ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological fu... more ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological functions for RNA. This suggests that RNA will be an expanding target for therapeutics. Genome sequencing is providing an avalanche of RNA sequences. There is relatively little RNA structural information, however. The thermodynamics of RNA folding facilitates finding structured RNA in genome sequences and, in combination with chemical mapping and NMR, determination of secondary structures. This lays a foundation for methods modeling 3D structure. Two new 3D motifs will be described that can contribute to homology modeling of structure and to benchmarking methods for predicting 3D structure. Additional tests of methods for predicting structure and energetics will also be presented. Recent predictions of secondary structures in influenza RNA will be discussed.
Recent experiments have demonstrated that the (13)C NMR spectra of iodoalkynes exhibit a strong s... more Recent experiments have demonstrated that the (13)C NMR spectra of iodoalkynes exhibit a strong solvent effect because of complexation with Lewis-basic solvents. This paper describes DFT NMR calculations (B3LYP-GIAO with LanL2DZ or Sadlej pVTZ basis set) of iodoalkynes and their Lewis acid-base complexes, interpreted by using Natural Chemical Shift (NCS) analysis within the framework of the Ramsey formalism for chemical shift. In particular, the paper presents calculations on diiodoethyne and its complexes with one and two ammonia molecules. Examination of the orbital changes upon forming the mono- and bisammonia complexes indicates that mixing of the nitrogen lone pair with the C-I antibonding orbital increases the paramagnetic deshielding at C1. Further increases can be attributed to increased polarization of the iodine lone-pair orbitals onto C1. The haloiodoalkyne series XCCI (X = F, Cl, Br, I) offers additional support for this model of the solvent effect.
Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. B... more Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. Base pairing in RNA is very favorable, but possibilities for RNA secondary structure of the influenza genomic RNA have not been investigated. This work presents the first experimentally-derived exploration of potential secondary structure in an influenza A naked (protein-free) genomic segment. Favorable folding regions are revealed by in vitro chemical structure mapping, thermodynamics, bioinformatics, and binding to isoenergetic microarrays of an entire natural sequence of the 875 nt segment 8 vRNA and of a smaller fragment. Segment 8 has thermodynamically stable and evolutionarily conserved RNA structure and encodes essential viral proteins NEP and NS1. This suggests that vRNA self-folding may generate helixes and loops that are important at one or more stages of the influenza life cycle.
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mamma... more The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to ...
Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, ... more Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy.
We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long ... more We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long non-coding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward transcripts (oriPtRs) are largely localized in the nucleus. While the oriPtLs are most likely non-coding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5' UTRs may partially serve non-coding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics and their expression is inhibited by phosphonoacetic acid. RNA-seq analysis showed that oriPtLs and oriPtRs exhibited extensive "hyper-editing" at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts suggesting that oriPts interacts with the paraspeckle-based innate anti-viral immune pathway. Knock-down and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade. Recent studies have revealed that the complexity of lytic herpesviral transcriptomes is significantly greater than previously appreciated with hundreds of viral long non-coding RNAs (vlncRNAs) being recently discovered. Work on cellular lncRNAs over the past several years has just begun to give us an initial appreciation for the array of functions they play in complex formation and regulatory processes in the cell. The…
ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological fu... more ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological functions for RNA. This suggests that RNA will be an expanding target for therapeutics. Genome sequencing is providing an avalanche of RNA sequences. There is relatively little RNA structural information, however. The thermodynamics of RNA folding facilitates finding structured RNA in genome sequences and, in combination with chemical mapping and NMR, determination of secondary structures. This lays a foundation for methods modeling 3D structure. Two new 3D motifs will be described that can contribute to homology modeling of structure and to benchmarking methods for predicting 3D structure. Additional tests of methods for predicting structure and energetics will also be presented. Recent predictions of secondary structures in influenza RNA will be discussed.
