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    Millipore rna library
    Diagrammatic representation of the various proteins used for <t>RNA</t> selections and aptamer analysis. (A) Wild-type HIV-1 Gag polyprotein. (B) The <t>DP6-Gag</t> protein used for selections lack the N-terminal myristate and the late domain p6. (C) 8N-Gag with eight
    Rna Library, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 50 article reviews
    Price from $9.99 to $1999.99
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    99
    Millipore rna seq library preparation
    Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells <t>transfected</t> with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the <t>RNA</t> Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated
    Rna Seq Library Preparation, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc rna library
    Modulation of MIR157c processing efficiency. ( A–C ) Small <t>RNA</t> gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P
    Rna Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 1370 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc rna truseq library
    Modulation of MIR157c processing efficiency. ( A–C ) Small <t>RNA</t> gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P
    Rna Truseq Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 73 article reviews
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    Image Search Results


    Diagrammatic representation of the various proteins used for RNA selections and aptamer analysis. (A) Wild-type HIV-1 Gag polyprotein. (B) The DP6-Gag protein used for selections lack the N-terminal myristate and the late domain p6. (C) 8N-Gag with eight

    Journal: Journal of Virology

    Article Title: RNA Aptamers Directed to Human Immunodeficiency Virus Type 1 Gag Polyprotein Bind to the Matrix and Nucleocapsid Domains and Inhibit Virus Production ▿RNA Aptamers Directed to Human Immunodeficiency Virus Type 1 Gag Polyprotein Bind to the Matrix and Nucleocapsid Domains and Inhibit Virus Production ▿ †

    doi: 10.1128/JVI.02626-09

    Figure Lengend Snippet: Diagrammatic representation of the various proteins used for RNA selections and aptamer analysis. (A) Wild-type HIV-1 Gag polyprotein. (B) The DP6-Gag protein used for selections lack the N-terminal myristate and the late domain p6. (C) 8N-Gag with eight

    Article Snippet: To perform RNA selections, ∼660 pmol of the DP6-Gag protein was incubated with equimolar quantities of the RNA library in binding buffer (20 mM Tris-HCl [pH 7.4], 250 mM NaCl, 5 mM MgCl2 , and 100 μM Tris(2-carboxyethyl)phosphine [TCEP]) for 15 min at 37°C, after which the reaction was filtered through HAWP nitrocellulose filters (Millipore, Bedford, MA).

    Techniques:

    Cathepsin B genes that are differentially expressed upon M. persicae host change belong predominantly to a single aphid-expanded clade and form gene clusters in the M. persicae genome. a Maximum likelihood phylogenic tree of arthropod cathepsin B protein sequences. The sequences were aligned with Muscle [ 76 ] and the phylogeny estimated using FastTree [ 92 ] (JTT + CAT rate variation). Circles on branches indicate SH-like local support values > 80%, scale bar below indicates 0.1 substitutions per site. Rings from outside to inside: ring 1, M. persicae cathepsin B (MpCathB) gene identities (IDs) with numbers in red indicating upregulation of these genes in M. persicae reared for one year on B. rapa relative to those reared for one year on N. benthamiana and bold font indicating location on the cathepsin B multigene clusters shown in ( b ); ring 2, red squares indicating MpCathB genes that are differentially expressed upon M. persicae host change; ring 3, cathB genes from different arthropods following the colour scheme of the legend in the upper left corner and matching the colours of the branches of the phylogenetic tree; ring 4, aphid-expanded (AE) clades with AE_Clade I labelled light green and AE_Clade II light blue . b MpCathB multigene clusters of the M. persicae genome. Lines indicate the genomic scaffolds on which the MpCathB genes are indicated with block arrows . Gene IDs above the genes match those of the phylogenetic tree in A, with block arrows and fonts highlighted in red being differentially expressed upon host change. Scale bar on right shows 1 kb. c Relative expression levels of MpCathB genes of M. persicae at seven weeks being reared on N. benthamiana (Nb), B. rapa (Br) and A. thaliana (At). Numbers under the graphs indicate MpCathB gene IDs with those in red font DE as in ( a ). Batches of five adult females were harvested for RNA extraction and quantitative real-time polymerase chain reaction assays. Bars represent expression values (mean ± standard deviation (SD)) of three independent biological replicates. * p

