Biology subjects

Ma, Q.

Publications and source records attributed to Ma, Q..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

A Substantia Innominata-midbrain Circuit Controls a General Aggressive State

While aggressive behaviors are universal and essential for survival, uncontrollable and abnormal aggressive behaviors in animals or humans may have severe adverse consequences or social costs. Neural circuits regulating specific forms of aggression under defined conditions have been described, but how brain circuits govern a general aggressive response remains unknown. Here, we found that posterior substantia innominata (pSI) neurons responded to several aggression-provoking cues with the graded activity of differential dynamics, predicting the aggressive state and the topography of aggression in mice. Activation of pSI neurons projecting to the periaqueductal gray (PAG) increased aggressive arousal and robustly initiated/promoted all the types of aggressive behavior examined in an activity level-dependent manner. Inactivation of the pSI circuit largely blocked diverse aggressive behaviors but not mating. By encoding a general aggressive response, the pSI-PAG circuit universally drives multiple aggressive behaviors and may provide a potential target for alleviating human pathological aggression. In BriefZhu et al. find that the posterior substantia innominata neurons universally drive aggressive behaviors by representing aggressive state and topography of aggression in mice. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/047670v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@19d72org.highwire.dtl.DTLVardef@7cc4corg.highwire.dtl.DTLVardef@1f5c3dborg.highwire.dtl.DTLVardef@d9743_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIpSI neuronal dynamics reflect aggressive state and the topography of aggression C_LIO_LIThe pSI-PAG circuit promotes arousal and elicits thirteen aggressive behaviors C_LIO_LIThe pSI controls various aggressive behaviors in an activity level-dependent manner C_LIO_LIInactivation of the pSI circuit blocks diverse aggressive behaviors but not mating C_LI

neuroscience↗

bioRxiv2020

MpsLDA-ProSVM: predicting multi-label protein subcellular localization by wMLDAe dimensionality reduction and ProSVM classifier

Proteins play a significant part in life processes such as cell growth, development, and reproduction. Exploring protein subcellular localization (SCL) is a direct way to better understand the function of proteins in cells. Studies have found that more and more proteins belong to multiple subcellular locations, and these proteins are called multi-label proteins. They not only play a key role in cell life activities, but also play an indispensable role in medicine and drug development. This article first presents a new prediction model, MpsLDA-ProSVM, to predict the SCL of multi-label proteins. Firstly, the physical and chemical information, evolution information, sequence information and annotation information of protein sequences are fused. Then, for the first time, use a weighted multi-label linear discriminant analysis framework based on entropy weight form (wMLDAe) to refine and purify features, reduce the difficulty of learning. Finally, input the optimal feature subset into the multi-label learning with label-specific features (LIFT) and multi-label k-nearest neighbor (ML-KNN) algorithms to obtain a synthetic ranking of relevant labels, and then use Prediction and Relevance Ordering based SVM (ProSVM) classifier to predict the SCLs. This method can rank and classify related tags at the same time, which greatly improves the efficiency of the model. Tested by jackknife method, the overall actual accuracy (OAA) on virus, plant, Gram-positive bacteria and Gram-negative bacteria datasets are 98.06%, 98.97%, 99.81% and 98.49%, which are 0.56%-9.16%, 5.37%-30.87%, 3.51%-6.91% and 3.99%-8.59% higher than other advanced methods respectively. The source codes and datasets are available at https://github.com/QUST-AIBBDRC/MpsLDA-ProSVM/.

bioinformatics↗

bioRxiv2020

Role of short-chain fatty acids in the gut-brain axis in schizophrenia: contribution to immune activation and pathophysiology in humans and mice

