May 2024
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10 Reads
Biochemistry
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May 2024
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10 Reads
Biochemistry
March 2024
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5 Reads
Nucleic Acids Research
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone nuclear receptor family. Due to its roles in regulating cell proliferation and differentiation, AR is tightly regulated to maintain proper levels of itself and the many genes it controls. AR dysregulation is a driver of many human diseases including prostate cancer. Though this dysregulation often occurs at the RNA level, there are many unknowns surrounding post-transcriptional regulation of AR mRNA, particularly the role that RNA secondary structure plays. Thus, a comprehensive analysis of AR transcript secondary structure is needed. We address this through the computational and experimental analyses of two key isoforms, full length (AR-FL) and truncated (AR-V7). Here, a combination of in-cell RNA secondary structure probing experiments (targeted DMS-MaPseq) and computational predictions were used to characterize the static structural landscape and conformational dynamics of both isoforms. Additionally, in-cell assays were used to identify functionally relevant structures in the 5′ and 3′ UTRs of AR-FL. A notable example is a conserved stem loop structure in the 5′UTR of AR-FL that can bind to Poly(RC) Binding Protein 2 (PCBP2). Taken together, our results reveal novel features that regulate AR expression.
January 2024
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22 Reads
MYC pre-mRNA is spliced with high fidelity to produce the transcription factor known to regulate cellular differentiation, proliferation, apoptosis, and alternative splicing. The mechanisms underpinning the pre-mRNA splicing of MYC , however, remain mostly unexplored. In this study, we examined the interaction of heterogeneous nuclear ribonucleoprotein C (HNRNPC) with MYC intron 2. Building off published eCLIP studies, we confirmed this interaction with poly(U) regions in intron 2 of MYC and found that full binding is correlated with optimal protein production. The interaction appears to be compensatory, as mutational disruption of all three poly(U) regions was required to reduce both HNRNPC binding capacity and fidelity of either splicing or translation. Poly(U) sequences in MYC intron 2 were relatively conserved across sequences from several different species. Lastly, we identified a short sequence just upstream of an HNRNPC binding region that when removed enhances MYC translation.
November 2023
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44 Reads
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1 Citation
The orphan gene of SARS-CoV-2, ORF10, is the least stud- ied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moder- ates innate immunity in vitro. However, whether ORF10 af- fects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ances- tral haplotype in 95% of genomes across five variants of con- cern (VOC). Four ORF10 variants are associated with less vir- ulent clinical outcomes in the human host: three of these af- fect ORF10 protein structure, one affects ORF10 RNA struc- tural dynamics. RNA-Seq data from 2070 samples from di- verse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 tran- scripts. Expression of ORF10 in A549 and HEK293 cells per- turbs immune-related gene expression networks, alters expres- sion of the majority of mitochondrially-encoded genes of oxida- tive respiration, and leads to large shifts in levels of 14 newly- identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
June 2023
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19 Reads
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1 Citation
MethodsX
Major advances in RNA secondary structural motif prediction have been achieved in the last few years; however, few methods harness the predictive power of multiple approaches to deliver in-depth characterizations of local RNA motifs and their potential functionality. Additionally, most available methods do not predict RNA pseudoknots. This work combines complementary bioinformatic systems into one robust discovery pipeline where: •RNA sequences are folded to search for thermodynamically favorable motifs utilizing ScanFold.•Motifs are expanded and refolded into alternate pseudoknot conformations by Knotty/Iterative HFold.•All conformations are evaluated for covariance via the cm-builder pipeline (Infernal and R-scape).
November 2022
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81 Reads
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11 Citations
A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural stability, evidence of sequence-ordered (potentially evolved) structure, and unique model structures comprised of recurring base pairs with the greatest structural bias. A key step in quantifying this propensity for ordered structure is the prediction of secondary structural stability for randomized sequences which, in the original implementation of ScanFold, is explicitly evaluated. This slow process has limited the rapid identification of ordered structures in large genomes/transcriptomes, which we seek to overcome in this current work introducing ScanFold 2.0. In this revised version of ScanFold, we no longer explicitly evaluate randomized sequence folding energy, but rather estimate it using a machine learning approach. For high randomization numbers, this can increase prediction speeds over 100-fold compared to ScanFold 1.0, allowing for the analysis of large sequences, as well as the use of additional folding algorithms that may be computationally expensive. In the testing of ScanFold 2.0, we re-evaluate the Zika, HIV, and SARS-CoV-2 genomes and compare both the consistency of results and the time of each run to ScanFold 1.0. We also re-evaluate the SARS-CoV-2 genome to assess the quality of ScanFold 2.0 predictions vs several biochemical structure probing datasets and compare the results to those of the original ScanFold program.
