Biology subjects

Cheng, S.

Publications and source records attributed to Cheng, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Divide and conquer: How avian 'prefrontal' and hippocampal neurons process extinction learning in complementary ways

Context-dependent extinction learning enables organisms to acquire an inhibition of responding to cues that no longer signal reward in specific environmental settings. Both the hippocampus and the prefrontal cortex play key but complementary roles in encoding extinction. To understand what drives the differential contributions of these two structures, we recorded single-unit responses from the pigeon hippocampus (HPC) and the prefrontal nidopallium caudolaterale (NCL), while the animals were engaged in a repeated appetitive ABA extinction learning paradigm. HPC carried more information about experimental phases (acquisition (context A), extinction (context B), and renewal (context A)) than NCL. In addition, hippocampal neurons with mixed selectivity integrated all contextual stimuli and conditioned cues, thereby possibly enabling context integration into phase-dependent extinction events. The mixed selectivity pattern of NCL neurons differed: They encoded all relevant task parameters separately, thereby possibly enabling the weighing and deciding between response alternatives. Repeatedly testing the same animals over many months enabled us to reveal that the activity of NCL neurons increasingly became predictive of the number of responses that animals made during renewal. Thus, NCL neurons possibly assumed a meta-learning ability that enabled a behavioral adaption to the deeper task structure that always followed the sequence of acquisition[->]extinction[->]renewal. Our results make it likely that different processing strategies of hippocampus and prefrontal NCL enable a differential encoding of experimental phase, context, decision-making, and meta-learning during extinction learning.

neuroscience↗

bioRxiv2025

Governed by surface amino acid composition: HIV capsid passage through the NPC barrier

Nuclear transport receptors (NTRs) carry cargo across the permeability barrier of nuclear pore complexes (NPCs) - an FG phase condensed from disordered but cohesive FG repeats. This phase repels normal macromolecules but allows NTR passage. When HIV infects non-dividing cells, its capsid is transported into nuclei not like cargo but crosses NPCs like NTRs. We now uncovered the molecular determinants of the capsids NTR behavior: The FG-binding pocket is insufficient. Hexameric and pentameric capsomers contribute. The highly exposed outer capsid surface is key. It lacks FG-repulsive charged residues (K,D,E) that are very abundant on normal protein surfaces. FG-attractive residues dominate the capsid surface. Introducing FG-repulsive ones impedes FG phase-partitioning, NPC-targeting and NPC-passage of assembled capsids. Capsids are thus made FG phase-soluble by myriads of transient FG-attractive interactions originating from individual surface sidechains. We discuss that CPSF6 releases the capsid from NPCs by switching its surface from FG-attractive to FG-repulsive.

cell biology↗

bioRxiv2025

Revealing the mechanisms underlying latent learning with successor representations

Latent learning experiments were critical in shaping Tolmans cognitive map theory. In a spatial navigation task, latent learning means that animals acquire knowledge of their environment through exploration, such that pre-exposed animals learn faster on a subsequent learning task than naive ones. This enhancement has been shown to depend on the design of the pre-exposure phase. Here, we hypothesize that the deep successor representation (DSR), a recent computational model for cognitive map formation, can account for the modulation of latent learning because it is sensitive to the statistics of behavior during exploration. In our model, exploration aligned with the future reward location significantly improves reward learning compared to random, misdirected, or no exploration, as reported by experiments. This effect generalizes across different action selection strategies. We show that these performance differences follow from the spatial information encoded in the structure of the DSR acquired in the pre-exposure phase. In summary, this study sheds light on the mechanisms underlying latent learning and how such learning shapes cognitive maps, impacting their effectiveness in goal-directed spatial tasks. Author summaryLatent learning enables animals to construct cognitive maps of their environment without direct reinforcement. This process facilitates efficient navigation when rewards are introduced later, that is, animals familiar with a maze through prior exposure learn rewarded tasks faster than those without pre-exposure. Evidence suggests that the design of the pre-exposure phase significantly impacts the effectiveness of latent learning. Targeted pre-exposure focused on future reward locations enhances learning more than generic pre-exposure. However, the underlying mechanisms driving these differences remain understudied. This study investigates how pre-exposure methods influence subsequent navigation task performance using an artificial agent based on deep successor representations -- a model for learning cognitive maps -- within a reinforcement learning framework. Our findings reveal that before reward learning, agents receiving targeted pre-exposure develop spatial features more closely aligned with those of agents learning from rewards, compared to agents experiencing generic pre-exposure. This alignment enables the targeted pre-exposure agent to take more effective targeted actions, resulting in accelerated initial learning. The persistence of this advantage, even when modifying the agents exploration policy, indicates a robust cognitive map within the successor representation.

