cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14790051.v2
title: Long non-coding RNA RP11-283G6.5 confines breast cancer development through modulating miR-188-3p/TMED3/Wnt/β-catenin signalling

description: The contributions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) to breast cancer are critical areas of investigation. In this study, we identified a novel lncRNA RP11-283G6.5 which was lowly expressed in breast cancer and whose low expression was correlated with poor overall survival and disease-free survival of breast cancer patients. Functional experiments revealed that ectopic expression of RP11-283G6.5 confined breast cancer cellular growth, migration, and invasion, and promoted cellular apoptosis. Conversely, RP11-283G6.5 silencing facilitated breast cancer cellular growth, migration, and invasion, and repressed cellular apoptosis. Moreover, RP11-283G6.5 was found to confine breast cancer tumour growth and metastasis <i>in vivo</i>. Mechanistically, RP11-283G6.5 competitively bound to ILF3, reduced the binding of ILF3to primary miR-188 (pri-miR-188), abolished the suppressive effect of ILF3 on pri-miR-188 processing, and therefore promoted pri-miR-188 processing, leading to the reduction of pri-miR-188 and the upregulation of mature miR-188-3p. The expression of RP11-283G6.5 was significantly positively correlated with that of miR-188-3p in breast cancer tissues. Through increasing miR-188-3p, RP11-283G6.5 decreased TMED3, a target of miR-188-3p. RP11-283G6.5 further suppressed Wnt/β-catenin signalling via decreasing TMED3. Rescue assays revealed that inhibition of miR-188-3p, overexpression of TMED3 or blocking Wnt/β-catenin signalling all attenuated the roles of RP11-283G6.5 in breast cancer. Collectively, these findings demonstrated that RP11-283G6.5 is a tumour suppressive lncRNA in breast cancer via modulating miR-188-3p/TMED3/Wnt/β-catenin signalling. This study indicated that RP11-283G6.5 might be a promising prognostic biomarker and therapeutic target for breast cancer.
DOI: 10.6084/m9.figshare.14790051.v1
title: Long non-coding RNA RP11-283G6.5 confines breast cancer development through modulating miR-188-3p/TMED3/Wnt/β-catenin signaling

description: The contributions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) to breast cancer are critical areas of investigation. In this study, we identified a novel lncRNA RP11-283G6.5 which was lowly expressed in breast cancer and whose low expression was correlated with poor overall survival and disease-free survival of breast cancer patients. Functional experiments revealed that ectopic expression of RP11-283G6.5 confined breast cancer cellular growth, migration, and invasion, and promoted cellular apoptosis. Conversely, RP11-283G6.5 silencing facilitated breast cancer cellular growth, migration, and invasion, and repressed cellular apoptosis. Moreover, RP11-283G6.5 was found to confine breast cancer tumor growth and metastasis <i>in vivo</i>. Mechanistically, RP11-283G6.5 competitively bound to ILF3, reduced the binding of ILF3to primary miR-188 (pri-miR-188), abolished the suppressive effect of ILF3 on pri-miR-188 processing, and therefore promoted pri-miR-188 processing, leading to the reduction of pri-miR-188 and the upregulation of mature miR-188-3p. The expression of RP11-283G6.5 was significantly positively correlated with that of miR-188-3p in breast cancer tissues. Through increasing miR-188-3p, RP11-283G6.5 decreased TMED3, a target of miR-188-3p. RP11-283G6.5 further suppressed Wnt/β-catenin signaling via decreasing TMED3. Recuse assays revealed that inhibition of miR-188-3p, overexpression of TMED3, or blocking Wnt/β-catenin signaling all attenuated the roles of RP11-283G6.5 in breast cancer. Collectively, these findings demonstrated that RP11-283G6.5 is a tumor suppressive lncRNA in breast cancer via modulating miR-188-3p/TMED3/Wnt/β-catenin signaling. This study indicated that RP11-283G6.5 might be a promising prognostic biomarker and therapeutic target for breast cancer.
DOI: 10.6084/m9.figshare.14922753
title: Pervasive transcription of the mitochondrial genome in <i>Candida albicans</i> is revealed in mutants lacking the mtEXO RNase complex