October 2022
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46 Reads
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3 Citations
NAR Genomics and Bioinformatics
Epstein–Barr virus (EBV) is a widely prevalent human herpes virus infecting over 95% of all adults and is associated with a variety of B-cell cancers and induction of multiple sclerosis. EBV accomplishes this in part by expression of coding and noncoding RNAs and alteration of the host cell transcriptome. To better understand the structures which are forming in the viral and host transcriptomes of infected cells, the RNA structure probing technique Structure-seq2 was applied to the BJAB-B1 cell line (an EBV infected B-cell lymphoma). This resulted in reactivity profiles and secondary structural analyses for over 10000 human mRNAs and lncRNAs, along with 19 lytic and latent EBV transcripts. We report in-depth structural analyses for the human MYC mRNA and the human lncRNA CYTOR. Additionally, we provide a new model for the EBV noncoding RNA EBER2 and provide the first reported model for the EBV tandem terminal repeat RNA. In-depth thermodynamic and structural analyses were carried out with the motif discovery tool ScanFold and RNAfold prediction tool; subsequent covariation analyses were performed on resulting models finding various levels of support. ScanFold results for all analyzed transcripts are made available for viewing and download on the user-friendly RNAStructuromeDB.
August 2022
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40 Reads
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2 Citations
Scientific Reports
RNA plays vital functional roles in almost every component of biology, and these functional roles are often influenced by its folding into secondary and tertiary structures. An important role of RNA secondary structure is in maintaining proper gene regulation; therefore, making accurate predictions of the structures involved in these processes is important. In this study, we have expanded on our previous work that led to the creation of the RNAStructuromeDB. Unlike this previous study that analyzed the human genome at low resolution, we have now scanned the protein-coding human transcriptome at high (single nt) resolution. This provides more robust structure predictions for over 100,000 isoforms of known protein-coding genes. Notably, we also utilize the motif identification tool, , to model structures with high propensity for ordered/evolved stability. All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the or ), and download of data—including unique highly-ordered motifs. Herein, we provide an example analysis of MAT2A to demonstrate the utility of at finding known and novel secondary structures, highlighting regions of potential functionality, and guiding generation of functional hypotheses through use of the data.
July 2022
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83 Reads
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10 Citations
Frontiers in Molecular Biosciences
Humans contain two nearly identical copies of Survival Motor Neuron genes, SMN1 and SMN2. Deletion or mutation of SMN1 causes spinal muscular atrophy (SMA), one of the leading genetic diseases associated with infant mortality. SMN2 is unable to compensate for the loss of SMN1 due to predominant exon 7 skipping, leading to the production of a truncated protein. Antisense oligonucleotide and small molecule-based strategies aimed at the restoration of SMN2 exon 7 inclusion are approved therapies of SMA. Many cis-elements and transacting factors have been implicated in regulation of SMN exon 7 splicing. Also, several structural elements, including those formed by a long-distance interaction, have been implicated in the modulation of SMN exon 7 splicing. Several of these structures have been confirmed by enzymatic and chemical structure-probing methods. Additional structures formed by inter-intronic interactions have been predicted by computational algorithms. SMN genes generate a vast repertoire of circular RNAs through inter-intronic secondary structures formed by inverted Alu repeats present in large number in SMN genes. Here, we review the structural context of the exonic and intronic cis-elements that promote or prevent exon 7 recognition. We discuss how structural rearrangements triggered by single nucleotide substitutions could bring drastic changes in SMN2 exon 7 splicing. We also propose potential mechanisms by which inter-intronic structures might impact the splicing outcomes.
May 2022
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17 Reads
RNA plays vital functional roles in almost every component of biology, and these functional roles are often influenced by its folding into secondary and tertiary structures. An important role of RNA secondary structure is in maintaining proper gene regulation; therefore, making accurate predictions of the structures involved in these processes is important. In this study, we have expanded on our previous work that led to the creation of the RNAStructuromeDB. Unlike this previous study that analyzed the human genome at low resolution, we have now scanned the protein-coding human transcriptome at high (single nt) resolution. This provides more robust structure predictions for over 100,000 isoforms of known protein-coding genes. Notably, we also utilize the motif identification tool, ScanFold, to model structures with high propensity for ordered/evolved stability. All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the Integrative Genomics Viewer or IGV), and download of ScanFold data—including unique highly-ordered motifs. Herein, we provide an example analysis of MAT2A to demonstrate the utility of ScanFold at finding known and novel secondary structures, highlighting regions of potential functionality, and guiding generation of functional hypotheses through use of the data.