EBER2 is an abundant nuclear noncoding RNA expressed by the Epstein-Barr virus (EBV). Probing its... more EBER2 is an abundant nuclear noncoding RNA expressed by the Epstein-Barr virus (EBV). Probing its possible chromatin localization by CHART revealed EBER2's presence at the terminal repeats (TRs) of the latent EBV genome, overlapping previously identified binding sites for the B cell transcription factor PAX5. EBER2 interacts with PAX5 and is required for the localization of PAX5 to the TRs. EBER2 knockdown phenocopies PAX5 depletion in upregulating the expression of LMP2A/B and LMP1, genes nearest the TRs. Knockdown of EBER2 also decreases EBV lytic replication, underscoring the essential role of the TRs in viral replication. Recruitment of the EBER2-PAX5 complex is mediated by base-pairing between EBER2 and nascent transcripts from the TR locus. The interaction is evolutionarily conserved in the related primate herpesvirus CeHV15 despite great sequence divergence. Using base-pairing with nascent RNA to guide an interacting transcription factor to its DNA target site is a previously undescribed function for a trans-acting noncoding RNA.
Analysis of the R2 retrotransposons from multiple silkmoth and fruitfly species have revealed thr... more Analysis of the R2 retrotransposons from multiple silkmoth and fruitfly species have revealed three segments that contain conserved RNA secondary structures. These conserved structures play important roles in the propagation of the R2 element, including R2 RNA processing and transposon integration into the host genome as well as a likely role in translation. Two of the structured regions comprise protein binding sites: one is located in the 3' UTR and the other is in the 5' UTR close to the putative start of the R2 open reading frame (ORF). The 3' structure was deduced from chemical mapping and sequence comparison. The 5' structure was determined using a combination of chemical mapping, oligonucleotide binding, NMR and sequence analysis and contains an unusual pseudoknot structure. The third structure occurs at the 5' end of the R2 RNA and is responsible for self-cleavage of the 5' end of the element from a 28S ribosomal RNA co-transcript. A structure for this fragment was proposed based on motif searching and sequence comparison. There is remarkable similarity in sequence and structure to the hepatitis delta virus (HDV) ribozyme. Seed alignments for the 5' structure and the R2 ribozyme, containing representative sequences and consensus structures, have been submitted to the Rfam database.
ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological fu... more ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological functions for RNA. This suggests that RNA will be an expanding target for therapeutics. Genome sequencing is providing an avalanche of RNA sequences. There is relatively little RNA structural information, however. The thermodynamics of RNA folding facilitates finding structured RNA in genome sequences and, in combination with chemical mapping and NMR, determination of secondary structures. This lays a foundation for methods modeling 3D structure. Two new 3D motifs will be described that can contribute to homology modeling of structure and to benchmarking methods for predicting 3D structure. Additional tests of methods for predicting structure and energetics will also be presented. Recent predictions of secondary structures in influenza RNA will be discussed.
Recent experiments have demonstrated that the (13)C NMR spectra of iodoalkynes exhibit a strong s... more Recent experiments have demonstrated that the (13)C NMR spectra of iodoalkynes exhibit a strong solvent effect because of complexation with Lewis-basic solvents. This paper describes DFT NMR calculations (B3LYP-GIAO with LanL2DZ or Sadlej pVTZ basis set) of iodoalkynes and their Lewis acid-base complexes, interpreted by using Natural Chemical Shift (NCS) analysis within the framework of the Ramsey formalism for chemical shift. In particular, the paper presents calculations on diiodoethyne and its complexes with one and two ammonia molecules. Examination of the orbital changes upon forming the mono- and bisammonia complexes indicates that mixing of the nitrogen lone pair with the C-I antibonding orbital increases the paramagnetic deshielding at C1. Further increases can be attributed to increased polarization of the iodine lone-pair orbitals onto C1. The haloiodoalkyne series XCCI (X = F, Cl, Br, I) offers additional support for this model of the solvent effect.
Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. B... more Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. Base pairing in RNA is very favorable, but possibilities for RNA secondary structure of the influenza genomic RNA have not been investigated. This work presents the first experimentally-derived exploration of potential secondary structure in an influenza A naked (protein-free) genomic segment. Favorable folding regions are revealed by in vitro chemical structure mapping, thermodynamics, bioinformatics, and binding to isoenergetic microarrays of an entire natural sequence of the 875 nt segment 8 vRNA and of a smaller fragment. Segment 8 has thermodynamically stable and evolutionarily conserved RNA structure and encodes essential viral proteins NEP and NS1. This suggests that vRNA self-folding may generate helixes and loops that are important at one or more stages of the influenza life cycle.
