Biology subjects

Xi, S.

Publications and source records attributed to Xi, S..

12 recordsLinked to original sources

bioRxiv2026

Spatiotemporal proteomic profiling of genome editing-associated microenvironment

Genome editing outcomes are influenced by local genomic context, yet the dynamic protein assemblies that form around genome editing sites remain poorly characterized. Here, we developed a Cas9-TurboID proximity labeling platform that combines programmable genomic targeting with rapid and minimally perturbative protein labeling, enabling spatiotemporal mapping of dynamic protein assemblies associated with distinct genome editing processes. Dynamic comparative profiling identified ACTL6A and H2A.Z as candidate regulators of genome editing, and Cas9 fusion with either ACTL6A or H2A.Z enhanced editing efficiency and improved editing outcomes in heterochromatic regions, which are generally refractory to genome editing due to limited DNA accessibility. We further extended the platform to prime editing and identified WRN as a functional regulator. Together, this study provides a strategy for systematically decoding editor-associated protein microenvironments, establishing a framework for understanding genome editing mechanisms and guiding the rational engineering of genome editors.

cell biology↗

bioRxiv2025

Metabolite accumulation mediates the shift between HOC and LOC phases in the Yeast Metabolic Cycle

The Yeast Metabolic Cycle (YMC) is a molecular system that serves as a model to study the internal clock that maintains homeostasis in complex organisms. Traditionally, this ultradian rhythm has been studied in the three phases where mature mRNA transcripts show peak accumulation. However, recent studies have shown that the YMC can be interpreted as a two-phase cycle based on altered redox states, known as the high (HOC) and low oxygen consumption (LOC) phases. The length of the HOC phase is fixed and its frequency is nutrient dependent but the nature of the HOC to LOC transition is poorly defined. Here, we use multivariate statistics to integrate metabolic, chromatin and transcriptional changes across the YMC to study the levels of organization that connect them. Our model reveals that both the HOC-LOC and LOC-HOC phase transitions in the YMC are coordinated by accumulating metabolites, reflecting cellular energetics and redox state. We propose that the cycling behavior of chromatin states, transcription and transcripts is a consequence of accumulating metabolites at phase transitions, which function by modulating protein activity and coordinating biochemical pathways to maintain cellular homeostasis.

cell biology↗

bioRxiv2025

A method for the detection and enrichment of endogenous cereblon substrates

C-Terminal cyclic imides are posttranslational modifications on proteins that are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN). Despite the observation of these modifications across the proteome by mass spectrometry-based proteomics, an orthogonal and generalizable method to visualize the C-terminal cyclic imide would enhance detection, sensitivity, and throughput of endogenous CRBN substrate characterization. Here we develop an antibody-like reagent, termed "cerebody," for visualizing and enriching C-terminal cyclic imide-modified proteins. We describe the engineering of CRBN derivatives to produce cerebody and use it to identify CRBN substrates by Western blot and enrichment from whole cell and tissue lysates. CRBN substrates identified by cerebody enrichment are mapped, validated, and further characterized for dependence on the C-terminal cyclic imide modification. These methods will accelerate the characterization of endogenous CRBN substrates and their regulation.

biochemistry↗

bioRxiv2025

Synthetic derivatives of vinpocetine as antiproliferative agents

Vincamine is an indole alkaloid initially isolated from plants of the Vinca genus and has previously been demonstrated to have antioxidant, hypoglycemic, and hypolipidemic activities. Vinpocetine, a synthetic derivative of vincamine with an enhanced pharmacological profile, has demonstrated promising antiproliferative properties. While previously reported vinpocetine derivatives have undergone extensive investigation for their pharmacological properties, the role of the E-ring ethyl ester in the anticancer properties of compounds with this scaffold has not yet been fully described. Here, we report the antiproliferative activity of two vinpocetine analogs with modifications at the E-ring. MTT assays revealed that reduction of the ethyl ester to an alcohol exhibited strong dose-dependent antiproliferative activity across five mammalian cell lines, but did not induce significant markers of apoptosis or necrotic death as determined by FITC/Annexin V and cell cycle flow cytometry, respectively. We further observe that vinpocetine and both analogs exhibit dose-dependent modulation of a TCF/LEF reporter cell, which appears to be decoupled from trends in antiproliferative activity Altogether, this work demonstrates the potential for E-ring modifications of vinpocetine as anticancer agents.

