL NEO-WEBERIAN STATE DALAM REVOLUSI BIROKRASI INTERNATIONAL

This research uses a literature review (SLR) study to investigate the application of the Neo-Weberian State (NWS) model in global bureaucratic reform, with an emphasis on economic, social and health issues. This research aims to provide a comprehensive understanding of the implementation of NWS, critically evaluate its success and provide recommendations for developing government governance and community services. This research applies a five-stage approach by Transfield to review the literature on the implementation of the Neo-Weberian State (NWS) over the past few decades. This review combines results from qualitative and quantitative research that has been published between 2021-2024 in various European countries. The results show that the Neo Weberian State (NWS) can increase efficiency in public services and overcome global challenges, despite facing internal obstacles, limited resources, complex regulations, and shortcomings in accountability and transparency. This research emphasizes the importance of adaptation according to context, capacity building, simpler deregulation, and strict supervision to ensure the effectiveness of the Neo Weberian State (NWS). The participation of government, civil society and the private sector is considered very important in creating new and creative public service solutions. This research outlines how the Neo-Weberian State (NWS) model faces broad challenges in carrying out bureaucratic reform. The NWS improves the quality of public services, addresses internal constraints, and emphasizes contextual adaptation, capacity building, modest deregulation, and strict supervision, which are critical to governance and public services. Although it provides a solution for solving problems in the current era of revolution, additional research is still needed to fully understand its impact and design more effective implementation models.

Complex regulation of tau phosphorylation by the endothelin system in brain microvascular endothelial cells (BMVECs): link to barrier function.

Endothelin-1 (ET-1), the most potent vasoconstrictor identified to date, contributes to cerebrovascular dysfunction. ET-1 levels in postmortem brain specimens from individuals diagnosed with Alzheimer's disease (AD) and related dementias (ADRD) were shown to be related to cerebral hypoxia and disease severity. ET-1-mediated vascular dysfunction and ensuing cognitive deficits have also been reported in experimental models of AD and ADRD. Moreover, studies also showed that ET-1 secreted from brain microvascular endothelial cells (BMVECs) can affect neurovascular unit integrity in an autocrine and paracrine manner. Vascular contributions to cognitive impairment and dementia (VCID) is a leading ADRD cause known to be free of neuronal tau pathology, a hallmark of AD. However, a recent study reported cytotoxic hyperphosphorylated tau (p-tau) accumulation, which fails to bind or stabilize microtubules in BMVECs in VCID. Thus, the study aimed to determine the impact of ET-1 on tau pathology, microtubule organization, and barrier function in BMVECs. Cells were stimulated with 1 μM ET-1 for 24 h in the presence/absence of ETA (BQ123; 20 μM) or ETB (BQ788; 20 μM) receptor antagonists. Cell lysates were assayed for an array of phosphorylation site-specific antibodies and microtubule organization/stabilization markers. ET-1 stimulation increased p-tau Thr231 but decreased p-tau Ser199, Ser262, Ser396, and Ser214 levels only in the presence of ETA or ETB antagonism. ET-1 also impaired barrier function in the presence of ETA antagonism. These novel findings suggest that (1) dysregulation of endothelial tau phosphorylation may contribute to cerebral microvascular dysfunction and (2) the ET system may be an early intervention target to prevent hyperphosphorylated tau-mediated disruption of BMVEC barrier function.

A human DCC variant causing mirror movement disorder reveals that the WAVE regulatory complex mediates axon guidance by netrin-1-DCC.

The axon guidance cue netrin-1 signals through its receptor DCC (deleted in colorectal cancer) to attract commissural axons to the midline. Variants in DCC are frequently associated with congenital mirror movements (CMMs). A CMM-associated variant in the cytoplasmic tail of DCC is located in a conserved motif predicted to bind to a regulator of actin dynamics called the WAVE (Wiskott-Aldrich syndrome protein-family verprolin homologous protein) regulatory complex (WRC). Here, we explored how this variant affects DCC function and may contribute to CMM. We found that a conserved WRC-interacting receptor sequence (WIRS) motif in the cytoplasmic tail of DCC mediated the interaction between DCC and the WRC. This interaction was required for netrin-1-mediated axon guidance in cultured rodent commissural neurons. Furthermore, the WIRS motif of Fra, the Drosophila DCC ortholog, was required for attractive signaling in vivo at the Drosophila midline. The CMM-associated R1343H variant of DCC, which altered the WIRS motif, prevented the DCC-WRC interaction and impaired axon guidance in cultured commissural neurons and in Drosophila. The findings reveal the WRC as a pivotal component of netrin-1-DCC signaling and uncover a molecular mechanism explaining how a human genetic variant in the cytoplasmic tail of DCC may lead to CMM.

