Biology subjects

Fei, J.

Publications and source records attributed to Fei, J..

At least 19 recordsLinked to original sources

bioRxiv2026

DuplexFM: Transferable small-RNA target representations link miRNA interactions to siRNA efficacy prediction

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) share Argonaute-mediated guide-target recognition, yet quantitative siRNA efficacy measurements are substantially scarcer and more costly to generate than miRNA-target interaction data. We therefore asked whether miRNA interaction data could provide transferable supervision for siRNA efficacy prediction. Here we present DuplexFM, a biologically grounded framework that uses sample-specific gates to integrate five evidence sources: pairing and sequence-context priors, duplex energetics, experimentally supervised mRNA accessibility, target-to-guide cross-attention, and contextual token-pair compatibility. The accessibility expert, trained on nucleotide-resolution icSHAPE measurements, achieved a held-out nucleotide-level Pearson correlation of 0.627 and evaluated accessibility at seed match and energy-supported candidate sites. On miRBench v7, three independently trained DuplexFM models achieved a macro APS of 0.873 (SD = 0.002), soft-voting increased this to 0.876 and yielded the highest APS on all four test sets. We then froze the miRNA-trained representation and trained only a lightweight residual head with 24 siRNA-specific descriptors. Transfer improved Pearson and Spearman correlations, AUPRC, and F1 over the descriptor-only baseline in all six evaluation settings. The ensemble achieved the highest Pearson and Spearman correlations in four settings, whereas OligoFormer remained stronger on Huesken and Takayuki. These findings show that experimentally grounded accessibility and miRNA-derived interaction representations provide complementary, transferable information, supporting a parameter-efficient route towards unified modeling of Argonaute-guided RNA regulation. Code and data are available at https://github.com/cbaiming/DuplexFM.

bioinformatics↗

bioRxiv2026

Super-resolved spatial organization of the nucleolar transcriptome

AbstractsMembraneless organelles (MLOs) often exhibit internal architecture, yet whether the local transcriptome differentially partitions across MLO subdomains remains largely uncharacterized. Here we combine super-resolution imaging with in situ reverse transcription-based sequencing to profile transcriptomes within MLO subdomains. Using the human tripartite nucleolus as a model system, we identify distinct RNA populations in the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). Pre-rRNA processing intermediates demonstrate a layered progression across nucleolar subdomains, reflecting the temporal order of the processing steps. Processing steps involved in large-small subunit separation show increased retention in the DFC in highly differentiated cells. Mature small nucleolar RNAs (snoRNAs) are preferentially enriched in the DFC and spatially segregated from their precursor transcripts. Many non-snoRNA-related transcripts, often derived from nucleolus-proximal genes, show modest enrichment in the GC. These results illustrate functional RNA organization across nucleolar subdomains and provide a framework for nanoscale transcriptome mapping of biomolecular condensates.

cell biology↗

bioRxiv2026

Cell Type Architecture and Positional Gene Gradients in an Adult Animal at Subcellular Resolution

The spatial organization of cell types and gene expression underlies tissue architecture and organismal physiology. However, resolving complete cellular and molecular landscapes within a three-dimensional context remains challenging, particularly in organisms with high cellular heterogeneity and complex geometry. Here, we developed a semi-supervised workflow to reconstruct high-resolution three-dimensional spatial transcriptomic models of the planarian Schmidtea mediterranea at single-cell resolution. Planarians are basal bilaterians capable of regenerating body structures after injury. Our reconstruction maps the distribution of cell types and spatially patterned gene expression across the intact organism and identifies 119 candidate positional control genes (PCGs). These genes are expressed across muscle, neural, and epidermal populations. Functional perturbation of selected candidates, including pitx3, ptpn11, pi4ka, upf3b, and cul1, revealed roles in regeneration following injury. In addition, we identify intestinal cells as prominent components of the microenvironment surrounding adult tgs1 pluripotent stem cells (neoblasts). Together, these results demonstrate the utility of three-dimensional spatial transcriptomic reconstruction for mapping cellular architecture and positional gene regulation in complex adult organisms.