neuroscience↗

bioRxiv2025

Glycogen Engineering Improves the Starvation Resistance of Mesenchymal stem cells and their Therapeutic Efficacy in Pulmonary Fibrosis

Mesenchymal stem cells (MSCs) are widely used in regenerative medicine, including the treatment of pulmonary fibrosis. However, implanted MSCs disappear within days, constraining therapeutic efficacy, which is largely attributed to nutrient deprivation. In this study, we established glycogen metabolism engineering strategies in mammalian cells. By expressing a functionally optimized glycogen synthase (GYSmut), MSCs could accumulate large amounts of glycogen rapidly as a reserve substance. Glycogen engineering significantly improved the survival of MSCs during starvation both in vitro and in vivo, enhancing cell viability post-implantation and their therapeutic efficacy in pulmonary fibrosis. Glycogen-engineered MSCs may serve as chassis cells for further applications. Our research highlights the importance of glucose metabolism regulation in cell-based therapy and demonstrates the great potential for the metabolic engineering of MSCs and other therapeutic cells.

bioengineering↗

bioRxiv2025

Cerebellar transcranial alternating current stimulation in the theta band facilitates extinction of learned fear responses

Fear extinction is a major component of exposure therapy for anxiety disorders. There is initial evidence that the cerebellum contributes to fear extinction learning, i.e., the ability to learn that certain stimuli are no longer associated with an aversive outcome. So far, however, knowledge of the cerebellums role in extinction is scarce. In the present study, 6 Hz cerebellar transcranial alternating current stimulation (ctACS) was used to modulate cerebellar function during extinction learning in young and healthy human participants in an MRI study. A two- day differential fear conditioning paradigm was used with acquisition and extinction training being performed on day 1, and fear extinction recall being tested on day 2. 6 Hz ctACS reduced spontaneous recovery of the initial fear association during recall, stabilizing extinction effects compared to sham ctACS. fMRI data during recall revealed significantly reduced activation in cortical areas involved in initial fear acquisition, such as the anterior cingulate and insula, in the verum ctACS group compared to the sham group. During extinction training, on the other hand, the verum group exhibited more widespread cerebral activation compared to the sham group. Group differences were significant in occipital cortical areas. Although direct stimulation effects cannot be excluded, increased activation in the visual cortex may reflect enhanced encoding and processing of visual information during fear extinction learning. The findings suggest that theta-range oscillatory interactions between the cerebellum and cortical areas support extinction processes and provide causal evidence of the cerebellar role in the human fear extinction network. Significance StatementWhile the cerebellum is well known for its role in associative learning, its contribution to fear extinction learning remains underexplored. This study used 6 Hz cerebellar transcranial alternating current stimulation (ctACS) to modulate cerebellar function during extinction training in healthy participants. The present data demonstrate that ctACS enhances cerebral cortical activation during extinction training which is followed by enhanced recall of the extinction memory and subsequently reduced activation of cerebral cortical areas associated to spontaneous recovery of fear memory. These findings provide causal evidence for the cerebelluar involvement in the human fear extinction network and suggest that enhancing cerebellar theta oscillations may be useful to support exposure therapy.

neuroscience↗

bioRxiv2024

An Investigation into Mechanomyography for Signal Extraction and Classification of Human Lower Limb Activity