cancer biology↗

bioRxiv2024

Axon initial segment plasticity caused by auditory deprivation degrades time difference sensitivity in a model of neural responses to cochlear implants

Synaptic and neural properties can change during periods of auditory deprivation. These changes may disrupt the computations that neurons perform. In the brainstem of chickens, auditory deprivation can lead to changes in the size and biophysics of the axon initial segment (AIS) of neurons in the sound source localization circuit. This is the phenomenon of axon initial segment (AIS) plasticity. Individuals who use cochlear implants (CIs) experience periods of hearing loss, and so we ask whether AIS plasticity in neurons of the medial superior olive (MSO), a key stage of sound location processing, would impact time difference sensitivity in the scenario of hearing with cochlear implants. The biophysical changes that we implement in our model of AIS plasticity include enlargement of the AIS and replacement of low-threshold Potassium conductance with the more slowly-activated M-type Potassium conductance. AIS plasticity has been observed to have a homeostatic effect with respect to excitability. In our model, AIS plasticity has the additional effect of converting MSO neurons from phasic firing type to tonic firing type. Phasic firing is known to have greater temporal sensitivity to coincident inputs. Consistent with this, we find AIS plasticity degrades time difference sensitivity in the auditory deprived MSO neuron model across a range of stimulus parameters. Our study illustrates a possible mechanism of cellular plasticity in a non-peripheral stage of neural processing that could impose barriers to sound source localization by bilateral cochlear implant users.

neuroscience↗

bioRxiv2023

USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC

Abnormal alternative splicing (AS) caused by alterations in spliceosomal factors is implicated in cancers. Standard models posit that splice site selection is mainly determined by early spliceosomal U1, U2 snRNPs. Whether and how other mid/late-acting spliceosome components such as USP39 modulate tumorigenic splice site choice remain largely elusive. We observed that hepatocyte-specific knock-in of USP39 promoted hepatocarcinogenesis and potently regulated splice site selection. In human liver cancer cells, USP39 promoted tumor proliferation in a spliceosome-dependent manner. USP39 depletion deregulated hundreds of AS events, including the oncogenic splice-switching of KANK2. Mechanistically, we developed a novel RBP-motif enrichment analysis and found that USP39 modulated exon inclusion/exclusion by interacting with SRSF6/HNRNPC in both humans and mice. Our data represent a paradigm for the control of splice site selection by mid/late-acting spliceosome proteins and their interacting RBPs. USP39 and possibly other mid/late-acting spliceosome proteins may represent potential prognostic biomarkers and targets for cancer therapy. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/525324v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@34cbc1org.highwire.dtl.DTLVardef@2d0ee2org.highwire.dtl.DTLVardef@2c4bd6org.highwire.dtl.DTLVardef@26db00_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