... Intron sequences were analyzed using ScanFold 2.0 [16] with default settings (no probing data, 120 nucleotide windows, 1 nucleotide step-size, global refold on, extract -2 z-score structures). Data were downloaded and z-average -1 dot-bracket structures were visually compared using VARNA [26]. ...
November 2022
... Since the tertiary structure of RNA is highly limited by the bi-dimensional structure [67], we analyzed the secondary structure of S03 generated by RNAFold Delta ( Figure 3B). An RNA molecule contains rigid and ecstatic structures and free highly dynamic ones [68], which can be organized into regions. ...
October 2022
NAR Genomics and Bioinformatics
... Existing probing data can be used as a constraint to inform the final model but are not required; purely in silico ScanFold results (especially -2 z-score motifs) correlate well with SHAPE and DMS reactivities [ 12 , 19 ]. A 120 nucleotide window size is sufficient for most structured RNAs (e.g., most known human cis-regulatory RNA structures are < ∼150 nucleotides [21] ), but the size can be reduced or increased depending on user needs. Window size can be increased to 150 nucleotides with little decline in accuracy, although it is not recommended to exceed 200 nucleotides [ 1 , 12 ]. ...
August 2022
Scientific Reports
... SMN protein plays a crucial role in the assembly of snRNPs, which are essential for mRNA splicing (37). Impaired snRNP assembly due to SMN deficiency leads to widespread splicing defects in various genes, further exacerbating motor neuron dysfunction (38). While SMA is primarily a disorder of motor neurons, the resulting muscle atrophy and weakness are critical clinical features. ...
July 2022
Frontiers in Molecular Biosciences
... We also asked whether the binding of HNRNPC to intron 2 of MYC could alter splicing of MYC pre-mRNA. To this end, a dual luciferase plasmid was generated containing MYC intron 2 inserted into the Firefly coding region (Fig 3C) at a location previously demonstrated not to adversely affect the resultant protein [22]. This approach also allowed introduction of mutations to each of the binding regions. ...
February 2022
... Subsequent bioinformatics analyses showed that the regions creating the highest amount of structure within the SARS-CoV-2 genome are in the 5 end and the regions corresponding to glycoproteins S and M [21]. Recently, RNA structure mapping of the complete SARS-CoV-2 genome and subgenomic RNA in vitro, in vivo, and in cellulo were published [22][23][24][25][26][27][28]. Moreover, the 3D folding of selected domains and motifs of genomic RNA was also proposed [29]. ...
February 2022
... Nucleotide positions 87 -130 of segment 5 are well conserved in IAV strains and predicted to form a pseudoknot structure in vRNA [10,47]. Interestingly, this region was not identified as a structural region in the recent study, where segments were scanned for local secondary structure and sequence covariance analysis [51]. Multiple structure modes in this region might trigger the weaker signals, but beyond the scope of this paper. ...
January 2022
Scientific Reports
... Similarly, a number of computational biology studies have been undertaken for this problem. The Moss laboratory published their findings in early 2021, describing eight highly likely structures predicted with their ScanFold-based computational pipeline [35,36]. The Pyle laboratory, at nearly the same time, described their findings using the SuperFold RNA secondary structure prediction utility, identifying 61% of the genome as being base paired [37]. ...
April 2021
NAR Genomics and Bioinformatics
... One attractive way to inhibit the viral frameshifting and interfere the viral replication is to develop the structure-specific binder to target the FES element. There have been drug-like small molecules identified to selectively bind to the AH structure and impair the frameshifting of virus 12,15 . These studies demonstrated the promise that the RNA genome of SARS-CoV-2 could be an ideal drug targets to disrupt the viral cellular functions. ...
October 2020
ACS Central Science
... Based on these findings, ordered thermodynamic stability can be measured to determine if a given RNA structure has undergone selection [1] . This is the basis for ScanFold, previously used to uncover unusually stable local motifs in human immunodeficiency virus (HIV-1) [1] , Zika virus (ZIKV) [1] , Epstein-Barr virus (EBV) [11] , severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [12] , and influenza virus [13] . ...
September 2020