developmental biology↗

bioRxiv2026

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

Regeneration relies on precise spatiotemporal gene expression and cellular responses to establish tissue identity and body patterning. Using high-resolution Stereo-seq (715 nm) on 353 sections from 16 whole animals at 8 regeneration timepoints, we constructed a 4D spatiotemporal transcriptomic map of planarian regeneration. Our analysis captured 36 refined cell types from 3,508,004 segmented cells, enabling genome-wide transcriptional imputation of gene expression dynamics across body axes at cellular, tissue, and organismal scales. We identified dynamic positional gradients and distinct spatially distributed cell types during regeneration, including an injury-induced Anterior Regenerative Zone (ARZ). The ARZ exhibited enriched positional signals in epidermal, muscle, and neural cells and was regulated by Mediator 8, which is crucial for polarity remodeling and blastema formation. This study provides a comprehensive spatial molecular and cellular map of regenerative processes, highlighting injury-induced spatial domains and key regulatory factors in planarian regeneration. We also provide an interactive web portal, offering a valuable resource for exploring and analyzing regeneration mechanisms in a spatiotemporal context.

developmental biology↗

bioRxiv2026

Tunable Chemical and Optical Control of ER-Plasma Membrane Contact Site Geometry and Dynamics with High-Fidelity Visualization

Endoplasmic reticulum-plasma membrane (ER-PM) contact sites are essential signaling hubs that regulate lipid transport, calcium homeostasis, and spatially organized signal transduction. Emerging evidence indicates that not only the presence but also the dynamics, stability, and geometry of ER-PM contacts critically shape cellular functions; however, tools that enable simultaneous high-fidelity visualization and reversible, quantitative control of these contacts in living cells remain limited. Here, we introduce a modular toolkit for inducible ER-PM contact-site reconstitution based on complementary chemical and optical dimerization strategies. We develop a nontoxic and reversible abscisic acid (ABA)-inducible system using the plant-derived ABIcs/PYLcs pair, and a rapidly reversible optogenetic system based on the iLID/SspB module, both of which allow robust visualization and dose-dependent control over contact-site formation kinetics, increasing contact-site density and total area fraction per cell without altering the size of individual contacts. In contrast, systematic variation of rigid -helical linker length or inducible tether abundance selectively tunes the lateral growth, stability, and lifetime of individual contact sites, without changing their density. By combining these two orthogonal strategies, we achieve independent control of both individual contact-site size and overall contact-site density, providing complementary mechanisms to adjust total contact area per cell. This versatile platform enables quantitative dissection of ER-PM contact site structure-function relationships and offers broad utility in studies of lipid exchange, calcium signaling, membrane repair, metabolic regulation, and disease-relevant dysregulation.

bioengineering↗

bioRxiv2025

tBid mediated genetic ablation of connective tissue cells reveal their key regulatory function during limb regeneration in axolotls

Limb regeneration in adulthood is a fascinating phenomenon unique to salamanders, requiring precise coordination and interaction of various cell types. Connective tissue (CT) constitutes a major component of the limb and serves as the primary reservoir of positional information during regeneration. However, the direct evidence and the extent of CT in positional contribution remain limited. Here we develop an inducible Cre-LoxP-mediated tBid cell ablation system in axolotls and demonstrate efficient elimination of targeted muscle tissue and muscle stem cells through transient electroporation or genetic approach. Ablation of CT cells at early stages of regeneration results in delayed regeneration and loss of proximal limb segments (e.g., upper and lower limb), with minimal impact on hand differentiation. CT ablation during development yields similar defects as observed during regeneration, indicating an essential role for CT cells in determining the positional identity of developing and regenerating limb structures. Further scRNA-seq reveal a progressive proximal-to-distal transition among CT cells and identify distinct CT subtypes that contribute to proximal and distal segments. CT ablation results in reduction of the differentiated CT1--a subpopulation that maintains proximal identity throughout regeneration, and a delay of distal transformation in the proliferative CT1--a major CT subtypes showing progenitor property. These cellular shifts likely lead to the observed morphological deficits in regenerating limbs after CT ablation. Moreover, differentiated CT1 cells enhanced their interactions with surrounding cell types after CT ablation, to modulate adaptive proliferation in other populations, e.g., muscle stem cells. Our work establishes a tBid-based ablation strategy for functional studies of CT and other cell types in axolotls, and provides direct evidence demonstrating pivotal roles of CT cells in guiding positional memory and segmental patterning during organ regeneration.

molecular biology↗

bioRxiv2025

Membrane-associated periodic skeleton regulates major forms of endocytosis in neurons through a signaling-driven positive feedback loop