    Journal: Genome Biology

    Article Title: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

    doi: 10.1186/s13059-016-1145-3

    Figure Lengend Snippet: Cathepsin B genes that are differentially expressed upon M. persicae host change belong predominantly to a single aphid-expanded clade and form gene clusters in the M. persicae genome. a Maximum likelihood phylogenic tree of arthropod cathepsin B protein sequences. The sequences were aligned with Muscle [ 76 ] and the phylogeny estimated using FastTree [ 92 ] (JTT + CAT rate variation). Circles on branches indicate SH-like local support values > 80%, scale bar below indicates 0.1 substitutions per site. Rings from outside to inside: ring 1, M. persicae cathepsin B (MpCathB) gene identities (IDs) with numbers in red indicating upregulation of these genes in M. persicae reared for one year on B. rapa relative to those reared for one year on N. benthamiana and bold font indicating location on the cathepsin B multigene clusters shown in ( b ); ring 2, red squares indicating MpCathB genes that are differentially expressed upon M. persicae host change; ring 3, cathB genes from different arthropods following the colour scheme of the legend in the upper left corner and matching the colours of the branches of the phylogenetic tree; ring 4, aphid-expanded (AE) clades with AE_Clade I labelled light green and AE_Clade II light blue . b MpCathB multigene clusters of the M. persicae genome. Lines indicate the genomic scaffolds on which the MpCathB genes are indicated with block arrows . Gene IDs above the genes match those of the phylogenetic tree in A, with block arrows and fonts highlighted in red being differentially expressed upon host change. Scale bar on right shows 1 kb. c Relative expression levels of MpCathB genes of M. persicae at seven weeks being reared on N. benthamiana (Nb), B. rapa (Br) and A. thaliana (At). Numbers under the graphs indicate MpCathB gene IDs with those in red font DE as in ( a ). Batches of five adult females were harvested for RNA extraction and quantitative real-time polymerase chain reaction assays. Bars represent expression values (mean ± standard deviation (SD)) of three independent biological replicates. * p

    Article Snippet: Construction of a small RNA library of M. persicae RNA was extracted from 450 M. persicae nymphs using Tri-Reagent (Sigma).

    Techniques: Blocking Assay, Expressing, RNA Extraction, Real-time Polymerase Chain Reaction, Standard Deviation

    RNAi-mediated knock-down of the expression of multiple cathepsin B genes reduces M. persicae survival and fecundity on A. thaliana . a Relative cathepsin B (CathB) expression levels (compared to aphids on dsGFP (control) plants) of M. persicae on three independent transgenic lines (lines 5–1, 17–5 and 18–2) producing double-stranded (ds) RNA corresponding to multiple M. persicae cathepsin B genes (dsCathB) (Fig. 3a , Additional file 20 : Figure S10). Aphids were reared on the transgenic lines for four generations. Batches of five adult females were harvested for RNA extraction and qRT-PCR assays. Bars represent expression values (mean ± standard deviation (SD)) of three independent biological replicates. b CathB-RNAi M. persicae produces less progeny compared to control (dsGFP-treated) aphids on A. thaliana . Five nymphs were transferred to single plants and produced nymphs on approximately day 5. Nymph counts were conducted on days 7, 9 and 11 and removed. Columns show the mean ± SD of the total nymph counts for these three days of three biological replicates, with each replicate consisting nymphs produced by 15 aphids at five aphids per plant (n = 3 plants). c , d Survival rates of CathB-RNAi and control (dsGFP-exposed) M persicae on non-transgenic A. thaliana (At) and N. benthamiana (Nb) plants. Ten third instar nymphs on dsCathB and dsGFP transgenic plants were transferred to non-transgenic plants; survival rates were recorded two days later. Bars represent mean ± SD of three biological replicates, with each replicate consisting of the survival rates of 30 aphids at 10 aphids per plants (n = 3 plants). e , f Fecundity rates of CathB-RNAi and control (dsGFP-exposed) M. persicae on non-transgenic A. thaliana (At) and N. benthamiana (Nb) plants. Nymph counts were conducted as in ( b ). Asterisks (*) and different letters ( a , b ) above the bars indicate significant difference at p