PRC2-RNA interactions: Viewpoint from Tom Cech, Chen Davidovich, and Richard Jenner

Diverse biochemical, structural, and invivo data support models for the regulation of polycomb repressive complex 2 (PRC2) activity by RNAs, which may contribute to the maintenance of epigenetic states. Here, we summarize this research and also suggest why it can be difficult to capture biologically relevant PRC2-RNA interactions in living cells.

Forecast, analytical and trend analysis of the development of the agro-industrial complex of Russia in the main agri-food markets as an area of state strategic guidelines

Abstract The modern structure of the Russian agro-industrial complex has the properties of consolidation, expansion and prevalence of agricultural organizations and agricultural holdings, as evidenced by the factor of their provision for about two-thirds of the total agricultural production. This circumstance states the growing dominance of large agricultural business and the progressive evolution of the agricultural sector, as well as the reduction in the importance of individual farms of the population. In the course of the study, the current state of development of the agro-industrial complex of Russia is considered, a forecast, analytical and trend analysis of the development of the domestic agro-industrial complex is carried out through the prism of the fundamental agri-food markets and the contours of the subsequent progress in the development of the agricultural sector in the context of the evolving restructuring of the social, economic and political situation are determined. The novelty of the research lies in the presentation of forecast estimates and trends in the development of the main agri-food markets of the Russian agro-industrial complex, which determine the presumptive transformation of the agrarian mechanism of Russia in the medium and long term: destabilization of international political and trade-economic cooperation, intensification of economic restrictive measures, as well as fundamentally new state priorities. The agricultural sector of the economy tends to react extremely sharply to the current situation in recent years, manifested in unstable international economic relations and foreign policy crises, which directly negatively affects the conditions for the functioning of the agricultural business. The presented forecast scenario for the development of agri-food markets will contribute to the formation of directions for state strategic management, planning and regulation of the agro-industrial complex for the medium and long term.

Patterns of corticosterone exposure affect the subcellular localisation of mineralocorticoid and glucocorticoid receptor complexes and gene expression

Mineralocorticoid (MR) and glucocorticoid receptors (GR) act as transcription factors and major mediators of glucocorticoid signalling, with pivotal roles in regulating the stress response and hormonal signalling, mood, cognition and memory. The MR and GR and share many target genes, have a high degree of homology in their DNA binding (DBD) and ligand binding domain (LBD) but differ considerably in the N-terminal domain (NTD). Using Proximity Ligation Assay (PLA) we quantitatively assessed MR-GR complex subcellular localisation and transcriptional regulation in murine neuroblastoma (N2A) cells stimulated by constant or pulsatile corticosterone (CORT) patterns. We observe that continuous receptor activation by CORT caused localisation at the periphery of the cell nucleus. Truncation of the receptor Ligand Binding Domain (LBD) led to a stronger localisation of MR-GR complexes at the periphery of the cell nuclei. This was also observed for GR immunofluorescence (IF), while in cells expressing only MR or GR the mRNA response to pulsatile hormone treatment was substantially attenuated. However, there was no clearcut correlation between the spatial distribution of MR-GR complexes and the mRNA levels of target genes. Overall, our findings suggest that longer presence in the cell nucleus favors more peripheral nuclear localisation.

GOLM1 promotes prostate cancer progression via interaction with PSMD1 and enhancing AR-driven transcriptional activation.

Aberrant transcriptional activation of the androgen receptor (AR) is a predominant cause of prostate cancer (PCa), including both in the initial and androgen-independent stages. Our study highlights Golgi membrane protein 1 (GOLM1) as a key regulator of AR-driven transcriptional activity in PCa progression. Utilizing local clinical data and TCGA data, we have established a robust association between GOLM1 and AR target genes, and further demonstrated that GOLM1 can enhance the expression of AR target genes. We discovered that GOLM1 interacts with PSMD1, a component of the 19S regulatory complex in the 26S proteasome, using mass spectrometry and Co-IP analysis. It is well known that ubiquitin-proteasome plays a vital role in AR expression and transcriptional regulation. Our findings demonstrate that GOLM1 enhances ubiquitin proteasome activity by binding to PSMD1, thereby facilitating AR-driven transcriptional activity and PCa progression. These results indicate that GOLM1 and its associated proteins may become potential therapeutic targets for PCa characterized by dysregulated AR-driven transcriptional activation.

