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opencc-by-4.0Feb 2022View details →

Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements

Polycomb Repressive Complex 2 (PRC2) maintains transcriptionally silent genes in a repressed state via deposition of histone H3 K27 trimethyl (me3) marks. PRC2 has also been implicated in silencing transposable elements (TEs), yet how PRC2 is targeted to TEs remains unclear. To address this question, we identified proteins that physically interact with the Paramecium Enhancer-of-zeste Ezl1 enzyme, which catalyzes H3K9me3 and H3K27me3 deposition at TEs. We show that the Paramecium PRC2 core complex comprises four subunits, each required in vivo for catalytic activity. We also identify PRC2 cofactors, including the RNA interference (RNAi) effector Ptiwi09, which are necessary to target H3K9me3 and H3K27me3 to TEs. We find that the physical interaction between PRC2 and the RNAi pathway is mediated by a RING finger protein and that small RNA recruitment of PRC2 to TEs is analogous to the small RNA recruitment of H3K9 methylation SU(VAR)3-9 enzymes.

opencc-by-4.0Jul 2024View details →

Additional data for publication: Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods.

Additional data and results are given in this repository. It contains the trimmed reads (fastp; raw reads also on SRA accession numbers SRR29851544-SRR29851549, Bioproject PRJNA1136254), full busco reports for individual transcriptomes, assembly of all six RNAseqs together (transcriptome as base for differential expression analysis) and results of salmon.

opencc-zeroDec 2022View details →

Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA: a benchmark dataset

Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA: a benchmark dataset.Ribonucleic acids (RNA) play crucial roles in living organisms as they are involved in key processes necessary for proper cell functioning. Some RNA molecules, such as bacterial ribosomes and precursor messenger RNA, are targets of small molecule drugs, while others, e.g., bacterial riboswitches or viral RNA motifs are considered as potential therapeutic targets. Thus, the continuous discovery of new functional RNA increases the demand for developing compounds targeting them and for methods for analyzing RNA—small molecule interactions. We recently developed fingeRNAt - a software for detecting non-covalent bonds formed within complexes of nucleic acids with different types of ligands. The program detects several non-covalent interactions, such as hydrogen and halogen bonds, ionic, Pi, inorganic ion- and water-mediated, lipophilic interactions, and encodes them as computational-friendly Structural Interaction Fingerprint (SIFt). Here we present the application of SIFts accompanied by machine learning methods for binding prediction of small molecules to RNA targets. We show that SIFt-based models outperform the classic, general-purpose scoring functions in virtual screening. We discuss the aid offered by Explainable Artificial Intelligence in the analysis of the binding prediction models, elucidating the decision-making process, and deciphering molecular recognition processes.

opencc-by-4.0Jun 2023View details →

RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia

Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis.  To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.

opencc-by-4.0Jul 2017View details →

Training material for small RNA-seq data analysis (Galaxy Training Network tutorial)

The data provided here are part of a Galaxy Training Network tutorial that analyzes small RNA-seq (sRNA-seq) data from a study published by Harrington et al. (DOI:10.1186/s12864-017-3692-8) to detect differential abundance of various classes of endogenous short interfering RNAs (esiRNAs). The goal of this study was to investigate "connections between differential retroTn and hp-derived esiRNA processing and cellular location, and to investigate the potential link between mRNA 3’ end cleavage and esiRNA biogenesis." To this end, sRNA-seq libraries were constructed from triplicate Drosophila tissue culture samples under conditions of either control RNAi or RNAi knockdown of a factor involved in mRNA 3’ end processing, Symplekin. This dataset (GEO Accession: GSE82128) consists of single-end, size-selected, non-rRNA-depleted sRNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to a subset of interesting transcript features including: (1) transposable elements, (2) Drosophila piRNA clusters, (3) Symplekin, and (4) genes encoding mass spectrometry-defined protein binding partners of Symplekin from Additional File 2 in the indicated paper by Harrington et al. More details on features 1 and 2 can be found here: https://github.com/bowhan/piPipes/blob/master/common/dm3/genomic_features (piRNA_Cluster, Trn). All features are from the Drosophila genome Apr. 2006 (BDGP R5/dm3) release.

opencc-by-4.0Feb 2010View details →

Fig. 1 in Phylogenetic position of the freshwater fish trypanosome, Trypanosoma ophiocephali (Kinetoplastida) inferred from the complete small subunit ribosomal RNA gene sequence

Fig. 1 The neighbor-joining tree of aquatic trypanosomes constructed from complete small subunit ribosomal RNA (SSrRNA) sequences indicating the systematic position of T. ophiocephali and phylogenetic relationships among the aquatic trypanosomes whose sequences are available. T. lewisi, T. theileri, and T. avium are taken as the outgroup. Bootstrap values are shown for the maximum parsimony/neighborjoining/Bayes analyses

opencc-by-4.0Mar 2018View details →

Arabidopsis RNA-seq seedling small training set (chr1 100k)

Arabidopsis seedling small training set for RNA-seq. FastQ files for reads mapping to the first 100k of the first chromosome of Arabidopsis are included. The sequencing was done using Illumina, 100 paired-end mode.