To mitigate the difficulties associated with the extraction of Mechanomyography (MMG) signals from raw Accelerometer (ACC) data and the subsequent classification of human lower limb activities based on MMG signals, the Feature Mode Decomposition (FMD) algorithm has been utilized for the isolation of the MMG signal. Simultaneously, surface Electromyography (sEMG) signals were recorded to perform correlation analyses, thereby validating the effectiveness of the extracted Mechanomyography (MMG) signals. The results demonstrate that the envelope entropy derived from the FMD was the lowest among the observed values, and the composite signal obtained via FMD displayed the highest correlation with the sEMG signal. This indicates that FMD is capable of efficiently isolating the MMG signal while maintaining the maximal quantity of muscle contraction data. To address the challenge of classifying human lower limb activities, a comprehensive feature extraction procedure was implemented, resulting in the derivation of 448 unique features from multi-channel mechanomyography (MMG) signals. Subsequently, Kernel Principal Component Analysis (KPCA) was employed to diminish the feature sets dimensionality. This was succeeded by the deployment of a Temporal Convolutional Network integrated with an Attention mechanism (TCN-Attention) to train the classification model. Additionally, an enhanced Northern Goshawk Optimization Algorithm was leveraged for optimization purposes. The findings indicate that FMD exhibited the minimum envelope entropy value of 8.13, concurrently attaining the maximum correlation coefficient of 0.87 between MMG and sEMG signals. Significantly, the SCNGO-TCN-Attention model demonstrated superior classification accuracy, attaining an exceptional accuracy rate of 98.44%.

bioengineering↗

bioRxiv2024

Human cerebellum and ventral tegmental area interact during extinction of learned fear

The key elements for fear extinction learning are unexpected omissions of expected aversive events, which are considered to be rewarding. Given its reception of reward information, we tested the hypothesis that the cerebellum contributes to reward-like prediction error processing driving extinction learning via its connections with the ventral tegmental area (VTA). Forty-three young and healthy participants performed a three-day fear conditioning paradigm in a 7T MR scanner. The cerebellum and VTA were active during unexpected omissions of aversive unconditioned stimuli in the initial extinction trials and in other learning phases, in line with the proposed role of prediction-error processing. Increased functional connectivity was observed between the cerebellum and VTA, indicating that they are functionally coupled during fear extinction learning. These results suggest that an interaction between the cerebellum and VTA should be incorporated into the existing model of the fear extinction network.

neuroscience↗

bioRxiv2024

WAVE1 and WAVE2 facilitate human papillomavirus-driven actin polymerization during cellular entry

Human Papillomavirus Type 16 (HPV16) is an etiological agent of human cancers that requires endocytosis to initiate infection. HPV16 entry into epithelial cells occurs through a non-canonical endocytic pathway that is actin-driven, but it is not well understood how HPV16-cell surface interactions trigger actin reorganization in a way that facilitates entry. This study provides evidence that Wiskott-Aldrich syndrome protein family verprolin-homologous proteins 1 and 2 (WAVE1 and WAVE2) are molecular mediators of the actin polymerization that facilitates HPV endocytosis and intracellular trafficking. We demonstrate through post-transcriptional gene silencing and genome editing that WAVE1 and WAVE2 are critical for efficient HPV16 infection, and that restoration of each in knockout cells rescues HPV16 infection. Cells lacking WAVE1, WAVE2, or both, internalize HPV16 at a significantly reduced rate. Analysis of fluorescently labeled cells exposed to HPV16 and acquired by confocal fluorescence microscopy revealed that HPV16, WAVE1, WAVE2, and actin are all colocalized at the cellular dorsal surface. We also found that HPV16 stimulates WAVE1 and WAVE2-mediated cellular dorsal surface filopodia formation during the viral endocytic process. Taken together, this study provides evidence that the HPV endocytic process needed for infection is controlled by actin reorganization into filopodial protrusions and that this process is mediated by WAVE1 and WAVE2. Author SummaryHuman Papillomavirus (HPV) is the most common sexually transmitted infection in the United States. While its mode of entry into cells has yet to be fully described, extensive studies indicate HPV entry occurs via a macropinocytosis-like pathway. Interestingly, more than 10 viruses enter cells via macropinocytosis-like entry, with no two viruses utilizing identical factors for entry. It is unclear whether these viruses are entering cells via the same pathway, or if the term "macropinocytosis" describes a subset of endocytic pathways. One unifying feature of entry for each of these viruses is their requirement of actin polymerization. In this study, we identify the cellular factors necessary for actin polymerization to participate in HPV endocytosis. The findings of this study are of importance to the field of virology as they may extend to the infection of other viruses. It is also of interest in cancer studies as macropinocytosis has been associated with the scavenging of nutrients and methuosis, a form of cell death in cancer cells that occurs from over- scavenging. Nanoparticle delivery can also occur via macropinocytosis. Therefore, the contribution of WAVE proteins to macropinocytosis and macropinocytosis-like endocytic events is informative to a broad audience.