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mamma... more The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to ...
Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, ... more Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy.
We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long ... more We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long non-coding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward transcripts (oriPtRs) are largely localized in the nucleus. While the oriPtLs are most likely non-coding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5' UTRs may partially serve non-coding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics and their expression is inhibited by phosphonoacetic acid. RNA-seq analysis showed that oriPtLs and oriPtRs exhibited extensive "hyper-editing" at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts suggesting that oriPts interacts with the paraspeckle-based innate anti-viral immune pathway. Knock-down and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade. Recent studies have revealed that the complexity of lytic herpesviral transcriptomes is significantly greater than previously appreciated with hundreds of viral long non-coding RNAs (vlncRNAs) being recently discovered. Work on cellular lncRNAs over the past several years has just begun to give us an initial appreciation for the array of functions they play in complex formation and regulatory processes in the cell. The…
ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological fu... more ABSTRACT Many discoveries in the past 30 years have revealed an unexpected range of biological functions for RNA. This suggests that RNA will be an expanding target for therapeutics. Genome sequencing is providing an avalanche of RNA sequences. There is relatively little RNA structural information, however. The thermodynamics of RNA folding facilitates finding structured RNA in genome sequences and, in combination with chemical mapping and NMR, determination of secondary structures. This lays a foundation for methods modeling 3D structure. Two new 3D motifs will be described that can contribute to homology modeling of structure and to benchmarking methods for predicting 3D structure. Additional tests of methods for predicting structure and energetics will also be presented. Recent predictions of secondary structures in influenza RNA will be discussed.
EBER2 is an abundant nuclear noncoding RNA expressed by the Epstein-Barr virus (EBV). Probing its... more EBER2 is an abundant nuclear noncoding RNA expressed by the Epstein-Barr virus (EBV). Probing its possible chromatin localization by CHART revealed EBER2's presence at the terminal repeats (TRs) of the latent EBV genome, overlapping previously identified binding sites for the B cell transcription factor PAX5. EBER2 interacts with PAX5 and is required for the localization of PAX5 to the TRs. EBER2 knockdown phenocopies PAX5 depletion in upregulating the expression of LMP2A/B and LMP1, genes nearest the TRs. Knockdown of EBER2 also decreases EBV lytic replication, underscoring the essential role of the TRs in viral replication. Recruitment of the EBER2-PAX5 complex is mediated by base-pairing between EBER2 and nascent transcripts from the TR locus. The interaction is evolutionarily conserved in the related primate herpesvirus CeHV15 despite great sequence divergence. Using base-pairing with nascent RNA to guide an interacting transcription factor to its DNA target site is a previously undescribed function for a trans-acting noncoding RNA.
Analysis of the R2 retrotransposons from multiple silkmoth and fruitfly species have revealed thr... more Analysis of the R2 retrotransposons from multiple silkmoth and fruitfly species have revealed three segments that contain conserved RNA secondary structures. These conserved structures play important roles in the propagation of the R2 element, including R2 RNA processing and transposon integration into the host genome as well as a likely role in translation. Two of the structured regions comprise protein binding sites: one is located in the 3' UTR and the other is in the 5' UTR close to the putative start of the R2 open reading frame (ORF). The 3' structure was deduced from chemical mapping and sequence comparison. The 5' structure was determined using a combination of chemical mapping, oligonucleotide binding, NMR and sequence analysis and contains an unusual pseudoknot structure. The third structure occurs at the 5' end of the R2 RNA and is responsible for self-cleavage of the 5' end of the element from a 28S ribosomal RNA co-transcript. A structure for this fragment was proposed based on motif searching and sequence comparison. There is remarkable similarity in sequence and structure to the hepatitis delta virus (HDV) ribozyme. Seed alignments for the 5' structure and the R2 ribozyme, containing representative sequences and consensus structures, have been submitted to the Rfam database.
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