Whole transcriptome sequencing analysis reveals the effect of circZFYVE9/miR-378a-3p/IMMT axis on mitochondrial function in adipocytes

Recent research highlights the complex regulation of lipid accumulation and mitochondrial function in adipocytes via non-coding RNAs like microRNAs and circular non-coding RNAs. Circular non-coding RNAs act as endogenous regulators, impacting lipid metabolism and mitochondrial function by interacting with miRNAs. Sequencing white and brown adipose tissues in mice revealed significant variations in 1936 mRNAs, 127 miRNAs, and 171 circRNAs. Analyses showed these RNAs' involvement in vital processes like mitochondrial biogenesis, oxidative phosphorylation, and the citric acid cycle, crucial for lipid metabolism. Focus on top differentially regulated miRNAs led to the construction of a regulatory network involving circRNAs, miRNAs, and mRNAs, illuminating the role of endogenous RNAs in lipid metabolism and mitochondrial function. The circZFYVE9/miR-378a-3p/IMMT axis was identified as influential in adipogenic differentiation of 3T3-L1 preadipocytes by regulating mitochondrial function. This study expands the understanding of non-coding RNAs in adipose tissue, particularly their connection to mitochondrial function and metabolism.

Differential expression of quick-to-court gene isoforms in Drosophila male and female

The quick-to-court (qtc) gene is expressed in both males and females but affects only the mating behavior of males, probably due to the different composition of isoforms in different sexes. We tested this hypothesis and examined the sex-specific expression of qtc transcripts in the tissues of male and female Oregon-R flies. It was found that some qtc transcripts, such as qtc-RM and qtc-RN, are testis-specific, while others like qtc-RH are found in ovaries but absent in testes. No sex-specific transcripts were identified in the brain, suggesting further investigation into specific brain structures may be needed. There is probably a complex regulation of qtc gene expression, which is potentially influenced by various factors in different tissues.

Regulatory role of Heparan sulfate in leptin signaling

Leptin, a hormone mainly secreted by adipocytes, has attracted significant attention since its discovery in 1994. Initially known for its role in appetite suppression and energy regulation, leptin is now recognized for its influence on various physiological processes, including immune response, bone formation, and reproduction. It exerts its effects by binding to receptors and initiating an intracellular signaling cascade. Heparan sulfate (HS) is known to regulate the intracellular signaling of various ligands. HS is present as the glycan portion of HSPGs on cell surfaces and in intercellular spaces, with diverse structures due to extensive sulfation and epimerization. Although HS chains on HSPGs are involved in many physiological processes, the detailed effects of HS chains on leptin signaling are not well understood.This study examined the role of HS chains on HSPGs in leptin signaling using Neuro2A cells expressing the full-length leptin receptor (LepR). We showed that cell surface HS was essential for efficient leptin signaling. Enzymatic degradation of HS significantly reduced leptin-induced phosphorylation of downstream molecules, such as signal transducer and activator of transcription 3 and p44/p42 Mitogen-activated protein kinase. In addition, HS regulated LepR expression and internalization, as treatment with HS-degrading enzymes decreased cell surface LepR. HS was also found to exhibit a weak interaction with LepR. Enzymatic removal of HS enhanced the interaction between LepR and low-density lipoprotein receptor-related protein 1, suggesting that HS negatively regulates this interaction. In conclusion, HS plays a significant role in modulating LepR availability on the cell surface, thereby influencing leptin signaling. These findings provide new insights into the complex regulation of leptin signaling and highlight potential therapeutic targets for metabolic disorders and obesity.

Whole cell affinity for 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in the marine bacterium Candidatus Pelagibacter st. HTCC7211 explains marine dissolved HMP concentrations.

