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21,320 results for “Transcription”
Fig 4 in Docosahexaenoic Acid (DHA) Reduces LPS-Induced Inflammatory Response Via ATF3 Transcription Factor and Stimulates Src/Syk Signaling-Dependent Phagocytosis in Microglia
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Single cell deletion of the transcription factors Trps1 and Sox9 reveals novel functions in adult cortical astrocytes
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Data from: Phenotypic plasticity through transcriptional regulation of the evolutionary hotspot gene tan in Drosophila melanogaster
Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. Phenotypic plasticity can be adaptive. Furthermore, it is thought to facilitate evolution. Although phenotypic plasticity is a widespread phenomenon, its molecular mechanisms are only beginning to be unravelled. Environmental conditions can affect gene expression through modification of chromatin structure, mainly via histone modifications, nucleosome remodelling or DNA methylation, suggesting that phenotypic plasticity might partly be due to chromatin plasticity. As a model of phenotypic plasticity, we study abdominal pigmentation of Drosophila melanogaster females, which is temperature sensitive. Abdominal pigmentation is indeed darker in females grown at 18°C than at 29°C. This phenomenon is thought to be adaptive as the dark pigmentation produced at lower temperature increases body temperature. We show here that temperature modulates the expression of tan (t), a pigmentation gene involved in melanin production. t is expressed 7 times more at 18°C than at 29°C in female abdominal epidermis. Genetic experiments show that modulation of t expression by temperature is essential for female abdominal pigmentation plasticity. Temperature modulates the activity of an enhancer of t without modifying compaction of its chromatin or level of the active histone mark H3K27ac. By contrast, the active mark H3K4me3 on the t promoter is strongly modulated by temperature. The H3K4 methyl-transferase involved in this process is likely Trithorax, as we show that it regulates t expression and the H3K4me3 level on the t promoter and also participates in female pigmentation and its plasticity. Interestingly, t was previously shown to be involved in inter-individual variation of female abdominal pigmentation in Drosophila melanogaster, and in abdominal pigmentation divergence between Drosophila species. Sensitivity of t expression to environmental conditions might therefore give more substrate for selection, explaining why this gene has frequently been involved in evolution of pigmentation.
Data from: Increased evolutionary rates and conserved transcriptional response following allopolyploidisation in brown algae
Genome mergers between independently evolving lineages, via allopolyploidy, can potentially lead to instantaneous sympatric speciation. However, little is known about the consequences of allopolyploidy and the resultant "genome shock" on genome evolution and expression beyond the plant and fungal branches of the Tree of Life. The aim of this study was to compare substitution rates and gene expression patterns in two allopolyploid brown algae (Phaeophyceae, Heterokonta) and their progenitors in the genus Pelvetiopsis N.L. Gardner in the north-east Pacific, and to date their relationships. We used RNA-seq data and putative single-copy loci for phylogenomic, divergence and gene expression analyses. The multispecies coalescent placed the origin of allopolyploids in the late Pleistocene (0.35 – 0.05 Ma). Homoeologues displayed increased non-synonymous divergence compared with parental orthologues, consistent with relaxed selective constraint following allopolyploidization, including for genes with no evidence of pseudogenization or neo-functionalization. Patterns of homeologue-orthologue expression conservation and expression-level dominance were shared with both natural plant and fungal allopolyploids. Interestingly, gene expression also appeared partially linked to the gender of origin of homoeologues. Our results provide further support for common cross-Kingdom patterns of allopolyploid genome evolution and transcriptional responses, here in the evolutionarily distinct marine heterokont brown algae.
Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices
<p>Readme.txt, 16.07.2021<br> Fontana et al.<br> “Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices”</p> <p>pre-print: https://doi.org/10.1101/2021.05.12.443786 (BioRxiv)</p> <p>The repository contains the raw data ("*.tif") files, data from subsequent analysis steps performed in Matlab ("*.mat") and obtained histograms.</p> <p>For further information, please contact<br> dr. Johannes Hohlbein @ Wageningen University & Research<br> (johannes.hohlbein@wur.nl)</p>
Transcriptional differentiation of UV-B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico
Globally, farmers cultivate and maintain crop landraces (i.e., traditional varieties). Landraces contain unique diversity shaped in part by natural and human-mediated selection and are an indispensable resource to farmers. Since environmental conditions change with elevation, crop landraces grown along elevational gradients have provided ideal locations to explore patterns of local adaptation. To further probe traits underlying this differentiation, transcriptome signatures can help provide a foundation for understanding the ways in which functional genetic diversity may be shaped by environment. In this study, we returned to an elevational gradient in Chiapas, Mexico, to assess transcriptional differentiation of genes underlying UV-B protection in locally adapted maize landraces from multiple elevations. We collected and planted landraces from three elevational zones (lowland, approximately 600 m; midland, approximately 1,550 m; highland approximately 2,100 m) in a common garden at 1,531 m. Using RNA-seq data derived from leaf tissue, we performed differential expression analysis between maize from these distinct elevations. Highland and lowland landraces displayed differential expression in phenylpropanoid and flavonoid biosynthesis genes involved in the production of UV-B protectants and did so at a rate greater than expected based on observed background transcriptional differentiation across the genome. These findings provide evidence for the differentiation of suites of genes involved in complex ecologically relevant pathways. Thus, while neutral evolutionary processes may have played a role in the observed patterns of differentiation, UV-B may have also acted as a selective pressure to differentiate maize landraces in the region. Studies of the distribution of functional crop genetic diversity across variable landscapes can aid us in understanding the response of diversity to abiotic/biotic change and, ultimately, may facilitate its conservation and utilization.
The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus
<p>Lateral organ boundaries domain (LBD) genes encode plant-specific transcription factors that participate in regulating various developmental processes. In this study, we genetically characterized PagLBD3 as an important regulator of secondary growth in Populus. Overexpression of PagLBD3 increased stem secondary growth in Populus with significantly higher rate of cambial cells differentiated into phloem, while dominant repression of PagLBD3 significantly decreased the rate of cambial cells differentiated into phloem. Furthermore, we identified 1756 PagLBD3 genome-wide putative direct target genes (DTGs) through RNA sequencing (RNA-seq) coupled DNA affinity purification followed by sequencing (DAP-seq) assays. Gene Ontology analysis revealed that genes regulated by PagLBD3 were enriched in biological pathways regulating meristem development, xylem development, and auxin transport. Several central regulator genes for vascular development, including phloem intercalated with xylem (PXY), wuschel related homeobox4 (WOX4), Secondary Wall-Associated NAC Domain 1s (SND1-B2) and Vascular-Related NAC-Domain 6s (VND6-B1), were identified as PagLBD3 DTGs. Together, our results suggested that PagLBD3 and its DTGs form a complex transcriptional network to modulate cambium activity and phloem/xylem differentiation.</p>
Figure 3 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 3. Localization of Lepeophtheirus salmonis Vasa (LsVasa) transcripts. (A) Light microscopy of sexually mature adult female with eggstrings attached. Most of the eggstrings extending from the genital segment have been cropped from the image. The position of various tissues is indicated: ∗ (ovaries), × (oocytes in the genital segment). Subcuticular tissue is found under the cuticula of most of the lice. The area used for in situ hybridization is indicated (+). Scale bar represents 5 mm. (B–F) In situ hybridization using an LsVasa-specific antisense RNA probe showing positive staining as dark colour. Small inserts illustrate corresponding locations in negative controls (using a LsVasa-sense RNA probe). (B) The two ovaries (Ov) of mature adult females. LsVasa transcripts are localized throughout the ovary including both proximal and the more distal zones. Scale bar represents 200 µm. (C) LsVasa is present in immature oocytes in the oviduct (ovd, scale bar 50 µm) as well as in mature oocytes in the unfertilized eggstring (D, scale bar 200 µm). LsVasa is also present in the gonads of earlier developmental stages (E, ovaries of preadult females, scale bar 200 µm) and in adult male testes (F, scale bar 100 µm).
Figure 2 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 2. Ontogenic analysis of Lepeophtheirus salmonis Vasa (LsVasa) transcript levels. LsVasa transcripts levels were determined by the use of quantitative reverse transcription-polymerase chain reaction at different developmental stages. Levels were quantified relative to the level found in the nauplius stage. Error bars show 95% confidence intervals calculated from the ΔΔCT values from each dilution.
