Mechanical force regulates a variety of cellular functions through inducing modulations in nuclear chromatin structures and epigenetic landscapes (outside in). The epigenetic modifications, in turn, regulate gene expressions and affect phenotypic outcomes, including cytoskeletal organization and cell–cell/cell–ECM interactions (inside out). While there have been significant advances in the understanding of mechanotransduction in the nucleus, there is still a lack of knowledge on the potential mechanisms through which mechanical cues affect epigenetic and chromatin regulations to determine genetic outcomes. This review firstly focuses on the current understanding of epigenetic regulations and then summarizes how mechanotransduction and epigenetic modification couple together to regulate molecular and cellular functions, eventually causing functional phenotype changes e.g. , diseases. Lastly, we introduce related technologies for mechanistic studies, particularly fluorescence resonance energy transfer (FRET) biosensors for the visualization of dynamic epigenetic regulations in single living cells, as well as the applications of FRET biosensors to visualize mechanotransduction events occurring in the nucleus. These studies could provide new insights into epigenetics in regulating the physiological and pathological processes in living cells under different mechanical environments.
In eukaryotic cells,the endoplasmic reticulum (ER) forms a continuous network of tubules and sheets.ER membranes are inter-connected by a class of dynamin-like GTPases termed atlastins (ATLs).Deletion or mutation of ATLs results in long and unbranched ER tubules in cells.Mutations in ATL1 in humans have been linked to the neurodegenerative disease hereditary spastic paraplegia.The basis of ATL-mediated membrane fusion has been studied extensively,but specific functions of ATL remain unclear.In this review,we summarize ER-related cellular processes that directly or indirectly involve ATL,including membrane trafficking,lipid metabolism,autophagy,microtubule dynamics,pathogen infections,calcium signaling,and protein homeostasis.These findings provide important clues for deciphering the physiological roles of the tubular ER network.
Tubulin posttranslational modifications (PTMs) add "tubulin code" to generate functional diversities of microtubules.Several types of tubulin PTMs accumulate on axonemes and basal bodies of cilia,including acetylation,glutamylation,glycylation and detyrosination.Among them,glutamylation,glycylation and detyrosination are mostly enriched in the B-tubules,whereas acetylation occurs on both A-and B-tubule of the microtubule doublets in a similar level.Recent studies indicate that tubulin PTMs are critical for the fine tuning of assembly/disassembly,maintenance,motility,and signaling of cilia.Dysregulated tubulin PTMs are strongly implicated in human disorders including ciliopathies and neuron degeneration.Here,we review the current understanding how tubulin PTMs regulate cilia formation and function,and their relevance to human health.
Noncoding RNAs play important roles in cell and their secondary structures are vital for understanding their tertiary structures and functions.Many prediction methods of RNA secondary structures have been proposed but it is still challenging to reach high accuracy,especially for those with pseudoknots.Here we present a coupled deep learning model,called 2dRNA,to predict RNA secondary structure.It combines two famous neural network architectures bidirectional LSTM and U-net and only needs the sequence of a target RNA as input.Benchmark shows that our method can achieve state-of-the-art performance compared to current methods on a testing dataset.Our analysis also shows that 2dRNA can learn structural information from similar RNA sequences without aligning them.
Mechanical properties of brain tissue can provide vital information for understanding the mechanism of traumatic brain injury (TBI).As mouse models were commonly adopted for TBI studies,a method to produce injury to the brain and characterize the injured tissue is desired.In this paper,a complete workflow of TBI induction,sample preparation,and biomechanical characterization is presented for measurement of the injured brain tissue.A controlled cortical impact device was used to induce injury to the brain.By setting the angle,speed,and position of the impact,the level of brain injuries could be controlled.Viscoelastic properties of both injured and non-injured brain tissues were measured using a ramp-hold indentation test.Regions of interests (ROIs) were tested and compared to contralateral corresponding counterparts.Methods introduced in this paper could be easily extended to produce and test a variety of other injured soft biological tissues.
