cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4665530
title: Molecular Dynamics of Janus Nanodimers Dispersed in Lamellar Phases of a Block Copolymer (Dataset 1 of 2)

description: <strong>Abstract:</strong> We investigate structural and dynamical properties of Janus nanodimers (NDs) dispersed in lamellar phases of a diblock copolymer. By performing Molecular Dynamics simulations, we show that an accurate tuning of the interactions between NDs and copolymer blocks can lead to a close control of NDs' space distribution and orientation. In particular, NDs are preferentially found within the lamellae if enthalpy-driven forces offset their entropic counterpart. By contrast, when enthalpic interactions are relatively mild, then excluded-volume effects become dominant and NDs are essentially observed within the inter-lamellar spacing. Not only does the degree of affinity between host and guest species drive the ND's distribution in the polymer matrix, but it also determines their space orientation. In turns, these key structural properties influence the long-time dynamics and the ability of NDs to diffuse through the polymer matrix. <strong>Dataset (1/2):</strong> <strong>Systems included:</strong> Pristine polymer (wpc0.*) 00-NDs (wpc1.N00.*.zip, wpc5.N00.*.zip, and wpc10.N00.*.zip) HH-NDs (wpc1.NHH.*.zip, wpc5.NHH.*.zip, and wpc10.NHH.*.zip) <strong>Data included:</strong> Lin-spaced trajectories: \(t=10^8\,\delta t\), \(\Delta t=5\cdot10^5\,\delta t\) (*.lintraj.zip). Log-spaced trajectories: \(t=10^8\,\delta t\). 74 configurations, i.e. 8 decades. (*.logtraj.zip). Results obtained from trajectories and LAMMPS log files (*.results.zip). Structural results were obtained from a file containing some ignored duplicated configurations that have been removed from the uploaded files. Dynamical results were obtained from 100 files containing 55 configurations, i.e. 6 decades, too big to be uploaded to this repository (instead, a minimal log-scaled trajectory with 74 configurations encompassing the same time length of time has been uploaded; this file should reproduce a noisy version of the MSDs included in the results).* LAMMPS files (*.inlammps_prod.zip), including script and data file to reproduce the trajectories, as well as log file from the production run. Equation of State of Pristine polymer (wpc0.eqstate.zip): LAMMPS files of expansion-compression runs. Initial pre-equilibration LAMMPS data files (wpcall.initial.zip). * The interested reader can contact the authors for the complete set of log-scaled trajectories (~3TB).
DOI: 10.5281/zenodo.4665529
title: Molecular Dynamics of Janus Nanodimers Dispersed in Lamellar Phases of a Block Copolymer (Dataset 1 of 2)

description: <strong>Abstract:</strong> We investigate structural and dynamical properties of Janus nanodimers (NDs) dispersed in lamellar phases of a diblock copolymer. By performing Molecular Dynamics simulations, we show that an accurate tuning of the interactions between NDs and copolymer blocks can lead to a close control of NDs' space distribution and orientation. In particular, NDs are preferentially found within the lamellae if enthalpy-driven forces offset their entropic counterpart. By contrast, when enthalpic interactions are relatively mild, then excluded-volume effects become dominant and NDs are essentially observed within the inter-lamellar spacing. Not only does the degree of affinity between host and guest species drive the ND's distribution in the polymer matrix, but it also determines their space orientation. In turns, these key structural properties influence the long-time dynamics and the ability of NDs to diffuse through the polymer matrix. <strong>Dataset (1/2):</strong> <strong>Systems included:</strong> Pristine polymer (wpc0.*) 00-NDs (wpc1.N00.*.zip, wpc5.N00.*.zip, and wpc10.N00.*.zip) HH-NDs (wpc1.NHH.*.zip, wpc5.NHH.*.zip, and wpc10.NHH.*.zip) <strong>Data included:</strong> Lin-spaced trajectories: \(t=10^8\,\delta t\), \(\Delta t=5\cdot10^5\,\delta t\) (*.lintraj.zip). Log-spaced trajectories: \(t=10^8\,\delta t\). 74 configurations, i.e. 8 decades. (*.logtraj.zip). Results obtained from trajectories and LAMMPS log files (*.results.zip). Structural results were obtained from a file containing some ignored duplicated configurations that have been removed from the uploaded files. Dynamical results were obtained from 100 files containing 55 configurations, i.e. 6 decades, too big to be uploaded to this repository (instead, a minimal log-scaled trajectory with 74 configurations encompassing the same time length of time has been uploaded; this file should reproduce a noisy version of the MSDs included in the results).* LAMMPS files (*.inlammps_prod.zip), including script and data file to reproduce the trajectories, as well as log file from the production run. Equation of State of Pristine polymer (wpc0.eqstate.zip): LAMMPS files of expansion-compression runs. Initial pre-equilibration LAMMPS data files (wpcall.initial.zip). * The interested reader can contact the authors for the complete set of log-scaled trajectories (~3TB).
DOI: 10.6084/m9.figshare.13140254
title: Introducing differential RNA-seq mapping to track the early infection phase for <i>Pseudomonas</i> phage ɸKZ