Figure 1 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 1. Domain structure and copy number of Lepeophtheirus salmonis Vasa (LsVasa). (A) LsVasa with position of conserved protein domains. Position of DEAD box helicase core motifs (reviewed by Hilbert et al. 2009) are indicated with Roman numerals: (I) Motif I, (II) Motif Ia, (III) GG doublet, (IV) Motif Ib, (V) Motif II, (VI) Motif III, (VII) Motif IV, (VIII) QxxR, (IX) Motif V and (X) Motif VI. Triangles indicate the position of the three introns. (B) Southern blot using LsVasa as a probe. Genomic DNA was digested with XhoI (lane 1), PstI (lane 2), ClaI (lane 3), KpnI (lane 4), SacI (lane 5) and XbaI (lane 6) and electrophoresed together with a DNA marker (M).
Analysis of antibody signal loss for elongating RNA polymerase II upon transcription inhibition
<p>This data set assesses the loss of antibody signal for elongating RNA polymerase II in zebrafish embryos upon transcription inhibition with flavopiridol. Polymerase was labeled by immunofluorescence, microscopy images were acquired by instant-SIM micrscopy, and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.</p>
Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures--Gene Validation FCS
<p>FCS files corresponding to the gene validation experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"</p> <p>Funding provided in part by the Aligning Science Across Parkinson’s ASAP-000375</p>
Data_Tab1_Deletion of the transcription factor Prox-1 specifically in the renal distal convoluted tubule causes hypomagnesemia via reduced expression of TRPM6 and NCC
<p>Data of Tab1 from “Deletion of the transcription factor Prox-1 specifically in the renal distal convoluted tubule causes hypomagnesemia via reduced expression of TRPM6 and NCC”</p> <p>Dataset (doi: 10.1007/s00424-020-02491-1) contains the original publication as PDF-format (10.1007_s00424-020-02491-1.pdf). Corresponding raw data obtained from LC-MS/MS analysis provided as one file in CSV format (31003A-179400_10.1007_s00424-020-02491-1_DW_4-1.csv). All further experiment related information provided as two meta-data-files (31003A-179400_10.1007_s00424-020-02491-1_DW _4-1_M_1.PDF, 31003A-179400_10.1007_s00424-020-02491-1_DW _4-1_M_2.pdf) as PDF format.</p>
Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens
Millions of putative transcriptional regulatory elements (TREs) have been cataloged in the human genome, yet their functional relevance in specific pathophysiological settings remains to be determined. This is critical to understand how oncogenic transcription factors (TFs) engage specific TREs to impose transcriptional programs underlying malignant phenotypes. Here, we combine cutting edge CRISPR screens and epigenomic profiling to functionally survey ≈15,000 TREs engaged by estrogen receptor (ER). We show that ER exerts its oncogenic role in breast cancer by engaging TREs enriched in GATA3, TFAP2C, and H3K27Ac signal. These TREs control critical downstream TFs, among which TFAP2C plays an essential role in ER-driven cell proliferation. Together, our work reveals novel insights into a critical oncogenic transcription program and provides a framework to map regulatory networks, enabling to dissect the function of the noncoding genome of cancer cells.
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>
Genes with transcripts predicted to be miR-195 or miR-26b targets by all 5 predictive algorithms included in starBase, or experimentally identified as targets by pulldown assay
<p>Genes with transcripts predicted to be miR-195 or miR-26b targets by all 5 predictive algorithms included in starBase, or experimentally identified as targets by pulldown assay</p>
Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer
<p>A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit fly embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity capture the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.</p>
cellsig: a Bayesian sparse random-effect model and large-scale human bulk transcriptional catalogue support cell-type marker selection
<p><strong>Human Bulk Cell-type Catalogue (HBCC): This database harmonises 1,435 samples of 67 cell types from 58 datasets which can be utilised in the cellsig method for estimating cell-type transcriptional profiles.</strong></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>
Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript
<p>## Overview</p> <p>This repository contains the data and R-scripts to reproduce the figures in the main text of the manuscript "Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript", which can be found here: (https://doi.org/10.1093/nar/gkad040).</p> <p> </p> <p>## Additional information</p> <p>The data can also be found on github via https://github.com/JeschekLab/uASPIre_UTR_CDS. The github repository also includes updates, scripts for NGS data analysis and additional code for data processing.</p> <p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.