Biology subjects

Nie, X. Y.

Publications and source records attributed to Nie, X. Y..

3 recordsLinked to original sources

bioRxiv2025

Thymine DNA Glycosylase Binds to R-Loops and Excises 5-Formyl and 5-Carboxyl Cytosine from DNA/RNA Hybrids

R-loops are three-stranded nucleic acid structures consisting of a DNA/RNA hybrid and a displaced single-stranded DNA. Once considered rare byproducts of transcription, R-loops are now recognized as important regulators of various nuclear processes. In particular, evidence indicates a role for R-loops in regulating DNA methylation dynamics. R-loops have been shown to promote active DNA demethylation--the enzymatic reversal of 5-methylcytosine (5mC) back into cytosine--by recruiting associated proteins, providing an attractive targeting mechanism. Nevertheless, many important aspects of this process, including whether the associated proteins bind to and function on R-loops, remain to be substantiated. In this study, we demonstrate for the first time that thymine DNA glycosylase (TDG), a key enzyme in the active DNA demethylation pathway, binds tightly to R-loops in vitro and can excise DNA demethylation intermediates 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) from DNA in DNA/RNA hybrid duplexes. We also show that R-loops guide the strand-specific activity of TDG at CpG sites, potentially explaining the asymmetric distribution of 5fC/5caC at gene promoters. Furthermore, we provide important mechanistic insights into base excision on DNA/RNA hybrid duplexes using 19F NMR. Finally, our findings suggest that TDG-R-loop interactions may be widespread in human cells. Collectively, our results provide strong evidence that R-loops play a critical role in DNA demethylation and support a mechanism in which 5fC/5caC are directly removed from DNA/RNA hybrids in cells. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/668694v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1ac2095org.highwire.dtl.DTLVardef@18f4952org.highwire.dtl.DTLVardef@16c403org.highwire.dtl.DTLVardef@9ed96c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver

Circadian rhythms are remarkably widespread across most organisms, regulating hormonal, metabolic, physiological, and behavioral oscillations through molecular clocks that orchestrate the rhythmic expression of thousands of genes. Here, we generate single-nucleus RNA and ATAC multiomics data to simultaneously characterize gene expression and chromatin accessibility of mouse liver cells across the 24-hour day. We interrogate multimodal circadian rhythmicity in both discretized cell types and transient sub-lobule cell states, capturing space-time omics profiles. We delve beyond mean cyclic patterns to characterize stochastic transcriptional bursting and infer spatiotemporal gene regulatory networks that control circadian rhythmicity and liver physiology. Our findings apply to existing single-cell data of mouse and Drosophila brains and are validated by time-series single-molecule fluorescence in situ hybridization and vast amounts of orthogonal omics data. Altogether, our study constructs a comprehensive map of the time-series transcriptomic and epigenomic landscapes that elucidate the function and mechanism of the liver peripheral clocks.

bioinformatics↗

bioRxiv2024

Circadian regulation of stereotypic chromatin conformations at enhancers

Cooperation between the circadian transcription factor (TF) CLOCK:BMAL1 and other TFs at cis-regulatory elements (CREs) is critical to daily rhythms of transcription. Yet, the mechanisms underlying this cooperation are unclear. Here, we analyzed the co-binding of multiple TFs on single DNA molecules in mouse liver using single molecule footprinting (SMF). We found that SMF reads clustered in stereotypic chromatin states that reflect distinguishable organization of TFs and nucleosomes, and that were remarkably conserved between all samples. DNA protection at CLOCK:BMAL1 binding motif (E-box) varied between CREs, from E-boxes being solely bound by CLOCK:BMAL1 to situations where other TFs competed with CLOCK:BMAL1 for E-box binding. SMF also uncovered CLOCK:BMAL1 cooperative binding at E-boxes separated by 250 bp, which structurally altered the CLOCK:BMAL1-DNA interface. Importantly, we discovered multiple nucleosomes with E-boxes at entry/exit sites that were removed upon CLOCK:BMAL1 DNA binding, thereby promoting the formation of open chromatin states that facilitate DNA binding of other TFs and that were associated with rhythmic transcription. These results demonstrate the utility of SMF for studying how CLOCK:BMAL1 and other TFs regulate stereotypical chromatin states at CREs to promote transcription.

molecular biology↗