ObjectiveGut microbiota dysbiosis and aberrant gut-brain functional modules including short-chain fatty acid (SCFA) production and long-lasting immune activation (IA) are presented in schizophrenia. Given the key roles of gut microbiota and SCFA in shaping immunity, we propose that dysbiosis-induced SCFA upregulation could contribute to IA and behavioral symptoms in schizophrenia. DesignGut microbiota, SCFA, and IA biomarkers were compared between schizophrenic patients and healthy controls. The roles of SCFA in schizophrenia-related IA were analyzed in cultured peripheral blood mononuclear cells (PBMCs) and a mouse model of schizophrenia. The effects of SCFAs on schizophrenia-related phenotypes were analyzed in both human and mouse. ResultsBoth microbial-derived SCFA and SCFA-producing bacteria were elevated in the guts of schizophrenic patients, and this increased SCFA production in gut was associated with IA in schizophrenia. The microbiome signature underpinning schizophrenia-related IA includes increased diversity and increased SCFA-producing bacteria and inflammation-associated bacteria. The impact of SCFAs on immune responses of cultured PBMC depend on the diagnosis and IA status of donors. Small-molecule serum filtrates from immune-activated schizophrenic patients increased the inflammatory response of PBMCs from healthy volunteers, which can be enhanced and attenuated by SCFAs supplementation and inhibition of SCFA signaling, respectively. Chronically elevated SCFAs in adolescence induced neuroinflammation and schizophrenia-like behaviors in adult mice. Moreover, chronically elevated SCFAs in adult mice prenatally exposed to IA potentiated their expression of schizophrenia-like behaviors. Conclusionmicrobiota-derived SCFAs are important mediators of dysregulated gut-brain axis and participant in pathogenesis via enhance IA in schizophrenia. SummaryO_ST_ABSSignificance of this studyC_ST_ABSO_LIWhat is already known about this subject? [tpltrtarr]Schizophrenia pathogenesis goes beyond the brain since increasing peripheral abnormalities are revealed including gut microbiota dysbiosis, GI dysfunction, and systemic immune activation (IA). [tpltrtarr]Systemic IA/inflammation contributes to the neuroinflammation and brain impairment underlying schizophrenia, and adjunctive immunotherapy can improve psychotic symptoms. [tpltrtarr]Short-chain fatty acids (SCFA) mediate the microbiota-gut-brain communication and modulate several pathways involved in schizophrenia, including pathways of immunity and neurotransmitters. C_LIO_LIWhat are the new findings? [tpltrtarr]Patients with schizophrenia displayed increased rates of IA and increased SCFA production compared with healthy controls, and increased SCFA is associated with IA in patients. [tpltrtarr]A unique microbiota signature including enriched SCFA-producing bacterial species can distinguish patients with IA from other patients and controls. [tpltrtarr]Small molecules in the serum of immune-activated patients with schizophrenia enhance LPS-induced immune response of cultured peripheral blood mononuclear cell (PBMCs), which is partially mediated by SCFA signaling. [tpltrtarr]SCFA intake upregulates both peripheral and brain inflammation and potentiates the expression of schizophrenia-like behaviors in mice prenatally exposed to IA. C_LIO_LIHow might it impact on clinical practice in the foreseeable future? [tpltrtarr]Interference of SCFA signaling or targeted destruction of SCFA-producing bacteria may provide a new approach for the prevention and treatment of schizophrenia. [tpltrtarr]Immune activation status of patients should be an important condition considered when selecting immunotherapy for future precision psychiatric therapy. C_LI

neuroscience↗

bioRxiv2020

Microvascular Injury in Mild Traumatic Brain Injury Accelerates Alzheimer-like Pathogenesis in Mice