cell biology↗

bioRxiv2024

Computational redesign of TALE proteins for DNA-templated assembly of protein fibers

Many viral proteins self-assemble into capsid structures, often using their genetic material as a template for assembly. To date, de novo designed capsid-like proteins do not require genetic material as a template for assembly, which can be both an advantage and a disadvantage depending on the use case. Templates are indispensable, for example, in the assembly of linear structures with well-defined lengths. As a first step towards fully de novo designed templated assembly, here we redesign proteins from the Transcription activator-like effector (TALE) family of transcriptional regulators to polymerize on double-stranded DNA (dsDNA) templates. Starting from natural TALE protein sequences, we created idealized repeat proteins with sequence-independent DNA binding properties that cooperatively self-assemble to form linear protein-DNA complexes with template-controlled lengths. We used high-resolution atomic force microscopy (AFM) and cryo electron microscopy (cryo-EM) to characterize the three-dimensional structures of the DNA-protein hybrid complexes. In these structures, a protein filament helically wraps around the dsDNA using a binding mode similar to that of natural TALE proteins. As an example application of these materials, we show the system can be used for repetitive peptide antigen display at precisely controlled repeat distances, and that such immunogens elicit robust antigen-specific antibodies in mice.

biochemistry↗

bioRxiv2024

Small-molecule Activation of TFEB Alleviates Niemann-Pick Disease Type C via Promoting Lysosomal Exocytosis and Biogenesis

Niemann-Pick disease type C (NPC) is a devastating lysosomal storage disease characterized by abnormal cholesterol accumulation in lysosomes. Currently, there is no treatment for NPC. Transcription factor EB (TFEB), a member of the microphthalmia transcription factors (MiTF), has emerged as a master regulator of lysosomal function and promoted the clearance of substrates stored in cells. However, it is not known whether TFEB plays a role in cholesterol clearance in NPC disease. Here, we show that transgenic overexpression of TFEB, but not TFE3 (another member of MiTF family) facilitates cholesterol clearance in various NPC1 cell models. Pharmacological activation of TFEB by sulforaphane (SFN), a previously identified natural small-molecule TFEB agonist by us, can dramatically ameliorate cholesterol accumulation in human and mouse NPC1 cell models. In NPC1 cells, SFN induces TFEB nuclear translocation via a ROS-Ca2+-calcineurin dependent but MTOR-independent pathway and upregulates the expression of TFEB-downstream genes, promoting lysosomal exocytosis and biogenesis. While genetic inhibition of TFEB abolishes the cholesterol clearance and exocytosis effect by SFN. In the NPC1 mouse model, SFN dephosphorylates/activates TFEB in brain and exhibits potent efficacy of rescuing the loss of Purkinje cells and body weight. Hence, pharmacological upregulating lysosome machinery via targeting TFEB represents a promising approach to treat NPC and related lysosomal storage diseases, and provides the possibility of TFEB agonists ie SFN as potential NPC therapeutic candidates.

