Biology subjects

Liew, S. W.

Publications and source records attributed to Liew, S. W..

4 recordsLinked to original sources

bioRxiv2025

Modification of RNAs in natural rG4 (MoRNiNG), A Database of RNA Modification Sites Associated with the Dynamics of RNA Secondary Structures

RNA structures are essential building blocks of functional RNA molecules. Profiling secondary structures in vivo and in real-time remains challenging because RNAs exhibit dynamic structures and complex conformations. Besides the stem-loop canonical secondary structure, the non-canonical structure RNA G-quadruplex (rG4) is of great interest for its potential as a drug target. Early studies have demonstrated that RNAs can form distinct secondary structures. However, it is not well understood how distinct RNA structures, formed from the same RNA sequences, function within the transcriptome. The factors driving and regulating structure transitions remain poorly investigated. Inspired by a segment in the HOXB9 mRNA capable of forming multiple structures, we found that many RNA segments across the transcriptome exhibit multi-faceted structure-forming potential. For the HOXB9 case, we demonstrated that RNA modification influences RNA structure and binding with RNA binding proteins. Therefore, we collected RNA modification sites naturally occurring in the putative G-quadruplex-forming sequences (PQSs) of transcripts and developed MoRNiNG, a freely accessible database at https://www.cityu.edu.hk/bms/morning. The database is designed and organized by reliability tiers determined by the resolution of RNA modification sites and capable of including various large datasets. We experimentally validated the influence of m6A, m5C, and A-to-I editing on rG4-forming sequences and provided evidence to support the modification switch concept. The diversity and transition of secondary structures from the same RNA segment offers valuable insights into the regulation of RNA structure dynamics.

systems biology↗

bioRxiv2025

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

G-quadruplexes (G4s) are alternative DNA structures with diverse biological roles, but their examination in highly repetitive parts of the human genome has been hindered by the lack of reliable sequencing technologies. Recent long-read based genome assemblies have enabled their characterization in previously inaccessible parts of the human genome. Here, we examine the topography and genomic instability of potential G4-forming sequences in the gap-less, reference human genome assembly and in 88 haplotypes of diverse ancestry. We report that G4s are highly enriched in specific repetitive regions, including in certain centromeric and pericentromeric repeat types, and in ribosomal DNA arrays, and experimentally validate the most prevalent G4s detected. G4s tend to have lower methylation than expected throughout the human genome and are genomically unstable, showing an excess of all mutation types, including substitutions, insertions and deletions and most prominently structural variants. Finally, we show that G4s are consistently enriched at PRDM9 binding sites, a protein involved in meiotic recombination. Together, our findings establish G4s as dynamic and functionally significant elements of the human genome and highlight new avenues for investigating their contributions to human disease and evolution.

genomics↗

bioRxiv2024

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

G-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability. These structures have demonstrably shaped organismal evolution. However, a comprehensive, organism-wide G-quadruplex map encompassing the diversity of life has remained elusive. Here, we introduce Quadrupia, the most extensive and well-characterized G-quadruplex database to date, facilitating the exploration of G-quadruplex structures across the evolutionary spectrum. Quadrupia has identified G-quadruplex sequences in 108,449 reference genomes, with a total of 140,181,277 G-quadruplexes. The database also hosts a collection of 319,784 G-quadruplex clusters of 20 or more members, annotated by taxonomic distributions, multiple sequence alignments, profile Hidden Markov Models and cross-references to G-quadruplex 3D structures. Examination of G-quadruplexes across functional genomic elements in different taxa indicates preferential orientation and positioning, with significant differences between individual taxonomic groups. For example, we find that G-quadruplexes in bacteria with a single replication origin display profound preference for the leading orientation. Finally, we experimentally validate the most frequently observed G-quadruplexes using CD-spectroscopy, UV melting, and fluorescent-based approaches. Quadrupia is publicly available through https://www.pavlopoulos-lab.org/quadrupia.

genomics↗

bioRxiv2021

Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA

RNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report that MALAT1 lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s in MALAT1 lncRNA can interact with NONO protein with high specificity and affinity in vitro and in nuclear cell lysate, and we provide in vivo data to support that NONO protein recognizes MALAT1 lncRNA via rG4 motifs. Notably, we demonstrate that rG4s in MALAT1 lncRNA can be targeted by rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation of MALAT1 rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s in MALAT1 lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targeting MALAT1 and its RNA-protein complex via its rG4 structure, and illustrates the prevalence and significance of rG4s in ncRNAs.

biochemistry↗