IntroductionTraumatic brain injury (TBI) is considered as the most robust environmental risk factor for Alzheimers disease (AD). Besides direct neuronal injury and neuroinflammation, vascular impairment is also a hallmark event of the pathological cascade after TBI. However, the vascular connection between TBI and subsequent AD pathogenesis remains underexplored. MethodsWe established a closed-head mild TBI (mTBI) model in mice with controlled cortical impact, and examined the time courses of microvascular injury, blood-brain barrier (BBB) dysfunction, gliosis and motor function impairment in wild type C57BL/6 mice. We also determined the brain clearance of {beta}-amyloid, as well as amyloid pathology and cognitive functions after mTBI in the 5xFAD mouse model of AD. ResultsmTBI induced microvascular injury with BBB breakdown, pericyte loss and cerebral blood flow reduction in mice, which preceded gliosis. mTBI also impaired brain amyloid clearance via the vascular pathways. More importantly, mTBI accelerated amyloid pathology and cognitive impairment in the 5xFAD mice. DiscussionOur data demonstrated that microvascular injury plays a key role in the pathogenesis of AD after mTBI. Therefore, restoring vascular functions might be beneficial for patients with mTBI, and potentially reduce the risk of developing AD.

neuroscience↗

bioRxiv2020

Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis

Centromeres pose an evolutionary paradox: strongly conserved in function, but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis exhibit within-species polymorphism for the location of centromeres on two of its eight chromosomes. Its old centromeres have an inverted-repeat (IR) structure, whereas its new centromeres have no obvious structural features, but are located within 30 kb of the old site. Centromeres can therefore move naturally from one chromosomal site to another, apparently spontaneously and in the absence of any significant changes in DNA sequence. Our observations are consistent with a model where all centromeres are genetically determined, such as by the presence of short or long IRs, or the ability to form cruciforms. We also find that centromeres have been hotspots for genomic rearrangements in the C. parapsilosis clade.

genomics↗

bioRxiv2020

β-alanine or L-carnosine prevents the development of pale, soft and exudative pork by inhibiting the glycolysis of porcine longissimus dorsi muscle

Carnosine plays an important role in regulating muscle buffering capacity and glycolysis. In order to investigate the effects of dietary {beta}-alanine, L-histidine, and L-carnosine supplementation on the pH value, glycolytic potential, the activities of AMP-activated protein kinase (AMPK) and pyruvate kinase (PK) activities in the porcine longissimus dorsi muscle, a total of 60 barrows with an average body weight (BW) of 50.5 {+/-} 1.7 kg were assigned into five groups which received diets containing basal diet (control, CON), 0.04% {beta}-alanine ({beta}-ALA), 0.06% L-histidine (L-HIS), 0.04% {beta}-alanine+0.06% L-histidine ({beta}-ALA+L-HIS), or 0.1% L-carnosine (L-CAR). The results showed that dietary supplementation of the combination of {beta}-ALA and L-HIS or L-CAR significantly increased (P < 0.05) the average daily gain (ADG) of pigs with 50-75 kg BW, compared with other three groups. Compared with L-CAR group, L-HIS supplementation significantly decreased (P < 0.05) the average daily feed intake (ADFI) of pigs. There were no significant difference (P > 0.05) in back fat thickness and loin eye area among treatments. At 0, 1 and 24 h postmortem (PM) the pH values in the longissimus dorsi muscle (LM) of pigs receiving L-CAR were higher (P < 0.05) than that of pigs receiving CON diet. The redness (a*) values of LM of pigs in the {beta}-ALA+L-HIS or L-CAR group were higher (P < 0.05) than those in other three groups. The glycolytic potential of LM was not significantly different (P > 0.05) among treatments. At 1, 24 h PM the AMPK activities in LM of pigs receiving {beta}-ALA, {beta}-ALA+L-HIS and L-CAR were much lower (P < 0.05) than those of pigs receiving CON diet or L-HIS. 0.1% L-carnosine or 0.04% {beta}-alanine supplemented to pigs diet was effective in regulating AMPK and PK activities in the porcine longissimus dorsi muscle and preventing the development of pale, soft and exudative (PSE) pork.

physiology↗

bioRxiv2020

A newly-identified inactive starch synthase simultaneously regulates starch synthesis and carbon allocation in storage roots of cassava (Manihot esculenta Crantz)