    Journal: Genome Biology

    Article Title: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

    doi: 10.1186/s13059-016-1145-3

    Figure Lengend Snippet: RNAi-mediated knock-down of the expression of multiple cathepsin B genes reduces M. persicae survival and fecundity on A. thaliana . a Relative cathepsin B (CathB) expression levels (compared to aphids on dsGFP (control) plants) of M. persicae on three independent transgenic lines (lines 5–1, 17–5 and 18–2) producing double-stranded (ds) RNA corresponding to multiple M. persicae cathepsin B genes (dsCathB) (Fig. 3a , Additional file 20 : Figure S10). Aphids were reared on the transgenic lines for four generations. Batches of five adult females were harvested for RNA extraction and qRT-PCR assays. Bars represent expression values (mean ± standard deviation (SD)) of three independent biological replicates. b CathB-RNAi M. persicae produces less progeny compared to control (dsGFP-treated) aphids on A. thaliana . Five nymphs were transferred to single plants and produced nymphs on approximately day 5. Nymph counts were conducted on days 7, 9 and 11 and removed. Columns show the mean ± SD of the total nymph counts for these three days of three biological replicates, with each replicate consisting nymphs produced by 15 aphids at five aphids per plant (n = 3 plants). c , d Survival rates of CathB-RNAi and control (dsGFP-exposed) M persicae on non-transgenic A. thaliana (At) and N. benthamiana (Nb) plants. Ten third instar nymphs on dsCathB and dsGFP transgenic plants were transferred to non-transgenic plants; survival rates were recorded two days later. Bars represent mean ± SD of three biological replicates, with each replicate consisting of the survival rates of 30 aphids at 10 aphids per plants (n = 3 plants). e , f Fecundity rates of CathB-RNAi and control (dsGFP-exposed) M. persicae on non-transgenic A. thaliana (At) and N. benthamiana (Nb) plants. Nymph counts were conducted as in ( b ). Asterisks (*) and different letters ( a , b ) above the bars indicate significant difference at p

    Article Snippet: Construction of a small RNA library of M. persicae RNA was extracted from 450 M. persicae nymphs using Tri-Reagent (Sigma).

    Techniques: Expressing, Transgenic Assay, RNA Extraction, Quantitative RT-PCR, Standard Deviation, Produced

    Expression profiles of HwHog-ChIP positive genes in adapted and stressed H. werneckii cells and ChIP results in adapted cells . RT-PCR was performed with RNA isolated from adapted cells (Adaptation) or cells exposed to hypersaline stress (Hyperosmotic stress) as indicated. 26S rRNA ( Hw26SRR ) was used as an internal control for template normalization. The HwHog1-ChIP and sequential RNA polymerase II/HwHog1-ChIP (SeqChIP) results for cells adapted to 3 M NaCl and 4.5 M NaCl are presented in parallel. The negative control for nonspecific binding of antibodies in both ChIP experiments is represented in the

    Journal: BMC Genomics

    Article Title: Differential gene expression and Hog1 interaction with osmoresponsive genes in the extremely halotolerant black yeast Hortaea werneckii

    doi: 10.1186/1471-2164-8-280

    Figure Lengend Snippet: Expression profiles of HwHog-ChIP positive genes in adapted and stressed H. werneckii cells and ChIP results in adapted cells . RT-PCR was performed with RNA isolated from adapted cells (Adaptation) or cells exposed to hypersaline stress (Hyperosmotic stress) as indicated. 26S rRNA ( Hw26SRR ) was used as an internal control for template normalization. The HwHog1-ChIP and sequential RNA polymerase II/HwHog1-ChIP (SeqChIP) results for cells adapted to 3 M NaCl and 4.5 M NaCl are presented in parallel. The negative control for nonspecific binding of antibodies in both ChIP experiments is represented in the "NoAB" line and the positive control for genomic DNA amplification from 100-fold diluted input samples is labeled as "INPUT". HwCOB1 and 26SRR genes were negative controls and HwGPD1A was the positive control for HwHog1 and RNA polymerase II cross-linking.

    Article Snippet: Suppression subtractive hybridization, mirror orientation selection and differential screening of subtracted library Total RNA from cells of H. werneckii was isolated using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions from mid-exponential phase cells grown in YNB media with 3 M or 4.5 M NaCl.

    Techniques: Expressing, Chromatin Immunoprecipitation, Reverse Transcription Polymerase Chain Reaction, Isolation, Negative Control, Binding Assay, Positive Control, Amplification, Labeling

    Expression profiles of HwHog-ChIP negative genes in adapted and stressed H. werneckii cells . RT-PCR was performed with RNA isolated from cells adapted to 3 M and 4.5 M NaCl (Adaptation) or cells exposed to hypersaline stress at indicated time points (Hyperosmotic stress). 26S rRNA ( Hw26SRR ) was used as an internal control for template normalization. Genes whose expression was not affected by salt-stress are presented in (A) and those that responded to salt stress are presented in (B).