description: The mitochondrial genome of the pathogenic yeast <i>Candida albicans</i> displays a typical organization of several (eight) primary transcription units separated by noncoding regions. Presence of genes encoding Complex I subunits and the stability of its mtDNA sequence make it an attractive model to study organellar genome expression using transcriptomic approaches. The main activity responsible for RNA degradation in mitochondria is a two-component complex (mtEXO) consisting of a 3ʹ-5ʹ exoribonuclease, in yeasts encoded by the <i>DSS1</i> gene, and a conserved Suv3p helicase. In <i>C. albicans</i>, deletion of either <i>DSS1</i> or <i>SUV3</i> gene results in multiple defects in mitochondrial genome expression leading to the loss of respiratory competence. Transcriptomic analysis reveals pervasive transcription in mutants lacking the mtEXO activity, with evidence of the entire genome being transcribed, whereas in wild-type strains no RNAs corresponding to a significant fraction of the noncoding genome can be detected. Antisense (‘mirror’) transcripts, absent from normal mitochondria are also prominent in the mutants. The expression of multiple mature transcripts, particularly those translated from bicistronic mRNAs, as well as those that contain introns is affected in the mutants, resulting in a decreased level of proteins and reduced respiratory complex activity. The phenotype is most severe in the case of Complex IV, where a decrease of mature COX1 mRNA level to ~5% results in a complete loss of activity. These results show that RNA degradation by mtEXO is essential for shaping the mitochondrial transcriptome and is required to maintain the functional demarcation between transcription units and non-coding genome segments.
DOI: 10.6084/m9.figshare.15050085
title: The enigmatic RNase MRP of kinetoplastids

description: The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.
DOI: 10.6084/m9.figshare.15050085.v1
title: The enigmatic RNase MRP of kinetoplastids

description: The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.
DOI: 10.6084/m9.figshare.14714912
title: Structural insights into dpCoA-RNA decapping by NudC

description: Various kinds of cap structures, such as m<sup>7</sup>G, triphosphate groups, NAD and dpCoA, protect the 5′ terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m<sup>7</sup>G, triphosphate group, and NAD caps. In contrast, few studies related to the cleavage of the RNA dpCoA cap have been conducted. Here, we report the hydrolytic activity of <i>Escherichia coli</i> NudC towards dpCoA and dpCoA-capped RNA <i>in vitro</i>. We also determined the crystal structure of dimeric NudC in complex with dpCoA at 2.0 Å resolution. Structural analysis revealed that dpCoA is recognized and hydrolysed in a manner similar to NAD. In addition, NudC may also remove other dinucleotide derivative caps of RNA, which comprise the AMP moieties. NudC homologs in <i>Saccharomyces cerevisiae</i> and <i>Arabidopsis thaliana</i> exhibited similar dpCoA decapping (deCoAping) activity. These results together indicate a conserved mechanism underpinning the hydrolysis of dpCoA-capped RNA in both prokaryotes and eukaryotes.
DOI: 10.6084/m9.figshare.14714912.v1
title: Structural insights into dpCoA-RNA decapping by NudC

description: Various kinds of cap structures, such as m<sup>7</sup>G, triphosphate groups, NAD and dpCoA, protect the 5′ terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m<sup>7</sup>G, triphosphate group, and NAD caps. In contrast, few studies related to the cleavage of the RNA dpCoA cap have been conducted. Here, we report the hydrolytic activity of <i>Escherichia coli</i> NudC towards dpCoA and dpCoA-capped RNA <i>in vitro</i>. We also determined the crystal structure of dimeric NudC in complex with dpCoA at 2.0 Å resolution. Structural analysis revealed that dpCoA is recognized and hydrolysed in a manner similar to NAD. In addition, NudC may also remove other dinucleotide derivative caps of RNA, which comprise the AMP moieties. NudC homologs in <i>Saccharomyces cerevisiae</i> and <i>Arabidopsis thaliana</i> exhibited similar dpCoA decapping (deCoAping) activity. These results together indicate a conserved mechanism underpinning the hydrolysis of dpCoA-capped RNA in both prokaryotes and eukaryotes.
DOI: 10.6084/m9.figshare.14922753.v1
title: Pervasive transcription of the mitochondrial genome in <i>Candida albicans</i> is revealed in mutants lacking the mtEXO RNase complex