molecular biology↗

bioRxiv2024

Blood cultures at baseline and during persistent candidemia contain populations of genetically diverse Candida albicans strains that may differ in echinocandin tolerance and virulence

It is unknown whether within-patient Candida albicans diversity is common during bloodstream infections (BSIs). We determined whole genome sequences of 10 C. albicans strains from blood cultures (BCs) in each of 4 patients. BCs in 3 patients contained mixed populations of strains that differed by large-scale genetic variants, including chromosome (Chr) 5 or 7 aneuploidy (n=2) and Chr1 loss of heterozygosity (n=1). Chr7 trisomy (Tri7) strains from patient MN were attenuated for hyphal and biofilm formation in vitro compared to euploid strains, due at least in part to NRG1 over-expression. Nevertheless, representative Tri7 strain M1 underwent filamentation during disseminated candidiasis (DC) in mice. M1 was more fit than euploid strain M2 during DC and mouse gastrointestinal colonization, and in blood ex vivo. M1 and M2 exhibited identical echinocandin minimum inhibitory concentrations, but M2 was more tolerant to micafungin in vitro. Furthermore, M2 was more competitive with M1 in mouse kidneys following micafungin treatment than it was in absence of micafungin. Tri7 strains represented 74% of patient MNs baseline BC population, but after 1d and 3d of echinocandin treatment, euploid strains were 93% and 98% of the BC population, respectively. Findings suggest that echinocandin tolerant, euploid strains were a subpopulation to more virulent Tri7 strains at baseline and then were selected upon echinocandin exposure. In conclusion, BCs in at least some patients are comprised of diverse C. albicans populations not recognized by the clinical lab, rather than single strains. Clinical relevance of C. albicans diversity and antifungal tolerance merits further investigation.

microbiology↗

bioRxiv2024

Patterned wireless transcranial optogenetics generates artificial perception

Synthesizing perceivable artificial neural inputs independent of typical sensory channels remains a fundamental challenge in the development of next-generation brain-machine interfaces. Establishing a minimally invasive, wirelessly effective, and miniaturized platform with long-term stability is crucial for creating a clinically meaningful interface capable of mediating artificial perceptual feedback. In this study, we demonstrate a miniaturized fully implantable wireless transcranial optogenetic encoder designed to generate artificial perceptions through digitized optogenetic manipulation of large cortical ensembles. This platform enables the spatiotemporal orchestration of large-scale cortical activity for remote perception genesis via real-time wireless communication and control, with optimized device performance achieved by simulation-guided methods addressing light and heat propagation during operation. Cue discrimination during operant learning demonstrates the wireless genesis of artificial percepts sensed by mice, where spatial distance across large cortical networks and sequential order-based analyses of discrimination performance reveal principles that adhere to general perceptual rules. These conceptual and technical advancements expand our understanding of artificial neural syntax and its perception by the brain, guiding the evolution of next-generation brain-machine communication.

neuroscience↗

bioRxiv2024

Single field evolution rule governs the dynamics of representational drift in mouse hippocampal dorsal CA1 region.

How the brain reconciles dynamism with stability to balance learning and reliable memory storage has not yet been fully understood. To address the critical question, we longitudinally recorded place cells in the hippocampal dorsal CA1 region over 7 to 56 days, utilizing multiple goal-oriented navigation paradigms across various environments. We found that over 80% of place cells displayed multiple fields, undergoing complex evolution events including field disappearance, formation, and retention. Place fields from the same neuron showed limited coordination ([~]5%), with a preference for synchronized changes. We further uncovered the single field evolution rule: the longer a field remains active, the more likely it is to continue being active; conversely, the longer a field remains inactive, the less likely it is to recover the future fate of a place field depends on its past activity. Mathematical modeling revealed that this rule sufficiently demonstrates the growing stability of the dCA1 spatial representation at the population level.