    Journal: BMC Genomics

    Article Title: Differential gene expression and Hog1 interaction with osmoresponsive genes in the extremely halotolerant black yeast Hortaea werneckii

    doi: 10.1186/1471-2164-8-280

    Figure Lengend Snippet: Expression profiles of HwHog-ChIP negative genes in adapted and stressed H. werneckii cells . RT-PCR was performed with RNA isolated from cells adapted to 3 M and 4.5 M NaCl (Adaptation) or cells exposed to hypersaline stress at indicated time points (Hyperosmotic stress). 26S rRNA ( Hw26SRR ) was used as an internal control for template normalization. Genes whose expression was not affected by salt-stress are presented in (A) and those that responded to salt stress are presented in (B).

    Article Snippet: Suppression subtractive hybridization, mirror orientation selection and differential screening of subtracted library Total RNA from cells of H. werneckii was isolated using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions from mid-exponential phase cells grown in YNB media with 3 M or 4.5 M NaCl.

    Techniques: Expressing, Chromatin Immunoprecipitation, Reverse Transcription Polymerase Chain Reaction, Isolation

    General characteristics of the small RNA libraries. 1A. T. pseudonana preparatory gel showing presence of small RNA bands after library construction and amplification, prior to 454 sequencing. Agarose gel electrophoretic separation of final amplified small RNA products. Right, zoomed gel detail highlights the presence of several predominant bands and size classes. 1B. T. pseudonana Agilent gel showing presence of small RNA band after library construction and amplification, prior to SOLiD sequencing. 1C - Length distribution of T. pseudonana small RNA candidate sequences. Length distribution of unique sequences was calculated after removal of RNA degradation products and alignment with the T. pseudonana genome. 1D - Nucleotide frequency at the 5′ end of the small RNA candidate sequences. Nucleotide frequency of unique sequences was tabulated after removal of RNA degradation products and alignment with the T. pseudonana genome.

    Journal: PLoS ONE

    Article Title: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

    doi: 10.1371/journal.pone.0022870

    Figure Lengend Snippet: General characteristics of the small RNA libraries. 1A. T. pseudonana preparatory gel showing presence of small RNA bands after library construction and amplification, prior to 454 sequencing. Agarose gel electrophoretic separation of final amplified small RNA products. Right, zoomed gel detail highlights the presence of several predominant bands and size classes. 1B. T. pseudonana Agilent gel showing presence of small RNA band after library construction and amplification, prior to SOLiD sequencing. 1C - Length distribution of T. pseudonana small RNA candidate sequences. Length distribution of unique sequences was calculated after removal of RNA degradation products and alignment with the T. pseudonana genome. 1D - Nucleotide frequency at the 5′ end of the small RNA candidate sequences. Nucleotide frequency of unique sequences was tabulated after removal of RNA degradation products and alignment with the T. pseudonana genome.

    Article Snippet: Small RNA cDNA library construction for SOLiD libraries Total RNA from T. pseudonana cell cultures was extracted with TriReagent (Sigma) as previously described .

    Techniques: Amplification, Sequencing, Agarose Gel Electrophoresis

    Percentage of small RNA sequences in each repetitive element class in the T. pseudonana genome for each library.

    Journal: PLoS ONE

    Article Title: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

    doi: 10.1371/journal.pone.0022870

    Figure Lengend Snippet: Percentage of small RNA sequences in each repetitive element class in the T. pseudonana genome for each library.

    Article Snippet: Small RNA cDNA library construction for SOLiD libraries Total RNA from T. pseudonana cell cultures was extracted with TriReagent (Sigma) as previously described .

    Techniques:

    Heatmaps and histograms of small RNA candidate abundance mapped along chromosomes 16a, 16b, 22, 24. All alignments to the T. pseudonana genome were binned, normalized, and then plotted along the length of the chromosome as a heatmap and as a histogram. The intensity of the spot on a heatmap denotes the abundance of sequences generated at the particular site relative to the total dataset for that sample, with darker colors depicting higher abundance. Additionally, the alignment coordinates of the sequences were binned into histograms along each chromosome. Values above the x-axis signify that the small RNA was transcribed along the plus strand of DNA, and below the x-axis for the minus strand. Each row of the heatmap represents a different sample library in the following order: Tp_454data, Tp_EF, Tp_EC. Bars above the line represent the plus strand and bars below the line represent the complimentary strand. A binsize of 10000 was used for both types of plots.

