Xin Ni Lim's research while affiliated with Genome Institute of Singapore and other places
What is this page?
This page lists the scientific contributions of an author, who either does not have a ResearchGate profile, or has not yet added these contributions to their profile.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
It was automatically created by ResearchGate to create a record of this author's body of work. We create such pages to advance our goal of creating and maintaining the most comprehensive scientific repository possible. In doing so, we process publicly available (personal) data relating to the author as a member of the scientific community.
If you're a ResearchGate member, you can follow this page to keep up with this author's work.
If you are this author, and you don't want us to display this page anymore, please let us know.
Publications (24)
Background
Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication.
Results
Here, we use proximity ligation sequencing to identify virus-host RNA interactions for four strains of Zika virus (ZIKV) and one strain of dengue virus (DENV-1) in human cells. W...
Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11...
SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different str...
SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified...
SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified...
Dengue virus (DENV) and Zika virus (ZIKV) are both positive sense single-stranded RNA viruses. They are packaged within the virion with a capsid (C) protein to form the nucleocapsid. Based on cryo-electron microscopy imaging, the nucleocapsid has been described as lacking symmetry, whilst there is distinguishable separation of the C proteins from t...
Dengue (DENV) and Zika (ZIKV) viruses are clinically important members of the Flaviviridae family with an 11 kb positive strand RNA genome that folds to enable virus function. Here, we perform structure and interaction mapping on four DENV and ZIKV strains inside virions and in infected cells. Comparative analysis of SHAPE reactivities across serot...
Dengue and Zika are clinically important members of the Flaviviridae family that utilizes an 11kb positive strand RNA for genome regulation. While structures have been mapped primarily in the UTRs, much remains to be learnt about how the rest of the genome folds to enable function. Here, we performed secondary structure and pair-wise interaction ma...
RNAs are well-suited to act as cellular sensors that detect and respond to metabolite changes in the environment, due to their ability to fold into complex structures. Here, we introduce a genome-wide strategy called PARCEL that experimentally identifies RNA aptamers in vitro, in a high-throughput manner. By applying PARCEL to a collection of proka...
Identifying pairwise RNA-RNA interactions is key to understanding how RNAs fold and interact with other RNAs inside the cell. We present a high-throughput approach, sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH), that maps pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. Applying SPLA...
Citations
... The search for SARS-CoV-2 treatments is continuing 3 and reductionist approaches vastly dominate experimental efforts. A stop-motion view of the SARS-CoV-2 infection cycle has emerged 4 , where its impact on the host cell is understood through key host/virus molecular entanglements 5 . Previous studies tackled the impact of the virus on a global cellular scale, employing fluorescence and electron microscopy 6,7 , and as, such were lacking the dimension of time. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/278089578893314-1443313130487_Q64/Danielle-Anderson-8.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272560965287945-1441995006340_Q64/Yue-Wan-6.jpg)
... Previously, in our study of identifying SARS-CoV-2 interactome, we had observed that SARS-CoV-2-interacting RNAs are preferentially stabilized during infection even though many transcripts are downregulated [14]. To examine how the host RNA changes in gene expression upon ZIKV infection, we performed RNA sequencing experiments at 0 and 24 h post-ZIKV or upon mock infection in Huh7 cells. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/995381823422468-1614328928058_Q64/Roland-Huber-2.jpg)
... Although we have seen flavivirus capsid's ability to essentially bind any nucleic acid, it is not clear if capsid has a preference for binding RNA motifs or secondary structures. Recently, Boon et al. showed that capsid's interactions with viral genome indicate some preference for G-quadruplexes in vitro [71]. It has also been shown that capsid proteins have the ability to anneal RNAs, indicating the ability to interact with both ss-and dsRNA [34], in contrast to predictions that capsid would specifically bind single-stranded RNA [10]. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/11431281230075903-1710783051874_Q64/Francisco-Enguita.jpg)
... The supernatant was collected and centrifuged for 5 minutes. The cell culture supernatant was kept at -80 o C, and then the titer of DENV-2 and DENV-3 was determined using a focus assay [13,14]. The method was done multiple times until the desired titer was achieved for the dose required in the study. ...
... The sequence for HIV-1 was from the genome chemically probed by Watts et al. (2009). SHAPE reactivity profiles for ZIKV were taken from extended data 6 in Huber et al. (2018) and for HIV-1 from supplementary dataset 2 in Watts et al. (2009). ...
... A major challenge for discovery of novel bacterial ncRNA classes is that current biochemical, genetic, or bioinformatic methods are limited in their ability to identify candidates efficiently and comprehensively. Most biochemical and genetic methods, such as RNA structural probing ( 11 ) or RNA transcriptomics ( 12 ), are generally limited to examining the RNAs produced in a single, culturable organism per experiment. Thus, other strategies are needed to effectively uncover additional ncRNA candidates more efficiently. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/598227611037701-1519639985750_Q64/Sidika-Tapsin.jpg)
... For example, LIGR-seq (LIGation of interacting RNA followed by high-throughput sequencing) led to the discovery of small nucleolar (sno)RNAs interacting with mRNAs in human cells ( 11 ), whereas RIL-seq (RNA interaction by ligation and sequencing) revealed novel RNA-RNA interactions and sRNA regulators in bacteria ( 12 ,13 ). Other key technologies for global RNA interactome analysis are CLASH ( 14 ), SPLASH ( 15 ), GRIL-seq ( 16 ) and PARIS ( 17 ), all of which enable the genome-wide annotation of RNA-RNA pairs. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/278625338314784-1443440865801_Q64/Andreas-Wilm-2.jpg)