Genomes are pervasively transcribed, leading to stable and unstable transcripts that influence 3-dimensional genome organisation and gene regulation. High sensitivity and nucleotide resolution are required to resolve mammalian nascent transcriptomes. Here, we exploit the sensitivity of 4-thio-uridine (4sU) metabolic pulse-labelling to develop two nucleotide-resolution methods: Single-Nucleotide resolution 4sU sequencing (SNU-Seq) and size-fractionated 4sU-Seq (sf4sU-Seq). sf4sU-Seq involves gel isolation of abundant 4sU-labelled promoter proximal nascent transcripts, enabling nucleotide resolution mapping of transcription start sites and promoter proximal pauses (PPPs) on the same transcript. SNU-Seq exploits 3 end RNA-Seq, using bacterial poly(A) polymerase (bPAP) to polyadenylate the 3 ends of nascent transcripts and create oligo(dT)-primed libraries. The artificial poly(A) tail marks the precise position of polymerase on a transcription unit. SNU-Seq read levels are similar at pre-mRNAs and enhancers genome-wide and read spikes in pre-mRNA outputs map pauses, PPPs and polyadenylation sites. SNU-Seq enables discovery of thousands of unannotated regions of divergent transcription and helps define hundreds of the more than 10,000 regions of primed non-transcribed acetylated open chromatin that induce divergent nascent transcripts within 0.5h of IFN-{gamma} treatment in Hep3B cells. Thus, combining chromatin analysis with SNU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome. HIGHLIGHTSO_LISNU-Seq maps nascent transcripts with bp resolution, high sensitivity and low cost C_LIO_LIsf4sU-Seq resolves TSS and PPP at the same gene, complementing SNU-Seq C_LIO_LI1000s of divergently transcribed enhancers resolved by SNU-Seq C_LIO_LIRapid IFN{gamma} dependent transcriptional induction from primed Hep3B epigenome C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/452379v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@da6239org.highwire.dtl.DTLVardef@16692c6org.highwire.dtl.DTLVardef@12e30f7org.highwire.dtl.DTLVardef@190c98f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2021

A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation

Zero-valent sulfur (ZVS) is a critical intermediate in the biogeochemical sulfur cycle. Up to date, sulfur oxidizing bacteria have been demonstrated to dominate the formation of ZVS. In contrast, formation of ZVS mediated by sulfate reducing bacteria (SRB) has been rarely reported. Here, we report for the first time that a typical sulfate reducing bacterium Desulfovibrio marinus CS1 directs the formation of ZVS via sulfide oxidation. In combination with proteomic analysis and protein activity assays, thiosulfate reductase (PhsA) and sulfide: quinone oxidoreductase (SQR) were demonstrated to play key roles in driving ZVS formation. In this process, PhsA catalyzed thiosulfate to form sulfide, which was then oxidized by SQR to form ZVS. Consistently, the expressions of PhsA and SQR were significantly up-regulated in strain CS1 when cultured in the deep-sea cold seep, strongly indicating strain CS1 might form ZVS in its real inhabiting niches. Notably, homologs of phsA and sqr widely distributed in the metagenomes of deep-sea SRB. Given the high abundance of SRB in cold seeps, it is reasonable to propose that SRB might greatly contribute to the formation of ZVS in the deep-sea environments. Our findings add a new aspect to the current understanding of the source of ZVS.

microbiology↗

bioRxiv2021

Predicting the current and future distribution of four original plants of Gentianae Macrophyllae Radix in China under climate change scenarios

The wild resources of the four original plants (Gentiana crasicaulis Duthie ex Burk, Gentiana daurica Fisch, Gentiana straminea Maxim, and Gentiana macrophylla Pall) of Gentianae Macrophyllae Radix are becoming exhausted. Predicting the distribution under current and future climate scenarios is of significance for the sustainable utilization of resources and ecological protection. In this study, we constructed four species distribution models (SDMs) combining species distribution informations, 19 bioclimatic variables, and the maximum entropy (MaxEnt) model. The results showed that these 4 plants prefer a cool and humid climate. Under the future climate scenarios, the areas of the highly suitable habitats for Gentiana crasicaulis Duthie ex Burk and Gentiana daurica Fisch were likely to decrease, while Gentiana straminea Maxim was likely to expand, and Gentiana macrophylla Pall was less affected. In addition, the centroids of the highly suitable habitats for the four species shifted north or west. Most notably, most of the highly suitable habitats for the four species remained unchanged, which would be the preferred area for semi-artificial cultivation. The above information in this study would contribute to the development of reasonable strategies to reduce the impact of climate change on the four original plants.