Endocytosis is an evolutionarily conserved process that enables neurons to internalize signaling receptors and membrane proteins, maintaining cellular homeostasis and supporting rapid responses to extracellular cues. The neuronal membrane-associated periodic skeleton (MPS), a lattice-like cytoskeletal structure composed of actin and spectrin, has been shown to restrict clathrin-mediated endocytosis (CME) at the axon initial segment (AIS) of neurons, by gating clathrin-coated pit (CCP) formation through membrane-localized "clearing" structures that are devoid of MPS. However, the extent to which the MPS regulates diverse forms of endocytosis across neuronal compartments, and how it is dynamically remodeled to permit trafficking on demand, remain unknown. While CME is relatively well characterized in neurons, the subcellular localization and physiological relevance of caveolin-mediated endocytosis, flotillin-mediated endocytosis, and fast endophilin-mediated endocytosis (FEME) have remained largely unclear. Here, we show that all four major endocytic pathways--CME, caveolin-, flotillin-, and FEME-- are spatially gated by the MPS and occur specifically within MPS-free "clearing" zones distributed across both axonal and somatodendritic compartments of mature neurons. These results, for the first time, map the spatial landscape of these lesser-understood pathways in neurons and reveal a unifying principle of cytoskeletal gating across endocytic mechanisms. Disruption of the MPS markedly enhances both basal and ligand-induced endocytosis across all four pathways, establishing its broad inhibitory role in pit initiation. We further discover that endocytosis can, in turn, remodel the MPS through a novel signaling-driven feedback loop: ligand-triggered endocytosis activates ERK signaling, which promotes calpain- and caspase-mediated spectrin cleavage. This targeted cytoskeletal degradation facilitates further rounds of endocytosis, forming a self-reinforcing circuit that couples membrane trafficking with cortical architecture remodeling. Finally, we show that the MPS limits amyloid precursor protein (APP) endocytosis and thereby suppresses amyloid-{beta} 1-42 (A{beta}42) production and neuronal apoptosis, implicating MPS integrity in the regulation of neurodegenerative processes such as Alzheimers disease. Together, our findings establish the MPS as a dynamic, signal-responsive modulator of endocytosis and neuronal health. This work uncovers a general spatial gating mechanism that applies to diverse endocytic pathways, introduces a cytoskeleton-centered feedback loop for signal-dependent remodeling, and expands the functional significance of the MPS from passive structural support to active regulation of neuronal homeostasis and disease susceptibility. TeaserMembrane skeleton gates endocytosis and remodels in response to signals, linking membrane dynamics to neuronal health and Alzheimers risk.

cell biology↗

bioRxiv2025

Inhibition of CGRP receptor ameliorates AD pathology by reprogramming lipid metabolism through HDAC11/LXRβ/ABCA1 signaling

The Calcitonin gene-related peptide (CGRP) receptor has gained attention in Alzheimers Disease (AD) research due to its involvement in regulating neuroinflammation. However, its role and mechanism in AD pathology remain unclear. Here, we demonstrate that CALCRL, a core component of the CGRP receptor, is upregulated in the hippocampus of AD dementia patients and 5xFAD mice. Knockout of the CGRP receptor ligand Calca or pharmacological blockade using Rimegepant (Rim), reduces soluble A{beta}1-42 oligomer-induced neuronal death and glial inflammation. Rim treatment also rescues neurobehavioral impairments, neurodegeneration, and lipid metabolism dysfunction in 5xFAD mice. Mechanistically, these effects are mediated through HDAC11 inhibition, which enhances LXR{beta} acetylation and ABCA1 expression, promoting the reprogramming of neuronal lipid metabolism. Importantly, this CALCRL/HDAC11/LXR{beta}/ABCA1 axis is conserved across both humans and mice. Our findings uncover a novel mechanism underlying AD pathogenesis and highlight the therapeutic potential of targeting CGRP signaling in AD. HIGHLIGHTSInhibition of CGRP receptor ameliorates disease pathology in models of AD HDAC11 mediates CGRP receptor function in AD HDAC11 is a pivotal regulator in lipid metabolism by LXR{beta}/ABCA1 signaling The HDAC11/LXR{beta}/ABCA1 axis is conserved in AD humans and mice

neuroscience↗

bioRxiv2025

A chemically inducible multimerization system for tunable and background-free RTK activation