Hepatitis B is caused by hepatitis B virus (HBV),and persistent HBV infection is a global public health problem,with 257 million people as HBV chronic carriers.Viral covalently closed circular DNA (cccDNA) is a key factor to establish persistent infection in infected hepatocytes.Current antiviral therapies have no direct impact on pre-existing cccDNA reservoir,which can be assembled into minichromosome by hijacking host factors.Understanding the mechanisms of epigenetic regulation in cccDNA minichromosome is crucial to develop new therapy on cccDNA,an attractive target for HBV cure.This review summarizes the current advances in epigenetic regulation of cccDNA minichromosome,which might provide clues to novel druggable targets to cure hepatitis B by either silencing or eliminating cccDNA reservoir.
The development of multi-photon microscopic technique has made it possible to image submicron structures deep in biological tissues.This technique is widely used for imaging of cortical structures in developing and adult animals,and there have been detail descriptions of in vivo imaging of synaptic structures in normal animals through a thinned-skull or open-skull cranial window.However,several challenges should be considered carefully for high-resolution imaging of cortical structures under pathological conditions.Here we describe a protocol for in vivo imaging of dendritic structures following ischemic stroke through thinned skull.This protocol can also be applied for acute or chronic imaging of neuronal structural plasticity,glial activation,cerebral microcirculation,or synaptic functions in other pathological conditions.
Molecular dynamics simulations can be a powerful tool to complement experiments in the study of the structures and dynamics of intrinsically disordered proteins. Though the accuracy of the physics-based all-atom force fields has improved significantly in simulating structured proteins over the past twenty years, most of these force fields face a big challenge to simulate flexible proteins. Recently, CHARMM36m with modified TIP3P model was proposed as a possible solution to simulate intrinsically disordered proteins. Here, we tested the proposed solution using an extensively studied protein, namely NCBD, to explore the performance of CHARMM36m plus modified TIP3P water. Our results suggest that the modified TIP3P water model does enhance the sampling of conformational space compared to the standard TIP3P water model. However, the new CHARMM36m force field still leads to over-compact structures and over-stabilized helices.
The toxin–antitoxin (TA) system is composed of a stable toxin and an unstable antitoxin that neutralizes the toxin. Being perhaps the most studied among the different TA types, type II TA systems are widely distributed and often exist in multiple copies within chromosomes of eubacteria and archaea. Exhibiting diverse molecular activities such as RNases, kinases, and acetyltransferases, type II TA systems have been confirmed to be involved in diverse biological processes including plasmid maintenance, phage inhibition, persistence, stress response, and biofilm formation. In this review, we summarize the current state of the research in the type II TA field, emphasizing the activation mechanism, structure–function relationship, and biological functions of type II TA systems.
The gallbladder is an important component of the hepatobiliary system whose primary function is to aid in digestion of foodstuffs, excretion of drugs and facilitate removal of waste products from the body. The gall bladder is principally a storage organ for bile, chemically modified salts and acids of cholesterol which are synthesized in the liver and which function as surfactants to solubilize fatty substances of limited aqueous solubility. Any disruption in the amount or activity of bile surfactant can lead to an accumulation of insoluble molecular clumps ( e.g., gallstones) that deposit in and obstruct fluid movement within the gallbladder, and which can lead to pathological congestion and tissue damage. The natural host defense response to any event that causes tissue damage is to stimulate inflammation, which non-specifically but aggressively reacts to the stimuli so to remove the cause and repair damaged tissues. The C-reactive protein (CRP) is a primarily hepatically produced serum protein whose blood levels increase within 6–10 h of any tissue-damaging event. The extent with which it increases correlates with the level of tissue damage and associated inflammation. CRP levels are reported to be of value in diagnosing acute cholecystitis severity, in predicting the outcome and prognosis of cancer-associated gallbladder resection, and in helping identify cystic structures during emergency laparoscopic cholecystectomies. As an understanding of distinctive CRP structural isoforms is evolving, its role not only as a biomarker but as regulator of both physiologic and pathophysiologic processes of inflammation may be relevant in the understanding of and treatment approaches for gallbladder-associated disease.
The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.