neuroscience↗

bioRxiv2024

Systematic Multi-Omics Investigation of Androgen Receptor Driven Gene Expression and Epigenetics changes in Prostate Cancer

Background: Prostate cancer, a common malignancy, is driven by androgen receptor (AR) signaling. Understanding the function of AR signaling is critical for prostate cancer research. Methods: We performed multi-omics data analysis for the AR+, androgen-sensitive LNCaP cell line, focusing on gene expression (RNAseq), chromatin accessibility (ATACseq), and transcription factor binding (ChIPseq). High-quality datasets were curated from public repositories and processed using state-of-the-art bioinformatics tools. Results: Our analysis identified 1004 up-regulated and 707 down-regulated genes in response to androgen deprivation therapy (ADT) which diminished AR signaling activity. Gene-set enrichment analysis revealed that AR signaling influences pathways related to neuron differentiation, cell adhesion, P53 signaling, and inflammation. ATACseq and ChIPseq data demonstrated that as a transcription factor, AR primarily binds to distal enhancers, influencing chromatin modifications without affecting proximal promoter regions. In addition, the AR-induced genes maintained higher active chromatin states than AR-inhibited genes, even under ADT conditions. Furthermore, ADT did not directly induce neuroendocrine differentiation in LNCaP cells, suggesting a complex mechanism behind neuroendocrine prostate cancer development. In addition, a publicly available online application LNCaP-ADT (https://pcatools.shinyapps.io/shinyADT/) was launched for users to visualize and browse data generated by this study. Conclusion: This study provides a comprehensive multi-omics dataset, elucidating the role of AR signaling in prostate cancer at the transcriptomic and epigenomic levels. The reprocessed data is publicly available, offering a valuable resource for future prostate cancer research.

cancer biology↗

bioRxiv2024

Computationally designed mRNA-launched protein nanoparticle vaccines

Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic1-6. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses7-10, while mRNA vaccines can be rapidly manufactured11 and elicit antigen-specific CD4 and CD8 T cells12,13. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells14 to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD)15, formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.

immunology↗

bioRxiv2024

Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways

Multicellularity was accompanied by the emergence of new classes of cell surface and secreted proteins. The nematode C. elegans is a favorable model to study cell surface interactomes, given its well-defined and stereotyped cell types and intercellular contacts. Here we report our C. elegans extracellular interactome dataset, the largest yet for an invertebrate. Most of these interactions were unknown, despite recent datasets for flies and humans, as our collection contains a larger selection of protein families. We uncover new interactions for all four major axon guidance pathways, including ectodomain interactions between three of the pathways. We demonstrate that a protein family known to maintain axon locations are secreted receptors for insulins. We reveal novel interactions of cystine-knot proteins with putative signaling receptors, which may extend the study of neurotrophins and growth-factor-mediated functions to nematodes. Finally, our dataset provides insights into human disease mechanisms and how extracellular interactions may help establish connectomes.

biochemistry↗

bioRxiv2024

Cellular and Molecular Changes During Aging in MEC: Unveiling the Role of Bglap3 Neurons in Cognitive Aging

Aging-correlated cognitive declines, including deficiencies in spatial orientation and memory, may reflect dysfunction in the hippocampus and medial entorhinal cortex (MEC). However, aging-related changes in MEC at the cellular and molecular levels remain unclear. In this study, we found fewer grid cells with reduced spatial stability in old mice. We compared gene expression profiles between young and old mice using 10x Genomics Visium technology. Among 1664 differentially expressed genes, we discovered Bglap3, a marker gene for subpopulation in MEC Layer III with decreased cell number with age. Silencing of Bglap3+ neurons in young mice impaired the spatial tuning of neurons in MEC and the spatial learning of a new platform location in water maze. These findings help us to understand the cellular and molecular changes in the MEC in healthy aging animals and the changes of Bglap3+ cells in old mice indicating a possible cause of aging-related MEC deficiency.

neuroscience↗

bioRxiv2024

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.

cancer biology↗