Starch is a glucose polymer synthesized by green plants for energy storage, and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis via forming protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII and MeISAII. The MeSSII-RNAi cassava lines showed increased amylose content and reduced intermediate chain of amylopectin (B1 type) biosynthesis in their storage roots, leading to altered starch physico-chemical properties. Further gel permeation chromatography analysis of starch biosynthetic enzymes between the wild type and MeSSII-RNAi lines confirmed the key rule of MeSSII in the organization of heteromeric starch synthetic protein complexes, including the MeSSII-MeSSI-MeGBSSI and MeSBEII-MeSSI-MeSSII-MeISAII-MeISAI complexes. The lack of MeSSII in cassava also reduced the binding capacity of the MeSSI, MeSBEII, MeISAI, and MeISAII to starch granules. Our results show a close coordination between granule-bound starch synthase and amylopectin biosynthetic enzymes, which implies that the processes of amylose synthesis and amylopectin synthesis are directly interrelated. These findings shed light on the key components of the starch biosynthesis machinery in root crops. One Sentence SummaryHere, by focusing on cassava SSII, we elucidated its function and the molecular mechanism by which it chaperones the starch synthase complex to regulate starch biosynthesis in cassava storage roots.

plant biology↗

bioRxiv2020

Calculation of fungal and bacterial inorganic nitrogen immobilization rates in soil

Microbial inorganic nitrogen (N) immobilization is an important mechanism in the retention of N in soils. However, as a result of the high diversity and complexity of soil microorganisms, there is still no effective approach to measuring the respective immobilization rates of inorganic N by fungi and bacteria, which are the two dominant microbial communities in soils. We propose a mathematical framework, combining the experimentally measurable gross inorganic N immobilization rate and proxies for fungal and bacterial inorganic N immobilization rates, to quantify the respective immobilization rates of inorganic N by fungal and bacterial communities in soil. Our approach will help to unravel the mechanisms of N retention in soils.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2020

Single-cell RNA sequencing of human, macaque, and mouse testes uncovers conserved and divergent features of mammalian spermatogenesis

Spermatogenesis is a highly regulated process that produces sperm to transmit genetic information to the next generation. Although extensively studied in mice, our current understanding of primate spermatogenesis is limited to populations defined by state-specific markers defined from rodent data. As between-species differences have been reported in the process duration and cellular differentiation hierarchy, it remains unclear how molecular markers and cell states are conserved or have diverged from mice to man. To address this challenge, we employ single-cell RNA-sequencing to identify transcriptional signatures of major germ and somatic cell-types of the testes in human, macaque and mice. This approach reveals differences in expression throughout spermatogenesis, including the stem/progenitor pool of spermatogonia, classical markers of differentiation, potential regulators of meiosis, the kinetics of RNA turnover during spermatid differentiation, and germ cell-soma communication. These datasets provide a rich foundation for future targeted mechanistic studies of primate germ cell development and in vitro gametogenesis.

genetics↗

bioRxiv2020

DMLDA-LocLIFT: Identification of multi-label protein subcellular localization using DMLDA dimensionality reduction and LIFT classifier

BackgroundMulti-label proteins occur in two or more subcellular locations, which play a vital part in cell development and metabolism. Prediction and analysis of multi-label subcellular localization (SCL) can present new angle with drug target identification and new drug design. However, the prediction of multi-label protein SCL using biological experiments is expensive and labor-intensive. Therefore, predicting large-scale SCL with machine learning methods has turned into a hot study topic in bioinformatics. MethodsIn this study, a novel multi-label learning means for protein SCL prediction, called DMLDA-LocLIFT, is proposed. Firstly, the dipeptide composition, encoding based on grouped weight, pseudo amino acid composition, gene ontology and pseudo position specific scoring matrix are employed to encode subcellular protein sequences. Then, direct multi-label linear discriminant analysis (DMLDA) is used to reduce the dimension of the fused feature vector. Lastly, the optimal feature vectors are input into the multi-label learning with Label-specIfic FeaTures (LIFT) classifier to predict the location of multi-label proteins. ResultsThe jackknife test showed that the overall actual accuracy on Gram-negative bacteria, Gram-positive bacteria, and plant datasets are 98.60%, 99.60%, and 97.90% respectively, which are obviously better than other state-of-the-art prediction methods. ConclusionThe proposed model can effectively predict SCL of multi-label proteins and provide references for experimental identification of SCL. The source codes and data are publicly available at https://github.com/QUST-AIBBDRC/DMLDA-LocLIFT/.

