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Srivastava M, Dukeshire MR, Mir Q, Omoru OB, Manzourolajdad A, Janga SC. Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes. Brief Funct Genomics 2024; 23:46-54. [PMID: 36752040 PMCID: PMC10799312 DOI: 10.1093/bfgp/elac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/24/2022] [Accepted: 11/11/2022] [Indexed: 02/09/2023] Open
Abstract
Long-range ribonucleic acid (RNA)-RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA-RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2's mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus-host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Biology, Indiana University, 1001 East 3 St, Bloomington, Indiana 47405, USA
| | - Matthew R Dukeshire
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Okiemute Beatrice Omoru
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Amirhossein Manzourolajdad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana 46202, USA
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana 46202, USA
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Fallatah A, Anastasakis DG, Manzourolajdad A, Sharma P, Wang X, Jacob A, Alsharif S, Elgerbi A, Coulombe PA, Hafner M, Chung BM. Keratin 19 binds and regulates cytoplasmic HNRNPK mRNA targets in triple-negative breast cancer. BMC Mol Cell Biol 2023; 24:26. [PMID: 37592256 PMCID: PMC10433649 DOI: 10.1186/s12860-023-00488-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Heterogeneous nuclear ribonucleoprotein K (HNRNPK) regulates pre-mRNA processing and long non-coding RNA localization in the nucleus. It was previously shown that shuttling of HNRNPK to the cytoplasm promotes cell proliferation and cancer metastasis. However, the mechanism of HNRNPK cytoplasmic localization, its cytoplasmic RNA ligands, and impact on post-transcriptional gene regulation remain uncharacterized. RESULTS Here we show that the intermediate filament protein Keratin 19 (K19) directly interacts with HNRNPK and sequesters it in the cytoplasm. Correspondingly, in K19 knockout breast cancer cells, HNRNPK does not localize in the cytoplasm, resulting in reduced cell proliferation. We comprehensively mapped HNRNPK binding sites on mRNAs and showed that, in the cytoplasm, K19-mediated HNRNPK-retention increases the abundance of target mRNAs bound to the 3' untranslated region (3'UTR) at the expected cytidine-rich (C-rich) sequence elements. Furthermore, these mRNAs protected by HNRNPK in the cytoplasm are typically involved in cancer progression and include the p53 signaling pathway that is dysregulated upon HNRNPK knockdown (HNRNPK KD) or K19 knockout (KRT19 KO). CONCLUSIONS This study identifies how a cytoskeletal protein can directly regulate gene expression by controlling the subcellular localization of RNA-binding proteins to support pathways involved in cancer progression.
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Affiliation(s)
- Arwa Fallatah
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America
| | - Amirhossein Manzourolajdad
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America
- Department of Computer Science, Colgate University, Hamilton, NY, United States of America
| | - Pooja Sharma
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Xiantao Wang
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America
| | - Alexis Jacob
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America
| | - Sarah Alsharif
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Ahmed Elgerbi
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Pierre A Coulombe
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States of America
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States of America.
| | - Byung Min Chung
- Department of Biology, The Catholic University of America, Washington, DC, United States of America.
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Omoru OB, Pereira F, Janga SC, Manzourolajdad A. A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2. PLoS One 2022; 17:e0260331. [PMID: 36048827 PMCID: PMC9436084 DOI: 10.1371/journal.pone.0260331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/22/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.
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Affiliation(s)
- Okiemute Beatrice Omoru
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
| | - Filipe Pereira
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- IDENTIFICA Genetic Testing, Maia, Portugal
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, Indianapolis, Indiana, United States of America
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), Indianapolis, Indiana, United States of America
| | - Amirhossein Manzourolajdad
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States of America
- Department of Computer Science, Colgate University, Hamilton, NY, United States of America
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Genzor P, Konstantinidou P, Stoyko D, Manzourolajdad A, Marlin Andrews C, Elchert AR, Stathopoulos C, Haase AD. Cellular abundance shapes function in piRNA-guided genome defense. Genome Res 2021; 31:2058-2068. [PMID: 34667116 PMCID: PMC8559710 DOI: 10.1101/gr.275478.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022]
Abstract
Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR-Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, whereas rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a 1000-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual, or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.
