Contributors:Herna de Wit, Louis Lategan Du Preez, Gerrit Koorsen
GH1x (PDB: 2LSO) or NGH1x (residues 1 – 120 of human H1x; UniProtKB: Q92522(H1X_HUMAN) were docked to the nucleosome structure (PDB: 4QLC) as described (De Wit, H., Koorsen, G. Docking data of selected human linker histone variants to the nucleosome. Data in Brief (2020) 30: 105580 https://doi.org/10.1016/j.dib.2020.105580) and superimposed on complete nucleosome structures (L.L. Du Preez, The structure and position of the histone terminal domains as a function of linker histone variants and post-translational modifications - A molecular dynamics study, Unpublished doctoral dissertation (2019) University of the Free State, South Africa.).
MD simulations were performed at the University of the Free State (UFS) High-Performance Computing (HPC) Cluster using GROMACS v 4.6.7. The AMBER03 all-atom force field and TIP3P water model were used. Periodic boundary conditions were applied, and long-range electrostatics were treated with the PME method (grid spacing: 0.16 nm and 0.8 nm cut-off).
The data provided gives the trajectory files of GH1x- and NGH1x-chromatosomes the in TPR, GRO and XTC formats.
Starting structures are provided in PDB format: GH1x-chromatosome_frame1.pdb and NGH1x-chromatosome_frame1.pdb.
Quality control of each trajectory was conducted after the 600 ns simulation run was complete (Quality_control_analyses.pdf).
Contributors:Christian Morabito, Riccardo Aiese Cigliano, Eric Marechal, Fabrice Rébeillé, Alberto Amato
- FASTA File containing the genomic sequence of Aurantiochytrium limacinum strain CCAP_4062/1
- Annotation File, GTF Format, containing the structure and the coordinates of the annotated genes
- Annotation File, TXT Format, containing the function annotation of the predced genes
Different strains of Saccharomyces cerevisiae were treated with Credit41, then isolated and sequenced. Whole genome sequencing of GSY147(S288c backgroud), YJM789, AWRI1631 and RM11, grown in YPD, YM or YM supplemented with WYF, treated or not with Cr41, using Illumina Miseq. The cells were grown for 6 passages, then screened for resistance. A single colony of resistant cells was used for genomic DNA extraction using phenol-chloroform method (Hirt, 1967). The library was built using Quanta-bio sparq DNA frag and library kit and sequenced on an Illumina Miseq platform. Basecalls performed with Illumina’s FASTQ Generation (v1.0.0) available in BaseSpace. The data for all strains was then aligned to S288c reference (release R64-2-1) by creating an index using GATK-126.96.36.199. The GATK HaplotypeCaller was used to generate the vcf files.
Contributors:Philippa Shellard, Thunyaporn Srisubin, Mirja Hartmann, Joe Butcher, Fan Fei, Henry Cox, Tom McNamara, Trevor McArdle, Ashley Shepherd, Robert Jacobs, Thomas Waigh, Sabine Flitsch, Christopher Blanford
Raw data files, figure components and Origin file containing data and figures
Contributors:Johannes Adrian Hildebrand, Oliver Weigert
Tumor cells orchestrate their microenvironment. Here, we provide biochemical,
structural, functional and clinical evidence that Cathepsin S ( CTSS ) alterations
induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We
found CTSS mutations at Y132 in 6% of FL (19/305). Another 13% (37/286) had
CTSS amplification, which was associated with higher CTSS expression. CTSS
Y132 mutations lead to accelerated autocatalytic conversion from pro-CTSS to active
CTSS and increase substrate cleavage, including CD74 which regulates MHC-IIrestricted
antigen presentation. Lymphoma cells with hyperactive CTSS more
efficiently activated antigen-specific CD4+ T-cells in vitro. Tumors with hyperactive
CTSS showed increased CD4+ T-cell infiltration and proinflammatory cytokine
perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune
microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive
FL had better treatment outcomes with standard immunochemotherapies, indicating
that these immunosuppressive regimens target both the lymphoma cells and the
tumor-promoting immune microenvironment.
Contributors:Caroline Isabel Kothe, Christine Delbarre-Ladrat, Pierre Renault, Delphine Passerini
Sequencing of Pseudoalteromonas sp. MIP2626 and Psychrobacter sp. BI730 genomes was performed by Illumina HiSeq platform (2×150 pb). De novo assemblies using Spades v3.9 generated 136 contigs for Pseudoalteromonas MIP2626 and 42 contigs for Psychrobacter BI730, representing a genome size of 3.9 Mb and 3.2 Mb, respectively. Phylogenetic based on 16S rRNA gene sequence and phylogenomic analyses were reported to compare the new sequences with Pseudoalteromonas and Psychrobacter representative strains available in the public databases.