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1,054 results for “Transcriptional control”
Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants
<p>In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically-interacting proteins, HYL1 and DCL1. However, the evolutionary history and structural basis of the HYL1-DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 <em>in vitro</em> and in <em>Arabidopsis thaliana </em>to better understand the origin and evolution of the HYL1-DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (~500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two double-stranded RNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1-DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in <em>A. thaliana</em> was sufficient to rescue many key aspects of plant development disrupted by HYL1<sup>-</sup> knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1-DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant ‘developmental toolkit’.</p>
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
<p>In this repository, we present the PacBio and ONT simulated datasets used for benchmarking transcriptome reconstruction tools, as evaluated in the manuscript titled "<i>SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark</i>". The dataset includes simulated long reads, short reads, CAGE peaks, and a reduced reference annotation. Additionally, we have included reconstructed transcriptomes from each method, along with SQANTI3 output files. The SQANTI-SIM software can be accessed on GitHub at the following URL: <a href="https://github.com/ConesaLab/SQANTI-SIM">https://github.com/ConesaLab/SQANTI-SIM</a>.</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Generation of transcriptional novelty by transposable element insertions in Arabidopsis, RNAseq Control Condition Sequencing Data
<p><strong>Arabidopsis stranded 150 bp paired end RNA sequencing data (Illumina) of plants that were grown under control conditions for the manuscript "Generation of transcriptional novelty by transposable element insertions in Arabidopsis"</strong></p> <p><strong><strong>Plant growth conditions</strong></strong></p> <p>Sequenced F4 seeds were sterilized for 10 minutes in 10% bleach, rinsed, and stratified at 4°C for four days in the dark before being sown on 0.5x Murashige & Skoog media (Du<em>schefa cat# M0222</em>) and transferred to growth chambers under long day conditions (16h of light at 24°C followed by 8h of darkness at 21°C; 20 seeds per plate, 6 replicate plates). Ten days after sowing, plants were subjected to 6°C for 24 hours and control plants were returned to normal long day growing conditions for 24 hours before harvesting (3 replicate plates per condition).</p> <p><strong><strong>RNA extraction and sequencing</strong></strong></p> <p>Seedlings were harvested and RNA extractions were done on pools of 5 plants. RNA extractions were performed for 3 biological replicate samples for each line in each condition (n=96) using the Macherey-Nagel NucleoSpin RNA kit (cat# 740955.50). Samples were sent to Novogene for Illumina 150bp paired-end sequencing using a stranded poly-A library.</p> <p><strong>RNAseq sample descriptions of the plants grown under control conditions</strong></p> <p>wt_control: wild-type plants.</p> <p>wtHS_control: wild-type plants that have been submitted to heat stress in a previous generation.</p> <p>wtAZ_control: wild-type plants that have been submitted to epigenetic drug treatments (alpha-amanitin and zebularine) in a previous generation.</p> <p>htLine#: plants carrying additional <em>ONSEN</em> transposable element insertions.</p> <p>Files description: Forward and reverse strand RNA seq data are combined in one file. The numbering at the end ("_1") denominates the biological replicate number.</p>
A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2 IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Transcriptional changes in macaques exposed to Sudan virus and treated with a vehicle controls or obeldesivir for 5 or 10 days
<p><span>Normalized Nanostring transcriptomic data (fold2-change- and Benjamini–Hochberg adjusted p-values) were exported as an .xlsx file. Groups include vehicle control (N=3), treated fatal (N=2), and treated survivor subjects administered ODV for 5 (N=3) or 10 days (N=5) compared against a pre-challenge baseline (0 DPI) at each collection timepoint. Any differentially expressed transcripts with a Benjamini-Hochberg false discovery rate (FDR) corrected p-value less than 0.05 were deemed significant. ODV, obeldesivir; DPI, days post infection.</span></p>
Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution
<p>Supplementary Tables for article "Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution"<br> </p>
Data from: Short activation domains control chromatin association of transcription factors
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A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
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Transcriptional changes in macaques exposed to Sudan virus and treated with a vehicle controls or obeldesivir for 5 or 10 days
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Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures
<p>Supplementary data for "Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures" by Toray S. Akcan, Matthias Heinig.</p>
Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription
<p>Dataset required for running leukemia associated structural variants scoring described in Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription manuscript.</p>
Dataset from: Functional divergence of mammalian TFAP2a and TFAP2b transcription factors for bidirectional sleep control
<p><span>Sleep is a conserved behavioral state that is found in all animals that have a nervous system. Invertebrates typically show quiet sleep, whereas in mammals, sleep is more complex, and consists of periods of non-rapid-eye-movement sleep (NREMS) and REM sleep (REMS). We previously found that the transcription factor AP-2 is required for sleep<i> </i>in<i> C. elegans </i>and <i>Drosophila</i> and that the <i>C. elegans </i>AP-2 gene <i>aptf-1</i> is required for sleep-active neurons to induce sleep. In mammals, several paralogous AP-2 transcription factors exist. Sleep-controlling genes are often conserved. However, little is known about how sleep genes evolved from controlling simpler types of sleep to govern complex mammalian sleep. Here, we studied the roles of <i>Tfap2a</i> and <i>Tfap2b</i> in sleep control in mice. Consistent with our results from <i>C. elegans</i> and <i>Drosophila</i>, the AP-2 transcription factors <i>Tfap2a</i> and <i>Tfap2b</i> also control sleep in mice. Surprisingly, however, the two AP-2 paralogs play contrary roles in sleep control. <i>Tfap2a</i> reduction of function causes stronger delta and theta power in both baseline and homeostasis analysis, thus indicating increased sleep quality, but did not affect sleep quantity. By contrast, <i>Tfap2b</i> reduction of function decreased NREM sleep time specifically during the dark phase, reduced NREMS and REMS power, and caused a weaker response to sleep deprivation. Consistent with the observed signatures of decreased sleep quality, stress resistance and memory were impaired in <i>Tfap2b</i> mutant animals. Also, the circadian period was slightly shortened. Taken together, AP-2 transcription factors control sleep behavior also in mice, but the role of the <i>AP-2</i> genes functionally diversified to allow for a bidirectional control of sleep quality. Divergence of AP-2 transcription factors might perhaps have supported the evolution of more complex types of sleep.</span></p>
Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of ANAC055 (encoding a transcription factor) increased in wild-type Arabidopsis under drought stress. Further analyses showed that CAU1 bound to the promoter of ANAC055 and suppressed its expression via H4R3sme2-type histone methylation in the promoter region. Thus, under drought stress, a decreased level of CAU1 led to an increased transcript level of ANAC055, which induced the expression of P5CS1 and increased proline level independently of CAS. Drought tolerance and the level of proline were found to be decreased in the cau1 anac055 double-mutant, while proline supplementation restored drought sensitivity in the anac055 mutant. Our results reveal the details of a novel pathway leading to drought tolerance mediated by CAU1.
The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon hdrBCA in Methanosarcina barkeri
<p><span>RNA-seq raw data and processed data are accessible at Zenodo.</span></p>
Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055
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Data from: The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development
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