Fig. 2 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 2. Phylogenetic tree of the centipedes based on the combined analysis of Edgecombe et al. (1999). The arrow indicates where the insertion of ca. 300 bp at region V7 occurred during the evolution of centipedes.

Fig. 5 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 5. Phylogenetic analysis of the data from fig. 4 using the ''fixed character states'' method of Wheeler (1999) implemented in the computer program POY (Gladstein and Wheeler, 1997). Commands: poy fixedstates noleading norandomizeoutgroup gap 1 maxtrees 20 multibuild 10 seed‾1 slop 2 checkslop 5. The two circles illustrate the insertions of the Geophilomorpha (ca. 300 bp), and the Scolopendridae (ca. 25 bp).

Fig. 1 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 1. Schematic representation of the 18S rRNA locus. The gray squares represent the variable regions V2, V4, V7, and V9 with insertions (V2: Onychophora, Geophilomorpha, Cephalopoda, Archaeogastropoda; V4: Hexapoda, Crustacea, Pauropoda, Holothuroidea, Chaetognatha, Platyhelminthes, Cephalopoda; V7: Onychophora, Hexapoda, Crustacea, Pauropoda, Chilopoda, Platyhelminthes, Hirudinea, Cephalopoda, Gastropoda; V9: Onychophora, Crustacea, Cephalopoda). The black arrowheads represent particular insertions (10: Pauropoda; 11: Onychophora; E23–7: Onychophora and Pauropoda; E23–8: Pauropoda; 29: Pauropoda; 46: Protura). The black bar represents the 500 bp deletion of the Symphyla.

Fig. 3 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 3. Phylogenetic tree based on 18S rRNA sequence data indicating the position of two symphylans (box) with respect to other myriapods (underlined taxa) in a phylogenetic analysis of arthropods (from Giribet, 1997). The two symphylans appear related to other myriapods.

opencc-by-4.0Dec 2020View details →

RNA modification 5-methylcytosine (m5C) is associated with small RNA biogenesis in Arabidopsis thaliana

Small RNAs (sRNAs) are essential in regulating the development in plants and animals. While the biogenesis pathways of many sRNAs is clear, the biogenesis pathway for novel small RNAs like tRNA- and rRNA-derived fragments (tRFs and rRFs) is less so. Many diverse cellular RNAs including mRNAs, long-non-coding RNAs, tRNAs and rRNAs in plants have covalent post-transcriptional modifications and their function is only starting to be elucidated. Here, we determine if the RNA modification 5-methylcytosine (m5C) plays a role in sRNA biogenesis in Arabidopsis thaliana. To this effect, we Illumina-sequenced sRNAs from wild type and m5C methyltransferase mutant tRNA methyltransferase 4b (trm4b). Our bioinformatics analysis identified 158 sRNAs loci that increased in abundance and two sRNA loci that decreased in abundance in the trm4b compared to the wild type control. Comparison with RNA bisulphite sequencing data confirmed that most of the top differentially abundant sRNAs have m5C sites. In summary, our results suggest that m5C RNA modifications is associated with sRNA biogenesis in Arabidopsis thaliana.

opencc-by-4.0Aug 2023View details →

Single-molecule Fluorescent In Situ Hybridization (smFISH) for RNA detection in the fungal pathogen Candida albicans small example dataset