Vitamin B1 is a universally required coenzyme in carbon metabolism. However, most marine microorganisms lack the complete biosynthetic pathway for this compound and must acquire thiamin, or precursor molecules, from the dissolved pool. The most common version of Vitamin B1 auxotrophy is for thiamin's pyrimidine precursor moiety, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). Frequent HMP auxotrophy in plankton and vanishingly low dissolved concentrations (approximately 0.1-50 pM) suggest that high-affinity HMP uptake systems are responsible for maintaining low ambient HMP concentrations. We used tritium-labelled HMP to investigate HMP uptake mechanisms and kinetics in cell cultures of Candidatus Pelagibacter st. HTCC7211, a representative of the globally distributed and highly abundant SAR11 clade. A single protein, the sodium solute symporter ThiV, which is conserved across SAR11 genomes, is the likely candidate for HMP transport. Experimental evidence indicated transport specificity for HMP and mechanistically complex, high-affinity HMP uptake kinetics. Km values ranged from 9.5 pM to 1.2 nM and were dramatically lower when cells were supplied with a carbon source. These results suggest that HMP uptake in HTCC7211 is subject to complex regulation and point to a strategy for high-affinity uptake of this essential growth factor that can explain natural HMP levels in seawater.

A governance and risk management framework for project management in the oil and gas industry

The oil and gas industry operates in an environment marked by high risks, complex regulations, and significant financial investments. Effective project management in this sector requires a robust governance and risk management framework to address operational, regulatory, financial, and environmental challenges. This review proposes a comprehensive governance and risk management framework tailored specifically to the unique needs of oil and gas projects. The framework integrates governance structures that define clear roles, responsibilities, and decision-making processes, ensuring that projects align with corporate objectives and compliance standards. Central to this framework is a risk management model that identifies, assesses, and mitigates potential project risks. The model emphasizes continuous risk monitoring, utilizing advanced technologies such as predictive analytics, AI, and digital twins to forecast risks and optimize decision-making. Additionally, it advocates for proactive stakeholder engagement strategies to ensure alignment among diverse stakeholders, including government agencies, investors, and local communities. The governance aspect of the framework promotes transparency, accountability, and sustainability, ensuring that projects meet both operational goals and regulatory requirements. It also introduces agile project management techniques to enhance flexibility and responsiveness throughout the project lifecycle. By integrating technological tools like blockchain for contract management and AI for predictive maintenance, the framework addresses both governance and risk management challenges. Ultimately, the review serves as a guide for oil and gas companies to enhance project efficiency, minimize risks, and meet the demands of an increasingly complex industry landscape.

Rural depopulation in Kazakhstan: mechanisms of regulation

The aim is to analyze depopulation trends in rural regions of Kazakhstan, including Kostanay region, and to propose mechanisms for their optimization. Methods - comparative analysis and dynamic methods were used to identify the main causes and annual decline in population in rural areas. Empirical methods were used to determine the factors of rural population reduction, as well as the formation of a system of complex regulation of demographic and social problems. The assessment of socio-economic indicators of the oblast was carried out on the basis of the evaluation approach. Results - the authors note that despite a number of existing documents on the development of rural areas of the country, since 2009 depopulation of the rural population of the country persists. In 2024 compared to 2008 the quantitative composition decreased by 9.1%. It is most characteristic for Kostanay region. In order to more deeply study the depopulation orientation in this region a comparative analysis of social parameters of 4 densely populated and 4 least densely populated areas, including data for the period from 2010 to 2023 was carried out. Conclusions - labor market indicators of Kazakhstan and Kostanay region are somewhat lower compared to urban indicators. In 2023, the labor force participation rate was observed to be higher in rural areas compared to urban areas, but the employment rate was significantly lower. Self-employed workers are 16% more in rural areas and 9% more in the oblast. The low size of income and its stable sources led to the outflow of economically active groups from villages to large cities. In order to comprehensively regulate these processes in rural areas, it is advisable to create an effective mechanism of social responsibility of business (SRB), which will reduce budget expenditures of the state.

Capture of RNA-binding proteins across mouse tissues using HARD-AP

RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly associated RNA regulatory complexes from cultured cells and fresh tissues. We successfully use HARD-AP to establish a comprehensive atlas of RBPs across mouse primary organs. We then systematically map RNA-binding sites of these RBPs using machine learning-based modeling. Notably, the modeling reveals that the LIM domain as an RNA-binding domain in many RBPs. We validate the LIM-domain-only protein Csrp1 as a tissue-dependent RNA binding protein. Taken together, HARD-AP is a powerful approach that can be used to identify RBPomes from any type of sample, allowing comprehensive and physiologically relevant networks of RNA-protein interactions.