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Affiliation(s)
- Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Parthena Konstantinidou
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Daniel Stoyko
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Amirhossein Manzourolajdad
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Celine Marlin Andrews
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
An RNA switch triggers biological functions by toggling between two conformations. RNA switches include bacterial riboswitches, where ligand binding can stabilize a bound structure. For RNAs with only one stable structure, structural prediction usually just requires a straightforward free energy minimization, but for an RNA switch, the prediction of a less stable alternative structure is often computationally costly and even problematic. The current sampling-clustering method predicts stable and alternative structures by partitioning structures sampled from the energy landscape into two clusters, but it is very time-consuming. Instead, we predict the alternative structure of an RNA switch from conditional probability calculations within the energy landscape. First, our method excludes base pairs related to the most stable structure in the energy landscape. Then, it detects stable stems (“seeds”) in the remaining landscape. Finally, it folds an alternative structure prediction around a seed. While having comparable riboswitch classification performance, the conditional-probability computations had fewer adjustable parameters, offered greater predictive flexibility, and were more than one thousand times faster than the sampling step alone in sampling-clustering predictions, the competing standard. Overall, the described approach helps traverse thermodynamically improbable energy landscapes to find biologically significant substructures and structures rapidly and effectively.
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Affiliation(s)
- Amirhossein Manzourolajdad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Manzourolajdad A, Gonzalez M, Spouge JL. Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic. PLoS One 2016; 11:e0163688. [PMID: 27685447 PMCID: PMC5042412 DOI: 10.1371/journal.pone.0163688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/13/2016] [Indexed: 02/04/2023] Open
Abstract
Because of a high mutation rate, HIV exists as a viral swarm of many sequence variants evolving under various selective pressures from the human immune system. Although the Nef gene codes for the most immunogenic of HIV accessory proteins, which alone makes it of great interest to HIV research, it also encodes an RNA structure, whose contribution to HIV virulence has been largely unexplored. Nef RNA helps HIV escape RNA interference (RNAi) through nucleotide changes and alternative folding. This study examines Historic and Modern Datasets of patient HIV-1 Nef sequences during the evolution of the North American epidemic for local changes in RNA plasticity. By definition, RNA plasticity refers to an RNA molecule’s ability to take alternative folds (i.e., alternative conformations). Our most important finding is that an evolutionarily conserved region of the HIV-1 Nef gene, which we denote by R2, recently underwent a statistically significant increase in its RNA plasticity. Thus, our results indicate that Modern Nef R2 typically accommodates an alternative fold more readily than Historic Nef R2. Moreover, the increase in RNA plasticity resides mostly in synonymous nucleotide changes, which cannot be a response to selective pressures on the Nef protein. R2 may therefore be of interest in the development of antiviral RNAi therapies.
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Affiliation(s)
- Amirhossein Manzourolajdad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Mileidy Gonzalez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Abstract
BACKGROUND RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. RESULTS We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. CONCLUSIONS Various tests show that there is in fact a relationship between higher structural entropy and the potential for the RNA sequence to have alternative structures, within the limitations of our methodology. This relationship, though modest, is consistent across various tests. Understanding the behavior of structural entropy as a fairly new feature for RNA conformational dynamics, however, may require extensive exploratory investigation both across RNA sequences and folding models.
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Affiliation(s)
- Amirhossein Manzourolajdad
- Institute of Bioinformatics, University of Georgia, Davison Life Sciences Bldg, Room B118B, 120 Green St, Athens, 30602, USA. .,National Center for Biotechnology Information (NCBI), NIH, Building 38A, RM 6S614K, 8600 Rockville Pike, Bethesda, 20894, USA.
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, Davison Life Sciences Bldg, Room B118B, 120 Green St, Athens, 30602, USA. .,Department of Genetics, University of Georgia, Davison Life Sciences Bldg, 120 Green St, Athens, 30602, USA.
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Manzourolajdad A, Wang Y, Shaw TI, Malmberg RL. Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. J Theor Biol 2012; 318:140-63. [PMID: 23160142 DOI: 10.1016/j.jtbi.2012.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 10/11/2012] [Accepted: 10/18/2012] [Indexed: 10/27/2022]
Abstract
UNLABELLED RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. AVAILABILITY URL http://www.plantbio.uga.edu/~russell/index.php?s=1&n=5&r=0.
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Affiliation(s)
- Amirhossein Manzourolajdad
- Institute of Bioinformatics, University of Georgia, Davison Life Sciences Bldg, Room B118B, 120 Green St, Athens, GA 30602, USA.
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