ecology↗

bioRxiv2020

ABACUS: A flexible UMI counter that leverages intronic reads for single-nucleus RNAseq analysis

Single-nucleus RNA sequencing (sNuc-RNAseq) is an emerging powerful genomics technology that combines droplet microfluidics with next-generation sequencing to interrogate transcriptome changes at single nucleus resolution. Here we developed Abacus, a flexible UMI counter software for sNuc-RNAseq analysis. Abacus draws extra information from sequencing reads mapped to introns of pre-mRNAs (~60% of total data) that are ignored by many single-cell RNAseq analysis pipelines. When applied to our pilot human brain sNuc-RNAseq data, ABACUS nearly doubled the number of nuclei identified by the CellRanger workflow, recovering a large number of nuclei from non-neuronal cells. By incorporating intronic reads into gene expression quantification, we showed that they encoded additional and valid transcription features of individual cells and could be used to improve cluster resolution of different cell types. By separately counting UMIs derived from forward and reverse intronic reads and from exonic reads, Abacus gives users flexibility in representing genes expressed at different abundance levels. In summary, Abacus represents a flexible, improved workflow for sNuc-RNAseq data processing and analysis.

bioinformatics↗

bioRxiv2020

Mosquito defensins enhance Japanese encephalitis virus infection by facilitating virus adsorption and entry within mosquito

Japanese encephalitis virus (JEV) is a viral zoonosis which can cause viral encephalitis, death and disability. Culex is the main vector of JEV, but little is known about JEV transmission by this kind of mosquito. Here, we found that mosquito defensin facilitated the adsorption of JEV on target cells via both direct and indirect pathways. Mosquito defensin bound the ED III domain of viral E protein and directly mediated efficient virus adsorption on the target cell surface, Lipoprotein receptor-related protein 2 expressed on the cell surface is the receptor affecting defensin dependent adsorption. Mosquito defensin also indirectly down-regulated the expression of an antiviral protein, HSC70B. As a result, mosquitos defensin enhances JEV infection in salivary gland while increasing the possibility of viral transmission by mosquito. These findings demonstrate that the novel effects of mosquito defensin in JEV infection and the mechanisms through which the virus exploits mosquito defensin for infection and transmission.

microbiology↗

bioRxiv2019

H3K4me3 is neither instructive for, nor informed by, transcription.

H3K4me3 is a near-universal histone modification found predominantly at the 5 region of genes, with a well-documented association with gene activity. H3K4me3 has been ascribed roles as both an instructor of gene expression and also a downstream consequence of expression, yet neither has been convincingly proven on a genome-wide scale. Here we test these relationships using a combination of bioinformatics, modelling and experimental data from budding yeast in which the levels of H3K4me3 have been massively ablated. We find that loss of H3K4me3 has no effect on the levels of nascent transcription or transcript in the population. Moreover, we observe no change in the rates of transcription initiation, elongation, mRNA export or turnover, or in protein levels, or cell-to-cell variation of mRNA. Loss of H3K4me3 also has no effect on the large changes in gene expression patterns that follow galactose induction. Conversely, loss of RNA polymerase from the nucleus has no effect on the pattern of H3K4me3 deposition and little effect on its levels, despite much larger changes to other chromatin features. Furthermore, large genome-wide changes in transcription, both in response to environmental stress and during metabolic cycling, are not accompanied by corresponding changes in H3K4me3. Thus, despite the correlation between H3K4me3 and gene activity, neither appear to be necessary to maintain levels of the other, nor to influence their changes in response to environmental stimuli. When we compare gene classes with very different levels of H3K4me3 but highly similar transcription levels we find that H3K4me3-marked genes are those whose expression is unresponsive to environmental changes, and that their histones are less acetylated and dynamically turned-over. Constitutive genes are generally well-expressed, which may alone explain the correlation between H3K4me3 and gene expression, while the biological role of H3K4me3 may have more to do with this distinction in gene class.

genomics↗