Receptor tyrosine kinases (RTKs) are key regulators of diverse cellular processes, including differentiation, migration, proliferation, survival, and intracellular communications, by transducing extracellular cues into intracellular responses. Upon oligomerization at the plasma membrane, RTKs become activated and initiate major downstream signaling cascades, such as the ERK pathway, which modulates cytoskeletal dynamics through phosphorylation of cytoskeletal regulators, regulation of actin-binding proteins, and transcriptional activation of immediate-early genes involved in cell structure and motility. Light-inducible RTK systems have been developed to achieve spatiotemporal control of RTK clustering and activation for both basic cell biology research, and engineered applications, such as controlling cell migration, proliferation, or differentiation. However, these systems are limited by high basal RTK activation, where substantial RTK activation occurs even before induction, leading to unintended ERK activation and downstream effects. Here, we report a chemically inducible RTK platform that minimizes basal activation while enabling direct visualization of RTK clustering at the plasma membrane upon induction. Single-cell imaging reveals visible RTK clusters after induction, with total RTK abundance in the clusters correlating with ERK phosphorylation levels. Using this system, we achieved precise and rapid control over multiple ERK-dependent cellular processes, including disassembly of spectrin-based membrane skeleton and nuclear entry of transcription factors STAT3 and CREB, while maintaining minimal basal activity before induction. In contrast to previously developed inducible RTK systems, which can perturb cytoskeletal structures or transcription factor dynamics even without stimulation, our design preserves native cellular architecture and nuclear signaling until activation is intentionally triggered. Collectively, these results establish our system as a robust and versatile platform for dissecting RTK signaling dynamics and engineering cell behaviors with precise, on-demand spatiotemporal control.

bioengineering↗

bioRxiv2025

RNA localization to nuclear speckles follows splicing logic

Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early splicesomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is tightly linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions. HighlightsO_LISequences containing hallmarks of pre-mRNA dictate speckle localization C_LIO_LIRNA speckle localization is coupled to early spliceosome assembly C_LIO_LIDisease-associated single nucleotide variants reduce localization of isolated exons C_LIO_LIRNA speckle localization strongly correlates with splicing kinetics C_LI O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/656493v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1efbb02org.highwire.dtl.DTLVardef@1deb7aaorg.highwire.dtl.DTLVardef@ec1ec2org.highwire.dtl.DTLVardef@1d78b72_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

biochemistry↗

bioRxiv2024

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

Stress-induced mRNP condensation is conserved across eukaryotes, resulting in stress granule formation under intense stresses, yet the mRNA composition and function of these condensates remain unclear. Exposure of ribosome-free mRNA following stress is thought to cause condensation and stress granule formation through mRNA-sequence-dependent interactions, leading to disproportionate condensation of long mRNAs. Here we show that, in striking contrast, virtually all mRNAs condense in response to multiple stresses in budding yeast with minor length dependence and often without stress granule formation. New transcripts escape mRNP condensation, enabling their selective translation. Inhibiting translation initiation causes formation of mRNP condensates that are distinct from stress granules and P-bodies; these translation-initiation-inhibited condensates (TIICs) are omnipresent, even in unstressed cells. Stress-induced mRNAs are excluded from TIICs due to the timing of their expression, indicating determinants of escape that are independent of sequence. Together, our results reveal a previously undetected level of translation-linked molecular organization and stress-responsive regulation.

cell biology↗

bioRxiv2024

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. Specifically, we find that stably-enriched transcripts contain inefficiently spliced introns. We show that nuclear speckles specifically facilitate splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, underscoring a tight interplay between genome organization, RNA cis-elements, and transcript speckle enrichment, and connecting transcript speckle localization with splicing efficiency. Finally, we show that speckles can act as hubs for the regulated retention of introns during cellular stress. Collectively, our data highlight a role of nuclear speckles in both co- and post-transcriptional splicing regulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/581881v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1a55b13org.highwire.dtl.DTLVardef@fe50baorg.highwire.dtl.DTLVardef@6610fborg.highwire.dtl.DTLVardef@e4df5b_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG

cell biology↗

bioRxiv2024

Translational T-box riboswitches bind tRNA by modulating conformational flexibility

T-box riboswitches, paradigmatic non-coding RNA elements involved in genetic regulation in most Gram-positive bacteria, are adept at monitoring amino acid metabolism through direct interactions with specific tRNAs. T-box riboswitches assess tRNA aminoacylation status, subsequently regulating the transcription or translation of downstream genes involved in amino acid metabolism. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a model of T-box translational regulation. The data supports a two-step binding model where the tRNA anticodon is recognized first, followed by interactions with the NCCA sequence. Specifically, after anticodon recognition, tRNA in the partially bound state can transiently dock into the discriminator domain, resembling the fully bound state, even in the absence of the tRNA NCCA-discriminator interactions. Establishment of the NCCA-discriminator interactions significantly stabilizes the fully bound state. Collectively, the data suggests higher conformational flexibility in translation-regulating T-box riboswitches, compared to transcription-regulating ones, and supports a conformational selection model for NCCA recognition. Furthermore, it was found that the conserved RAG sequence is pivotal in maintaining specific interactions with the tRNA NCCA sequence by preventing sampling of an aberrant conformational state, while Stem IIA/B-linker interactions impact the conformational dynamics and the stability of both the partially bound and fully bound states. The present study provides a critical kinetic basis for how specific sequences and structural elements in T-box riboswitches enable the binding efficiency and specificity required to achieve gene regulation.