    Journal: PLoS ONE

    Article Title: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

    doi: 10.1371/journal.pone.0022870

    Figure Lengend Snippet: Heatmaps and histograms of small RNA candidate abundance mapped along chromosomes 16a, 16b, 22, 24. All alignments to the T. pseudonana genome were binned, normalized, and then plotted along the length of the chromosome as a heatmap and as a histogram. The intensity of the spot on a heatmap denotes the abundance of sequences generated at the particular site relative to the total dataset for that sample, with darker colors depicting higher abundance. Additionally, the alignment coordinates of the sequences were binned into histograms along each chromosome. Values above the x-axis signify that the small RNA was transcribed along the plus strand of DNA, and below the x-axis for the minus strand. Each row of the heatmap represents a different sample library in the following order: Tp_454data, Tp_EF, Tp_EC. Bars above the line represent the plus strand and bars below the line represent the complimentary strand. A binsize of 10000 was used for both types of plots.

    Article Snippet: Small RNA cDNA library construction for SOLiD libraries Total RNA from T. pseudonana cell cultures was extracted with TriReagent (Sigma) as previously described .

    Techniques: Generated

    Summary of the small RNA sequence distribution in the T. pseudonana genome for each library.

    Journal: PLoS ONE

    Article Title: Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

    doi: 10.1371/journal.pone.0022870

    Figure Lengend Snippet: Summary of the small RNA sequence distribution in the T. pseudonana genome for each library.

    Article Snippet: Small RNA cDNA library construction for SOLiD libraries Total RNA from T. pseudonana cell cultures was extracted with TriReagent (Sigma) as previously described .

    Techniques: Sequencing

    Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells transfected with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the RNA Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated

    Journal: Nature Communications

    Article Title: Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

    doi: 10.1038/s41467-018-02894-w

    Figure Lengend Snippet: Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells transfected with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the RNA Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated

    Article Snippet: RNA extraction and RNA-seq library preparation For RNA-seq, DIvA cells (transfected with the control siRNA) were lysed using TRI reagent (SIGMA) and spiked-in with ERCC RNA Spike-In Mix (Thermo Fisher Scientific).

    Techniques: Polymerase Chain Reaction, DNA Sequencing, Amplification, Real-time Polymerase Chain Reaction, Transfection, Activity Assay, Translocation Assay

    Modulation of MIR157c processing efficiency. ( A–C ) Small RNA gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P

    Journal: Nucleic Acids Research

    Article Title: Efficiency and precision of microRNA biogenesis modes in plants

    doi: 10.1093/nar/gky853

    Figure Lengend Snippet: Modulation of MIR157c processing efficiency. ( A–C ) Small RNA gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P

    Article Snippet: The small RNA library was constructed using the Illumina TruSeq sRNA kit, and sequenced on the Illumina HiSeq platform at the University of Delaware.

    Techniques: Transgenic Assay, Expressing, Plasmid Preparation, Autoradiography, Construct

    Small RNA sequence variation caused by variability in the position of the first cut. (A–P) miRNAs for which the biogenesis is base-to-loop are displayed on the left panels (turquoise bars) (A–H), while loop-to-base miRNAs are displayed on the right panels (blue bars) (I–P). ( A ) miR165a, ( B ) miR168ab, ( C ) miR390ab, ( D ) miR396a ( E ) miR398bc ( F ) miR173, ( G ) miR824, and ( H ) average base-to-loop miRNA; ( I ) miR156a-f, ( J ) miR157ab, ( K ) miR157c, ( L ) miR160a-c, ( M ) miR408, ( N ) miR400, ( O ) miR825, ( P ) average loop-to-base miRNA. The miRNA sequence is indicated below each graph. The bar shows the frequency of the small RNAs ending at that position. For the average miRNA ( H and P ) the bases are depicted as squares.

    Journal: Nucleic Acids Research

    Article Title: Efficiency and precision of microRNA biogenesis modes in plants

    doi: 10.1093/nar/gky853

    Figure Lengend Snippet: Small RNA sequence variation caused by variability in the position of the first cut. (A–P) miRNAs for which the biogenesis is base-to-loop are displayed on the left panels (turquoise bars) (A–H), while loop-to-base miRNAs are displayed on the right panels (blue bars) (I–P). ( A ) miR165a, ( B ) miR168ab, ( C ) miR390ab, ( D ) miR396a ( E ) miR398bc ( F ) miR173, ( G ) miR824, and ( H ) average base-to-loop miRNA; ( I ) miR156a-f, ( J ) miR157ab, ( K ) miR157c, ( L ) miR160a-c, ( M ) miR408, ( N ) miR400, ( O ) miR825, ( P ) average loop-to-base miRNA. The miRNA sequence is indicated below each graph. The bar shows the frequency of the small RNAs ending at that position. For the average miRNA ( H and P ) the bases are depicted as squares.

    Article Snippet: The small RNA library was constructed using the Illumina TruSeq sRNA kit, and sequenced on the Illumina HiSeq platform at the University of Delaware.

    Techniques: Sequencing