description: The mitochondrial genome of the pathogenic yeast <i>Candida albicans</i> displays a typical organization of several (eight) primary transcription units separated by noncoding regions. Presence of genes encoding Complex I subunits and the stability of its mtDNA sequence make it an attractive model to study organellar genome expression using transcriptomic approaches. The main activity responsible for RNA degradation in mitochondria is a two-component complex (mtEXO) consisting of a 3ʹ-5ʹ exoribonuclease, in yeasts encoded by the <i>DSS1</i> gene, and a conserved Suv3p helicase. In <i>C. albicans</i>, deletion of either <i>DSS1</i> or <i>SUV3</i> gene results in multiple defects in mitochondrial genome expression leading to the loss of respiratory competence. Transcriptomic analysis reveals pervasive transcription in mutants lacking the mtEXO activity, with evidence of the entire genome being transcribed, whereas in wild-type strains no RNAs corresponding to a significant fraction of the noncoding genome can be detected. Antisense (‘mirror’) transcripts, absent from normal mitochondria are also prominent in the mutants. The expression of multiple mature transcripts, particularly those translated from bicistronic mRNAs, as well as those that contain introns is affected in the mutants, resulting in a decreased level of proteins and reduced respiratory complex activity. The phenotype is most severe in the case of Complex IV, where a decrease of mature COX1 mRNA level to ~5% results in a complete loss of activity. These results show that RNA degradation by mtEXO is essential for shaping the mitochondrial transcriptome and is required to maintain the functional demarcation between transcription units and non-coding genome segments.
DOI: 10.6084/m9.figshare.15035377
title: SRSF5 regulates alternative splicing of <i>DMTF1</i> pre-mRNA through modulating SF1 binding

description: Among the three DMTF1 splicing isoforms, DMTF1α acts as a tumour suppressor through promoting p14ARF expression, while DMTF1β exhibits an oncogenic role likely through antagonizing DMTF1α. However, the molecular mechanism underlying alternative splicing of <i>DMTF1</i> pre-mRNA has not been delineated. In the current study, we discovered SRSF5 as a regulatory protein binding to a region located between <i>DMTF1β</i> and <i>α</i> acceptor splice sites to promote <i>DMTF1β</i> and <i>γ</i> splicing. We demonstrated that SRSF5 expression positively correlated with <i>DMTF1β</i>/<i>α</i> ratio in breast cancer samples, and ectopically expressed SRSF5 promoted the splicing of <i>DMTF1β</i> and <i>γ</i>, but not <i>DMTF1α</i>, when testing endogenous <i>DMTF1</i> pre-mRNA and a reporter construct. Upon SRSF5 knockdown, we observed significantly decreased <i>DMTF1β</i> and <i>γ</i> ratios of endogenous transcripts. An RNA sequence just upstream of the <i>α</i> acceptor site contains two adjacent SRSF5 binding elements, one of which overlaps with an SF1 binding site. Our mechanistic studies revealed that SRSF5 binding to both elements in this region could consign SF1 to its distal-binding sites close to the <i>β</i> and <i>γ</i> acceptor sites, favouring splicing of their isoforms. Overall, our study revealed SRSF5 as a key regulator to promote <i>DMTF1β</i> and <i>γ</i> splicing, and consequently reduce <i>DMTF1α</i> splicing. ARF: alternative reading frame, that is, p14ARF, or CDKN2A (cyclin-dependent kinase inhibitor 2A); β-gal: β-galactosidase; CLIP-seq: crosslinking and immunoprecipitation-sequencing; <i>DMTF1</i>: the cyclin D binding myb-like transcription factor 1; ESS/ESE: exonic splicing silencer/enhancer; Ex: exon; FBS: fetal bovine serum; Gluc: Gaussia luciferase; hnRNPs: heterogeneous nuclear ribonucleoproteins; In: intron; ISS/ISE: intronic splicing silencer/enhancer; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; PSI: percent-splice-in; qPCR: quantitative real-time PCR; RIP: RNA immunoprecipitation; RNAseq: RNA sequencing; RT: reverse transcription; SF1: splicing factor 1; SR: serine/arginine-rich proteins; SRSF5: serine and arginine-rich splicing factor 5; TCGA: the cancer genome atlas; UCSC: University of California, Santa Cruz. WT: Wild type
DOI: 10.6084/m9.figshare.15035377.v1
title: SRSF5 regulates alternative splicing of <i>DMTF1</i> pre-mRNA through modulating SF1 binding