biophysics↗

bioRxiv2023

Comparative genetic, biochemical, and biophysical analyses of the four E. coli 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 Escherichia coli 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 {Delta}uup knockout, like {Delta}ettA, exhibits strongly reduced fitness when growth is restarted from long-term stationary phase, but neither {Delta}ybiT nor {Delta}yheS exhibits this phenotype. All four proteins nonetheless functionally interact with ribosomes based on in vitro translation and single-molecule fluorescence resonance energy transfer experiments employing variants harboring glutamate-to-glutamine active-site mutations (EQ2) that trap them in the ATP-bound conformation. These variants all strongly stabilize the same global conformational state of a ribosomal elongation complex harboring deacylated tRNAVal in the P site. However, EQ2-Uup uniquely exchanges on/off the ribosome on a second timescale, while EQ2-YheS-bound ribosomes uniquely sample alternative global conformations. At sub-micromolar concentrations, EQ2-EttA and EQ2-YbiT fully inhibit in vitro translation of an mRNA encoding luciferase, while EQ2-Uup and EQ2-YheS only partially inhibit it at ~10-fold higher concentrations. Moreover, tripeptide synthesis reactions are not inhibited by EQ2-Uup or EQ2-YheS, while EQ2-YbiT inhibits synthesis of both peptide bonds and EQ2-EttA specifically traps ribosomes after synthesis of the first peptide bond. These results support the four E. coli ABCF paralogs all having different activities on translating ribosomes, and they suggest that there remains a substantial amount of functionally uncharacterized "dark matter" involved in mRNA translation.

biochemistry↗

bioRxiv2023

Enhanced selectivity of transcutaneous spinal cord stimulation by multielectrode configuration

ObjectiveTranscutaneous spinal cord stimulation (tSCS) has been gaining momentum as a non-invasive rehabilitation approach to restore movement to paralyzed muscles after spinal cord injury (SCI). However, its low selectivity limits the types of movements that can be enabled and, thus, its potential applications in rehabilitation. ApproachIn this cross-over study design, we investigated whether muscle recruitment selectivity of individual muscles could be enhanced by multielectrode configurations of tSCS in 16 neurologically intact individuals. We hypothesized that due to the segmental innervation of lower limb muscles, we could identify muscle-specific optimal stimulation locations that would enable improved recruitment selectivity over conventional tSCS. We elicited leg muscle responses by delivering biphasic pulses of electrical stimulation to the lumbosacral enlargement using conventional and multielectrode tSCS. ResultsAnalysis of recruitment curve responses confirmed that multielectrode configurations could improve the rostrocaudal and lateral selectivity of tSCS. To investigate whether motor responses elicited by spatially selective tSCS were mediated by posterior root-muscle reflexes, each stimulation event was a paired pulse with a conditioning-test interval of 33.3 ms. Muscle responses to the second stimulation pulse were significantly suppressed, a characteristic of post-activation depression suggesting that spatially selective tSCS recruits proprioceptive fibers that reflexively activate muscle-specific motor neurons in the spinal cord. Moreover, the combination of leg muscle recruitment probability and segmental innervation maps revealed a stereotypical spinal activation map in congruence with each electrodes position. SignificanceImprovements in muscle recruitment selectivity could be essential for the effective translation into stimulation protocols that selectively enhance single-joint movements in neurorehabilitation.

neuroscience↗

bioRxiv2022

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed "positional information". How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.

developmental biology↗

bioRxiv2022

Nuclear speckle-localized RNAs exhibit preferential positioning and orientation

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. Specifically, we image transcripts containing a region enriched in SR protein binding motifs and another region enriched in hnRNP binding motifs. We show that these transcripts localize to the outer shell of speckles, with the SR motif-rich region localized closer to the speckle center relative to the hnRNP motif-rich region. Further, we identify that this intra-speckle RNA organization is driven by the strength of RNA-protein interactions inside and outside speckles. Our results hint at novel functional roles of nuclear speckles and likely other membraneless organelles in organizing RNA substrates for biochemical reactions.

biophysics↗

bioRxiv2022

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. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here we dissect the free energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free energy landscape). We propose that such ligand-dependent entropic control of free energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

biophysics↗