description: As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of <i>Pseudomonas aeruginosa</i> jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (<i>cdrAB</i>) and iron storage (<i>bfrB</i>), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (<i>atpCDGHF</i> and <i>cyoABCDE</i>). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
DOI: 10.6084/m9.figshare.13140254.v1
title: Introducing differential RNA-seq mapping to track the early infection phase for <i>Pseudomonas</i> phage ɸKZ

description: As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of <i>Pseudomonas aeruginosa</i> jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (<i>cdrAB</i>) and iron storage (<i>bfrB</i>), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (<i>atpCDGHF</i> and <i>cyoABCDE</i>). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
DOI: 10.6084/m9.figshare.13140262.v1
title: PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region

description: Bacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform ‘PresRAT’. PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on the identification of the probable sRNA-mRNA binding regions. Using PresRAT, we have identified a total of 66,209 potential sRNA sequences from 292 bacterial genomes and 2247 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets, and their corresponding 3D models with structural dynamics information.
DOI: 10.6084/m9.figshare.13140262
title: PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region

description: Bacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform ‘PresRAT’. PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on the identification of the probable sRNA-mRNA binding regions. Using PresRAT, we have identified a total of 66,209 potential sRNA sequences from 292 bacterial genomes and 2247 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets, and their corresponding 3D models with structural dynamics information.
DOI: 10.6084/m9.figshare.13312256.v1
title: Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs

description: We have previously reported that not only transcripts of RNA polymerase II (pol II), but also one type of RNA transcribed by RNA polymerase III (pol III), undergo AAUAAA-dependent polyadenylation. Such an unusual feature is inherent in Short Interspersed Elements (SINEs) from genomes of certain mammals. For polyadenylation of its transcript, SINE should contain, besides an AATAAA hexamer and a transcription terminator, two specific regions: β, located downstream of box B of a promoter, and τ, preceding AATAAA. Here, using nucleotide substitutions in SINEs B2 (mouse) and Ves (bat), we identified nucleotides of β regions necessary for polyadenylation of their transcripts. These sequences (β signals) are the following: ACCACATgg in B2 and GGGCATGT in Ves. Using this approach, we identified τ signal of SINE B2 (GCTACagTGTACTTACAT), where TGTA tetramer is most important for polyadenylation. In Ves, τ region is a long polypyrimidine motif which is able to interact with PTB protein in Ves transcripts. We demonstrated by knockdown that B2 and Ves transcript polyadenylation is performed by canonical poly(A) polymerase with the participation of proteins CSPF-160 and Fip1, the known factors of mRNA polyadenylation. We also showed that a factor CFIm partaking in polyadenylation of many mRNAs, is involved only in polyadenylation of B2 transcripts. CFIm seems to interact with τ signal of В2 RNA and thereby facilitates the recruiting of other proteins engaged in polyadenylation. Thus, SINEs utilize at least some proteins involved in polyadenylation of pol II transcripts to polyadenylate their pol III transcripts.
DOI: 10.6084/m9.figshare.13312256
title: Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs

description: We have previously reported that not only transcripts of RNA polymerase II (pol II), but also one type of RNA transcribed by RNA polymerase III (pol III), undergo AAUAAA-dependent polyadenylation. Such an unusual feature is inherent in Short Interspersed Elements (SINEs) from genomes of certain mammals. For polyadenylation of its transcript, SINE should contain, besides an AATAAA hexamer and a transcription terminator, two specific regions: β, located downstream of box B of a promoter, and τ, preceding AATAAA. Here, using nucleotide substitutions in SINEs B2 (mouse) and Ves (bat), we identified nucleotides of β regions necessary for polyadenylation of their transcripts. These sequences (β signals) are the following: ACCACATgg in B2 and GGGCATGT in Ves. Using this approach, we identified τ signal of SINE B2 (GCTACagTGTACTTACAT), where TGTA tetramer is most important for polyadenylation. In Ves, τ region is a long polypyrimidine motif which is able to interact with PTB protein in Ves transcripts. We demonstrated by knockdown that B2 and Ves transcript polyadenylation is performed by canonical poly(A) polymerase with the participation of proteins CSPF-160 and Fip1, the known factors of mRNA polyadenylation. We also showed that a factor CFIm partaking in polyadenylation of many mRNAs, is involved only in polyadenylation of B2 transcripts. CFIm seems to interact with τ signal of В2 RNA and thereby facilitates the recruiting of other proteins engaged in polyadenylation. Thus, SINEs utilize at least some proteins involved in polyadenylation of pol II transcripts to polyadenylate their pol III transcripts.
DOI: 10.6084/m9.figshare.13077376.v1
title: Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species

description: Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated <i>in vivo</i> with MS2-tagged <i>trans</i>-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in the nitrogen-fixing α-rhizobia <i>Sinorhizobium meliloti</i>. The three proteomes were rather distinct, with that of EcpR1 particularly enriched in cell cycle-related enzymes, whilst sharing several transcription/translation-related proteins recurrently identified associated with sRNAs. Strikingly, MetK, the synthetase of the major methyl donor S-adenosylmethionine, was reliably recovered as a binding partner of the three sRNAs, which reciprocally co-immunoprecipitated with a FLAG-tagged MetK variant. Induced (over)expression of the <i>trans</i>-sRNAs and MetK depletion did not influence canonical riboregulatory traits, `for example, protein titration or sRNA stability, respectively. An <i>in vitro</i> filter assay confirmed binding of AbcR2, NfeR1 and EcpR1 to MetK and further revealed interaction of the protein with other non-coding and coding transcripts but not with the 5S rRNA. These findings uncover a broad specificity for RNA binding as an unprecedented feature of this housekeeping prokaryotic enzyme.
DOI: 10.6084/m9.figshare.13077376
title: Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species

description: Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated <i>in vivo</i> with MS2-tagged <i>trans</i>-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in the nitrogen-fixing α-rhizobia <i>Sinorhizobium meliloti</i>. The three proteomes were rather distinct, with that of EcpR1 particularly enriched in cell cycle-related enzymes, whilst sharing several transcription/translation-related proteins recurrently identified associated with sRNAs. Strikingly, MetK, the synthetase of the major methyl donor S-adenosylmethionine, was reliably recovered as a binding partner of the three sRNAs, which reciprocally co-immunoprecipitated with a FLAG-tagged MetK variant. Induced (over)expression of the <i>trans</i>-sRNAs and MetK depletion did not influence canonical riboregulatory traits, `for example, protein titration or sRNA stability, respectively. An <i>in vitro</i> filter assay confirmed binding of AbcR2, NfeR1 and EcpR1 to MetK and further revealed interaction of the protein with other non-coding and coding transcripts but not with the 5S rRNA. These findings uncover a broad specificity for RNA binding as an unprecedented feature of this housekeeping prokaryotic enzyme.
DOI: 10.6084/m9.figshare.13092846.v2
title: Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster

description: One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3ʹ end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional ‘fine-tuning’ can differentiate among miRNAs that are expressed simultaneously from a common precursor.
DOI: 10.6084/m9.figshare.13092846
title: Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster

description: One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3ʹ end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional ‘fine-tuning’ can differentiate among miRNAs that are expressed simultaneously from a common precursor.