bioinformatics↗

bioRxiv2020

Prediction of Protein-Protein Interactions Based on L1-Regularized Logistic Regression and Gradient Tree Boosting

Protein-protein interactions (PPIs) are of great importance to understand genetic mechanisms, disease pathogenesis, and guide drug design. With the increase of PPIs sequence data and development of machine learning, the prediction and identification of PPIs have become a research hotspot in proteomics. In this paper, we propose a new prediction pipeline for PPIs based on gradient tree boosting (GTB). First, the initial feature vector is extracted by fusing pseudo amino acid composition (PseAAC), pseudo-position-specific scoring matrix (PsePSSM), reduced sequence and index-vectors (RSIV) and autocorrelation descriptor (AD). Second, to remove redundancy and noise, we employ L1-regularized logistic regression to select an optimal feature subset. Finally, GTB-PPI model based on GTB is constructed. Five-fold cross-validation showed GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori, respectively. In addition, GTB-PPI could be applied to predict Caenorhabditis elegans, Escherichia coli, Homo sapiens, and Mus musculus independent test sets, the one-core PPIs network for CD9, and the crossover PPIs network. The results show that GTB-PPI can significantly improve prediction accuracy of PPIs. The code and datasets of GTB-PPI can be downloaded from https://github.com/QUST-AIBBDRC/GTB-PPI/.

bioinformatics↗

bioRxiv2020

Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication

The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued structure-based design of peptidomimetic -ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease:inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the -ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against Middle East Respiratory Syndrome coronavirus.

biochemistry↗

bioRxiv2020

Measuring aptamer folding energy using a molecular clamp

Folding energy offers a useful metric for characterizing the stability and function of aptamers. However, experimentally measuring the folding energy is challenging and there is currently no general technique to measure this parameter directly. In this work, we present a simple approach for measuring aptamer folding energy. First, the aptamer is stretched under equilibrium conditions with a double-stranded DNA "molecular clamp" that is coupled to the aptamer ends. We then measure the total internal energy of stressed DNA molecules using time-lapse gel electrophoresis and compare the folding and unfolding behavior of molecular clamp-stressed molecules that incorporate either the aptamer or unstructured random single-stranded DNA in order to derive the aptamer folding energy. Using this approach, we measured a folding energy of 10.40 kJ/mol for the HD22 thrombin aptamer, which is consistent with other predictions and estimates. We also analyzed a simple hairpin structure, generating a folding energy result of 9.05 kJ/mol, consistent with the value predicted by computational models (9.24 kJ/mol). We believe our strategy offers an accessible and generalizable approach for obtaining such measurements with virtually any aptamer.

biophysics↗

bioRxiv2020

Isolation and long-term expansion of a single adult human renal epithelial cell with efficient kidney regeneration capacity