description: Among the three DMTF1 splicing isoforms, DMTF1α acts as a tumour suppressor through promoting p14ARF expression, while DMTF1β exhibits an oncogenic role likely through antagonizing DMTF1α. However, the molecular mechanism underlying alternative splicing of <i>DMTF1</i> pre-mRNA has not been delineated. In the current study, we discovered SRSF5 as a regulatory protein binding to a region located between <i>DMTF1β</i> and <i>α</i> acceptor splice sites to promote <i>DMTF1β</i> and <i>γ</i> splicing. We demonstrated that SRSF5 expression positively correlated with <i>DMTF1β</i>/<i>α</i> ratio in breast cancer samples, and ectopically expressed SRSF5 promoted the splicing of <i>DMTF1β</i> and <i>γ</i>, but not <i>DMTF1α</i>, when testing endogenous <i>DMTF1</i> pre-mRNA and a reporter construct. Upon SRSF5 knockdown, we observed significantly decreased <i>DMTF1β</i> and <i>γ</i> ratios of endogenous transcripts. An RNA sequence just upstream of the <i>α</i> acceptor site contains two adjacent SRSF5 binding elements, one of which overlaps with an SF1 binding site. Our mechanistic studies revealed that SRSF5 binding to both elements in this region could consign SF1 to its distal-binding sites close to the <i>β</i> and <i>γ</i> acceptor sites, favouring splicing of their isoforms. Overall, our study revealed SRSF5 as a key regulator to promote <i>DMTF1β</i> and <i>γ</i> splicing, and consequently reduce <i>DMTF1α</i> splicing. ARF: alternative reading frame, that is, p14ARF, or CDKN2A (cyclin-dependent kinase inhibitor 2A); β-gal: β-galactosidase; CLIP-seq: crosslinking and immunoprecipitation-sequencing; <i>DMTF1</i>: the cyclin D binding myb-like transcription factor 1; ESS/ESE: exonic splicing silencer/enhancer; Ex: exon; FBS: fetal bovine serum; Gluc: Gaussia luciferase; hnRNPs: heterogeneous nuclear ribonucleoproteins; In: intron; ISS/ISE: intronic splicing silencer/enhancer; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; PSI: percent-splice-in; qPCR: quantitative real-time PCR; RIP: RNA immunoprecipitation; RNAseq: RNA sequencing; RT: reverse transcription; SF1: splicing factor 1; SR: serine/arginine-rich proteins; SRSF5: serine and arginine-rich splicing factor 5; TCGA: the cancer genome atlas; UCSC: University of California, Santa Cruz. WT: Wild type
DOI: 10.6084/m9.figshare.15060842
title: A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy

description: lncRNAs are at the core of many regulatory processes and have also been recognized to be involved in various complex diseases. They affect gene regulation through direct interactions with RNA, DNA or proteins. Accordingly, lncRNA structure is likely to be essential for their regulatory function. Point mutations, which manifest as SNPs (single nucleotide polymorphisms) in genome screens, can substantially alter their function and, subsequently, the expression of their downstream regulated genes. To test the effect of SNPs on structure, we investigated lncRNAs associated with dilated cardiomyopathy. Among 322 human candidate lncRNAs, we demonstrate first the significant association of an SNP located in lncRNA H19 using data from 1084 diseased and 751 control patients. H19 is generally highly expressed in the heart, with a complex expression pattern during heart development. Next, we used MFE (minimum free energy) folding to demonstrate a significant refolding in the secondary structure of this 861 nt long lncRNA. Since MFE folding may overlook the importance of sub-optimal structures, we showed that this refolding also manifests in the overall Boltzmann structure ensemble. There, the composition of structures is tremendously affected in their thermodynamic probabilities through the genetic variant. Finally, we confirmed these results experimentally, using SHAPE-Seq, corroborating that SNPs affecting such structures may explain hidden genetic variance not accounted for through genome wide association studies. Our results suggest that structural changes in lncRNAs, and lncRNA H19 in particular, affect regulatory processes and represent optimal targets for further in-depth studies probing their molecular interactions.
DOI: 10.6084/m9.figshare.15060842.v1
title: A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy

description: lncRNAs are at the core of many regulatory processes and have also been recognized to be involved in various complex diseases. They affect gene regulation through direct interactions with RNA, DNA or proteins. Accordingly, lncRNA structure is likely to be essential for their regulatory function. Point mutations, which manifest as SNPs (single nucleotide polymorphisms) in genome screens, can substantially alter their function and, subsequently, the expression of their downstream regulated genes. To test the effect of SNPs on structure, we investigated lncRNAs associated with dilated cardiomyopathy. Among 322 human candidate lncRNAs, we demonstrate first the significant association of an SNP located in lncRNA H19 using data from 1084 diseased and 751 control patients. H19 is generally highly expressed in the heart, with a complex expression pattern during heart development. Next, we used MFE (minimum free energy) folding to demonstrate a significant refolding in the secondary structure of this 861 nt long lncRNA. Since MFE folding may overlook the importance of sub-optimal structures, we showed that this refolding also manifests in the overall Boltzmann structure ensemble. There, the composition of structures is tremendously affected in their thermodynamic probabilities through the genetic variant. Finally, we confirmed these results experimentally, using SHAPE-Seq, corroborating that SNPs affecting such structures may explain hidden genetic variance not accounted for through genome wide association studies. Our results suggest that structural changes in lncRNAs, and lncRNA H19 in particular, affect regulatory processes and represent optimal targets for further in-depth studies probing their molecular interactions.
DOI: 10.6084/m9.figshare.16699561.v1
title: MustSeq, an alternative approach for multiplexible strand-specific 3’ end sequencing of mRNA transcriptome confers high efficiency and practicality

description: RNA-seq has been widely used to reveal the molecular mechanism of variants of life process. We have developed an alternative method, MustSeq, which generates multiple second strands along a single 1<sup>st</sup> strand cDNA by random-priming initiation, immediately after reverse transcription for each RNA extract using sample-barcoded poly-dT primers, then 3ʹ ends-enriching PCR is applied to construct the library. Unlike the conventional RNA seq, MustSeq avoids procedures such as mRNA isolation, fragmentation and RNA 5ʹ-end capture, enables early pooling of multiple samples, and requires only one twentieth of sequencing reads of full-length sequencing. We demonstrate the power and features of MustSeq comparing with TruSeq and NEBNext RNA-seq, two conventional full-length methods and QuantSeq, an industrial 3ʹ end method. In cancer cell lines, the reads distribution of CDS-exon as well as genes, lncRNAs and GO terms detected by MustSeq are closer than QuantSeq to TruSeq. In mouse hepatocarcinoma and healthy livers, MustSeq enriches the same pathways as by NEBNext, and reveals the molecular profile of carcinogenesis. Overall MustSeq is a robust and accurate RNA-seq method allowing efficient library construction, sequencing and analysis, particularly valuable for analysis of differentially expressed genes with a large number of samples. MustSeq will greatly accelerate the application of bulk RNA-seq on different fields, and potentially applicable for single cell RNA-seq.
DOI: 10.6084/m9.figshare.25451749
title: Recombination analysis raw data

description: This research delves into the understanding of the formation of recombinant forms between HIV-1 and HIV-2. Since both HIV-1 and HIV-2 infect the same cell type, they can certainly reside in the same cell and undergo recombination. Recombination between HIV-1 and HIV-2 might have important ramifications for the disease progression phenotype observed in HIV-1 and HIV-2 co-infected individuals. We developed a bioinformatics analysis pipeline which performs an in-depth analysis of recombination to detect these recombinant forms. We found HIV-1/HIV-2 recombinants in circulation based on our analysis. Thus, we conclude that there are HIV-1/HIV-2 recombinants in circulation, and these recombinants are likely to contribute to the observed slow progression of disease in dually infected individuals. Our analysis pipeline is reproducible and can be adopted for the recombination analysis of any retrovirus.