This small example dataset is connected to the protocol article titled: Single-molecule Fluorescent In Situ Hybridization (smFISH) for RNA detection in the fungal pathogen Candida albicans Abstract: Candida albicans is the most prevalent human fungal pathogen. Its pathogenicity is linked to the ability of C. albicans to reversibly change morphology and to grow as yeast, pseudohyphal or hyphal cells in response to environmental stimuli. Understanding the molecular regulation controlling those morphological switches remains a challenge that, if solved, could help fight C. albicans infections. While numerous studies investigated gene expression changes occurring during C. albicans morphological switches using bulk approaches (e.g., RNA sequencing), here we describe a single-cell and single-molecule RNA imaging and analysis protocol to measure absolute mRNA counts in morphologically intact cells. To detect endogenous mRNAs in single fixed cells, we optimized a single molecule fluorescent in situ hybridization (smFISH) protocol for C. albicans, which allows one to quantify the differential expression of mRNAs in yeast, pseudohyphae or hyphal cells. We quantified the expression of two mRNAs, cell cycle-controlled mRNA (CLB2) and a transcription regulator (EFG1), which show differential expression in the different morphological cell types and in different nutrient conditions. In this protocol, we described in detail the major steps of this approach: growth and fixation, hybridization, imaging, cell-segmentation and mRNA spot analysis. Raw data is provided with the protocol to favour reproducibility. This approach could benefit the molecular characterization of C. albicans and other filamentous fungi, pathogenic or non-pathogenic. Data description: This dataset consists of a FISH experiment spanning two different mRNAs, EFG1 and CLB2, and one nutrient condition, SPIDER37, in Candida albicans. For culturing, the C. albicans wildtype strain SC5314 was inoculated at 30 degrees overnight (~15 hours) in 10 mL of TSB medium in a 30 °C shaking incubator. Next, samples were diluted to a density of 10^5 cells/ mL and inoculated for 6 hours in 30 mL Spider medium at 37 °C in falcon tubes on an orbital microplate shaker. Then, samples were fixated by adding PFA to a final concentration of 4% to the medium. For hybridization, both mRNAs were hybridized independently by specific DNA oligo labelled with a Quasar670 dye to enable the visualisation of single mRNA molecules. As both genes are labelled by the same dye, these oligos were not co-applied to the same sample but to independent samples. Microscopy For smFISH imaging we use an Olympus BX-63 epifluorescence microscope equipped with Ultrasonic stage and UPlanApo 100x 1.35NA oil-immersion objective (Olympus). Lumencore SOLA FISH light source, a Hamamatsu ORCA-Fusion sCMOS camera (6.5 µm-pixel size) mounted using U-CMT C-Mount Adapter, and zero-pixel shift filter sets: F36-500 DAPI HC Brightline Bandpass Filter, F36-502 FITC HC BrightLine Filter, F36-542 Cy3 HC BrightLine Filter, and F36-523 Cy5 HC BrightLine Filter. Images are acquired across 61-81 optical sections (depending on the sample thickness) with a z-step size of 0.2 μm. The CellSens software (Olympus) is used for instrument control and image acquisition. For the DAPI  channel 10-50 ms of exposure was used. Whilst, for the CY5 channel, used for imaging the FISH probes, 750 ms was applied.

dryad40/100

Data from: Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase

Open the record for dataset details and reuse information.

publicOct 2025View details →

opencc-by-4.0Dec 2023View details →

Transcription start sites from capped small RNA-seq of rat nucleus accubmens and prefrontal cortex

Small RNAs of &sim;15–60 nt were size selected by denaturing gel electrophoresis starting from total RNA extracted from 14 rat brain tissue dissections. For csRNA libraries, cap selection was followed by decapping, adapter ligation, and sequencing. For input libraries, 10% of small RNA input was used for decapping, adapter ligation, and sequencing. After library quality check by gel electrophoresis, the samples were sequenced using the Illumina NextSeq 500 platform using 75 cycles single end. Sequencing reads were aligned to the rat mRatBN7.2 genome assembly using STAR v2.5.3a aligner with default parameters. Transcriptional start regions were defined using HOMER’s findPeaks tool.  Duttke, S.H., Montilla-Perez, P., Chang, M.W., Li, H., Chen, H., Carrette, L.L.G., de Guglielmo, G., George, O., Palmer, A.A., Benner, C., et al. (2022). Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction. Front. Neurosci. 16, 858427.

opencc-by-4.0Apr 2019View details →

Training material for analysis small RNA-seq data (Galaxy Training Network tutorial)

The data provided here is part of the Galaxy Training Network tutorial for analysis of small RNA-seq (sRNA-seq) data using mirdeep2 and miranda. This dataset is provided by INRA (Le Rheu, France).

Fig. 4 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

Fig. 4. Variable region (V7) of the 18S rRNA locus of 17 species of centipedes.

opencc-by-4.0Dec 2021View details →

Non-cell autonomous small RNA silencing in Arabidopsis female gametes

Raw data tables as well as R script