A wide spectrum of lethal kidney diseases involves the irreversible destruction of the tubular structures which leads to loss of renal function. A reliable technological platform to culture and transplant adult human-derived cells with nephrogenic potential offers great hope to facilitate human kidney regeneration. Here, we show that in an appropriate feeder cell-based culture system, it is feasible to isolate and long-term expand the progenitor-like SOX9+ renal epithelial cells (SOX9+ RECs) from adult mammalians. Single cell-derived SOX9+ REC lines can be established from human needle biopsy or urine samples with molecular homogeneity and genomic stability maintained during culture. Such cells grown in 3D culture system could self-organize into renal organoids composed of proximal tubular, Loop of Henle (LOH) and distal tubular cells as illustrated by single cell transcriptomic analysis. Once being transplanted into the physically injured mouse kidney, the expanded single human SOX9+ RECs incorporated into the damaged area and demonstrated capacity of regenerating functional tubules in vivo. Altogether, the ability to extensively propagate human SOX9+ REC in culture whilst concomitantly maintaining their intrinsic lineage differentiation commitment suggests their future application in regenerative medicine.

cell biology↗

bioRxiv2019

Single Cell Profiling of Acute Kidney Injury Reveals Novel Transcriptional Signatures, Mixed Identities and Epithelial-to-Stromal Crosstalk

Acute kidney injury (AKI) is a rapid decline of renal function, with an incidence of up to 67% of intensive care unit patients. Current treatments are merely supportive, emphasizing the need for deeper understanding that could lead to improved therapies. We used single cell RNA sequencing, in situ hybridization and protein expression analyses to create comprehensive renal cell specific transcriptional profiles of multiple AKI stages. We revealed that AKI induces marked dedifferentiation, renal developmental gene activation and mixed identities in injured renal tubules. Moreover, we identified potential pathologic crosstalk between epithelial and stromal cells, and several novel genes involved in AKI. We also demonstrated the definitive effects of age on AKI outcome, and showed that renal developmental genes hold a potential as novel AKI markers. Moreover, our study provides the resource power which will aid in unraveling the molecular genetics of AKI.

developmental biology↗

bioRxiv2019

Gene regulatory networks associated with lateral root and nodule development in soybean

Legume plants such as soybean produce two major types of root lateral organs, lateral roots and root nodules. A robust computational framework was developed to predict potential gene regulatory networks (GRNs) associated with root lateral organ development in soybean. A genome-scale expression dataset was obtained from soybean root nodules and lateral roots and subjected to biclustering using QUBIC. Biclusters (BCs) and transcription factor (TF) genes with enriched expression in lateral root tissues were converged using different network inference algorithms to predict high confident regulatory modules that are repeatedly retrieved in different methods. The ranked combination of results from all different network inference algorithms into one ensemble solution identified 21 GRN modules of 182 co-regulated genes networks potentially involved in root lateral organ development stages in soybean. The pipeline correctly predicted previously known nodule- and LR-associated TFs including the expected hierarchical relationships. The results revealed high scorer AP2, GRF5, and C3H co-regulated GRN modules during early nodule development; and GRAS, LBD41, and ARR18 co-regulated GRN modules late during nodule maturation. Knowledge from this work supported by experimental validation in the future is expected to help determine key gene targets for biotechnological strategies to optimize nodule formation and enhance nitrogen fixation.

plant biology↗

bioRxiv2019

Testosterone Changes in Female Pandas in Estrus

Currently, the majority of giant panda breeding is carried out by cage-mating or artificial insemination based on estrogen levels and behavior in female pandas. However, studies have shown that testosterone levels both in women and in non-human primate females have a significant effect on the desire to mate. In this study, we wanted to explain how testosterone levels of female giant pandas would change during estrous. In this study, 23 accounts of rutting were recorded in 10 female pandas from 2009 to 2012. Changes in urinal testosterone levels were monitored and compared with estradiol values. Our data showed that, for female pandas in estrus, testosterone levels after the estradiol peak was significantly higher than before, and the testosterone peak occurred 4 days after the estradiol peak. Furthermore, testosterone and estradiol level were only significantly correlated after peak estradiol levels peaked, and not before. Finally, out findings suggest that testosterone could help us better understand hormone variation during panda estrus, as well as help aid in the natural breeding of pandas.

zoology↗

bioRxiv2019

Structural modularity of the XIST ribonucleoprotein complex

Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.

molecular biology↗