Biology subjects

CHEN, S.

Publications and source records attributed to CHEN, S..

4 recordsLinked to original sources

bioRxiv2026

Small Molecule-Directed RNA Modification via Proximity-Driven Catalysis

Selective chemical modification of RNA is essential for RNA functionalization, probing RNA structure-function relationships and developing RNA-targeted therapeutics. Existing chemical strategies often rely on guanine accessibility or multiple helper DNA strands, restricting their generality and biological applicability. Inspired by DNA-guided DMAP catalysis and small-molecule binding-induced crosslinking, we report a small molecule-directed, DMAP-catalyzed, proximity-driven strategy for site-selective RNA functionalization. By appending a catalytic DMAP moiety to RNA-binding ligands, 2'-OH groups are selectively acylated in the presence of azide-bearing acyl donors, enabling subsequent installation of bioorthogonal handles. This approach was validated across diverse RNAs, including Pepper and Clivia RNA aptamers, G-quadruplex Broccoli RNA, and endogenous FMN riboswitch RNA. For a 400-nt Pepper-7SK fusion, selective modification of the Pepper motif was achieved with minimal perturbation to the nucleus localization function of 7SK RNA. Optimized PEG-pentafluorophenyl (PFP) acyl donors provided enhanced reactivity and low background. The method operates catalytically, decouples ligand recognition from the labeling moiety, and enables selective enrichment of target RNAs, offering a versatile platform for RNA functionalization, ligand profiling, and potentially live-cell applications.

biochemistry↗

bioRxiv2025

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains unclear whether such approaches can operate within the regulatory complexity of mammalian tissues in vivo. Here, we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks (CNNs) on genome-wide chromatin accessibility and fine-tune them via transfer learning on validated human and mouse enhancers. Guided by these models, we design fifteen synthetic enhancers for the heart, limb, and central nervous system (CNS) in mouse embryos, all of which are active in their intended target tissue. Our work establishes a generalizable framework for programmable control of mammalian gene expression in vivo, opening new avenues in functional genomics, synthetic biology, and gene therapy.

synthetic biology↗

bioRxiv2025

Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Nanopore RNA004 Technology

RNA modifications are critical regulators of diverse cellular processes, yet their roles in prokaryotic mRNAs remain poorly understood. Recent advances in Oxford Nanopore sequencing--especially the RNA004 kit--have enabled higher yields, reduced signal-to-noise ratio, and improved read accuracy, making them promising tools for investigating bacterial epitranscriptomes. Here, we presented a comprehensive walkthrough for Escherichia coli RNA modification analysis based on RNA004. Using both native (WT) and in vitro-transcribed (IVT) RNA samples, we first evaluated the Dorado modification detection models ({Psi}, mA, mC, and A-to-I). While each model successfully identified known rRNA modification sites, it also generated many false positives, emphasizing the need for careful data interpretation. To address these limitations, we introduced nanoSundial (https://github.com/lrslab/nanoSundial), a new comparative method that leveraged raw current features from WT and IVT samples to detect multiple types of RNA modifications in prokaryotes. We optimized nanoSundial on well-studied rRNA sites and validated its effectiveness with tRNA modifications. Through technical and biological replicate analyses, nanoSundial demonstrated reproducibility exceeding 95% in tRNA, rRNA, and ncRNA regions, albeit with lower reproducibility ([~]61%) in mRNA. We further found enrichment of mRNA modifications at the start or end of coding sequences. In total, 190 stably modified CDS regions were identified in E. coli, many of which cluster near the end of highly expressed transcriptional units (TUs) in each operon. Overall, this study highlighted the strengths and limitations of current nanopore-based modification detection methods on bacterial RNA, introduced a robust new comparative tool, and elucidated previously uncharacterized mRNA modification landscapes. Our findings open new avenues for understanding the functional impacts of bacterial RNA modifications and advancing epitranscriptomic research in prokaryotes.

bioinformatics↗

bioRxiv2024

Catalytic-independent functions of INTAC in conferring sensitivity to BET inhibition

Chromatin and transcription regulators are critical to defining cell identity through shaping epigenetic and transcriptional landscapes, with their misregulation being closely linked to oncogenesis. Pharmacologically targeting these regulators, particularly the transcription activating BET proteins, has emerged as a promising approach in cancer therapy, yet intrinsic or acquired resistance frequently occurs with poorly understood mechanisms. Using genome-wide CRISPR screens, we find that BET inhibitor efficacy in mediating transcriptional silencing and growth inhibition depends on the auxiliary module of the INTAC complex, a global regulator of polymerase pause-release dynamics. This process bypasses a requirement for INTACs catalytic activities and instead leverages direct engagement of the auxiliary module with the RACK7/ZMYND8-KDM5C complex to remove histone H3K4 methylation. Targeted degradation of the COMPASS subunit WDR5 to attenuate H3K4 methylation restores sensitivity to BET inhibitors, highlighting how simultaneously targeting coordinated chromatin and transcription regulators can circumvent drug-resistant tumors.

molecular biology↗