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  1. Article ; Online: The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions.

    Rouse, Warren B / Tompkins, Van S / O'Leary, Collin A / Moss, Walter N

    Nucleic acids research

    2024  

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2024-03-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation.

    Peterson, Jake M / O'Leary, Collin A / Moss, Walter N

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 310

    Abstract: Influenza virus is a persistent threat to human health; indeed, the deadliest modern pandemic was in 1918 when an H1N1 virus killed an estimated 50 million people globally. The intent of this work is to better understand influenza from an RNA-centric ... ...

    Abstract Influenza virus is a persistent threat to human health; indeed, the deadliest modern pandemic was in 1918 when an H1N1 virus killed an estimated 50 million people globally. The intent of this work is to better understand influenza from an RNA-centric perspective to provide local, structural motifs with likely significance to the influenza infectious cycle for therapeutic targeting. To accomplish this, we analyzed over four hundred thousand RNA sequences spanning three major clades: influenza A, B and C. We scanned influenza segments for local secondary structure, identified/modeled motifs of likely functionality, and coupled the results to an analysis of evolutionary conservation. We discovered 185 significant regions of predicted ordered stability, yet evidence of sequence covariation was limited to 7 motifs, where 3-found in influenza C-had higher than expected amounts of sequence covariation.
    MeSH term(s) Antiviral Agents/pharmacology ; Influenza A virus/drug effects ; Influenza A virus/genetics ; Betainfluenzavirus/drug effects ; Betainfluenzavirus/genetics ; Gammainfluenzavirus/drug effects ; Gammainfluenzavirus/genetics ; Models, Molecular ; Nucleic Acid Conformation ; Nucleotide Motifs ; RNA Stability ; RNA, Viral/drug effects ; RNA, Viral/genetics ; RNA, Viral/ultrastructure ; Sequence Analysis, RNA ; Structure-Activity Relationship
    Chemical Substances Antiviral Agents ; RNA, Viral
    Language English
    Publishing date 2022-01-10
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-03767-x
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  3. Article ; Online: Identification of MYC intron 2 regions that modulate expression.

    Tompkins, Van S / Xue, Zheng / Peterson, Jake M / Rouse, Warren B / O'Leary, Collin A / Moss, Walter N

    PloS one

    2024  Volume 19, Issue 1, Page(s) e0296889

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Introns/genetics ; RNA Precursors/genetics ; RNA Splicing ; Alternative Splicing ; Mutation
    Chemical Substances RNA Precursors
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0296889
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  4. Article: Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis.

    Peterson, Jake M / O'Leary, Collin A / Coppenbarger, Evelyn C / Tompkins, Van S / Moss, Walter N

    MethodsX

    2023  Volume 11, Page(s) 102275

    Abstract: 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 ... ...

    Abstract 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).
    Language English
    Publishing date 2023-06-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2830212-6
    ISSN 2215-0161
    ISSN 2215-0161
    DOI 10.1016/j.mex.2023.102275
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  5. Article ; Online: Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis

    Peterson, Jake M. / O'Leary, Collin A. / Coppenbarger, Evelyn C. / Tompkins, Van S. / Moss, Walter N.

    MethodsX. 2023 Dec., v. 11 p.102275-

    2023  

    Abstract: 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 ... ...

    Abstract 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).
    Keywords RNA ; bioinformatics ; covariance ; prediction ; sequence analysis ; thermodynamics ; RNA structure ; Motif discovery ; Covariance analysis ; Cobretti
    Language English
    Dates of publication 2023-12
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 2830212-6
    ISSN 2215-0161
    ISSN 2215-0161
    DOI 10.1016/j.mex.2023.102275
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes.

    Andrews, Ryan J / Rouse, Warren B / O'Leary, Collin A / Booher, Nicholas J / Moss, Walter N

    PeerJ

    2022  Volume 10, Page(s) e14361

    Abstract: 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, ... ...

    Abstract 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
    MeSH term(s) Humans ; RNA/genetics ; Nucleic Acid Conformation ; Base Sequence ; Transcriptome/genetics ; SARS-CoV-2/genetics ; COVID-19/genetics ; Neoplasm Recurrence, Local/genetics ; Zika Virus/genetics ; Zika Virus Infection/genetics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2022-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.14361
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  7. Article: Structural Context of a Critical Exon of Spinal Muscular Atrophy Gene.

    Singh, Natalia N / O'Leary, Collin A / Eich, Taylor / Moss, Walter N / Singh, Ravindra N

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 928581

    Abstract: Humans contain two nearly identical copies ... ...

    Abstract Humans contain two nearly identical copies of
    Language English
    Publishing date 2022-07-01
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.928581
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  8. Article ; Online: Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control.

    Tompkins, Van S / Rouse, Warren B / O'Leary, Collin A / Andrews, Ryan J / Moss, Walter N

    PloS one

    2022  Volume 17, Issue 2, Page(s) e0264025

    Abstract: Experimental breakthroughs have provided unprecedented insights into the genes involved in cancer. The identification of such cancer driver genes is a major step in gaining a fuller understanding of oncogenesis and provides novel lists of potential ... ...

    Abstract Experimental breakthroughs have provided unprecedented insights into the genes involved in cancer. The identification of such cancer driver genes is a major step in gaining a fuller understanding of oncogenesis and provides novel lists of potential therapeutic targets. A key area that requires additional study is the posttranscriptional control mechanisms at work in cancer driver genes. This is important not only for basic insights into the biology of cancer, but also to advance new therapeutic modalities that target RNA-an emerging field with great promise toward the treatment of various cancers. In the current study we performed an in silico analysis on the transcripts associated with 800 cancer driver genes (10,390 unique transcripts) that identified 179,190 secondary structural motifs with evidence of evolutionarily ordered structures with unusual thermodynamic stability. Narrowing to one transcript per gene, 35,426 predicted structures were subjected to phylogenetic comparisons of sequence and structural conservation. This identified 7,001 RNA secondary structures embedded in transcripts with evidence of covariation between paired sites, supporting structure models and suggesting functional significance. A select set of seven structures were tested in vitro for their ability to regulate gene expression; all were found to have significant effects. These results indicate potentially widespread roles for RNA structure in posttranscriptional control of human cancer driver genes.
    MeSH term(s) Evolution, Molecular ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Nucleic Acid Conformation ; Phylogeny ; RNA Processing, Post-Transcriptional ; RNA Stability ; RNA, Neoplasm/genetics ; RNA, Neoplasm/metabolism
    Chemical Substances RNA, Neoplasm
    Language English
    Publishing date 2022-02-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0264025
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  9. Article ; Online: Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome.

    Rouse, Warren B / O'Leary, Collin A / Booher, Nicholas J / Moss, Walter N

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 14515

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Gene Expression Regulation ; Genome, Human ; Genomics ; Humans ; Methionine Adenosyltransferase/genetics ; RNA/chemistry ; RNA/genetics ; Transcriptome/genetics
    Chemical Substances RNA (63231-63-0) ; MAT2A protein, human (EC 2.5.1.6) ; Methionine Adenosyltransferase (EC 2.5.1.6)
    Language English
    Publishing date 2022-08-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-18699-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome.

    O'Leary, Collin A / Van Tompkins, S / Rouse, Warren B / Nam, Gijong / Moss, Walter N

    NAR genomics and bioinformatics

    2022  Volume 4, Issue 4, Page(s) lqac082

    Abstract: 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 ...

    Abstract 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
    Language English
    Publishing date 2022-10-21
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqac082
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