ABSTRACT: Gene expression during in different LSD1 (KO, recovery, catalitically-inert) stem cell models in mice, in order to determine its molecular function
Project description:The aim of this study was to investigate transcriptional changes underlying the zinc (Zn) deficiency response in root and shoot tissues of bread wheat. Triticum aestivum cv. Paragon seedlings were hydroponically grown and subjected to Zn starvation (0 μM ZnCl₂) starting at 14 days after germination. Samples were collected at 1, 3, 5, and 7 days following Zn withdrawal. RNA-seq was performed on whole root and shoot tissues, with three biological replicates per treatment and time point. Control plants supplied with 8 μM ZnCl₂ were included to distinguish Zn deficiency transcriptional responses.
Project description:Lysine-specific demethylase 1 (LSD1) is a histone demethylase that promotes stemness and cancer cell survival, including in prostate cancer. Most prostate malignancies are adenocarcinomas with luminal differentiation. However, a subset of tumors undergoes cellular reprogramming to a more lethal neuroendocrine prostate cancer (NEPC) with neuronal differentiation. The frequency of NEPC is increasing since widespread use of potent androgen receptor signaling inhibitors. Currently, there are no effective treatments for NEPC. We previously determined that LSD1 promotes survival of prostate adenocarcinoma tumors. However, role of LSD1 in NEPC is largely unknown. We sought to identify key genes and molecular pathways controlled by LSD1 in NEPC. We therefore inhibited LSD1 with SP2509 and performed RNA-seq in LASCPC-01, LNCaP-N-Myc, and MR42D cell lines. The vast majority of differentially expressed genes after SP2509 treatment were upregulated, suggesting that LSD1 may primarily function as a transcriptional repressor in NEPC. RNA-seq analysis reveals that LSD1 represses pathways linked to luminal differentiation and TP53 is the top pathway reactivated after LSD1 suppression. Taken together, these data suggest that LSD1 may be an important regulator of TP53 function in prostate cancer.
Project description:We aim to investigate the role of METTL3 and METTL14, the catalytic enzyme responsible for m⁶A methylation, in high-grade serous ovarian carcinoma (HGSOC) cells like OVCAR8 human cell line. In addition, we aimed to identify m⁶A-modified transcripts using MeRIP-seq in the same cell line.
Project description:We report the identification of LSD1 binding genomic regions in mouse embryonic stem cells (ESC) by high throughput sequencing. By obtaining over 10 million 36 bp reads of sequence from each chromatin immunoprecipitated DNA, we generated genome-wide maps for LSD1 and histone H3 dimethylated on lysine 4 (H3K4me2), the substrate for LSD1 in mouse ESCs. Our results showed an extensive overlap between the LSD1 and H3K4me2 genomic regions and a correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ESC genes. LSD1 is recruited to the chromatin of cells in the G1/S/G2 phases and is displaced from the chromatin of M phase cells, suggesting that LSD1 or H3K4me2 alternatively occupies LSD1 genomic regions during cell cycle progression. LSD1 knockdown by RNA interference or its displacement from the chromatin by anti-neoplastic agents caused an increase in the levels of a subset of LSD1 target genes. Taken together, these results suggest that cell-cycle dependent association and dissociation of LSD1 with chromatin mediates short-time scale gene expression changes during ES cell cycle progression. Examination of LSD1 and lysine 4 dimethylated histone H3 (H3K4me2) binding genomic regions in embryonic stem cells. Input genomic DNA and DNA immunoprecipitaed with control IgG was included as controls.
Project description:This experiment seeks to elucidate the functional role of MYB73 in Arabidopsis thaliana siliques via differential gene expression (DGE) analysis. Total RNA were extracted from pooled Arabidopsis siliques at 12 days after flowering (DAF) for 3 biological replicates from WT and MYB73-OE lines. RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) for Illumina according to the manufacturer’s instruction and sequenced with Novaseq-6000 (Illumina) using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.
Project description:This experiment seeks to elucidate the functional role of the ZFP2 transcription factor in Arabidopsis thaliana siliques via differential gene expression analysis. Total RNA extracted from pooled Arabidopsis siliques 12 days after flowering (DAF) was used for the assay, with 3 biological replicates each for WT and zfp2-2. For each sample, RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and sequenced with Illumina Novaseq-6000 using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.
Project description:This experiment seeks to elucidate the functional role of DREB2G in Arabidopsis thaliana seeds via differential gene expression (DGE) analysis. Total RNA were extracted from pooled Arabidopsis thaliana seeds at 10-2 days after flowering (DAF) for 3 biological replicates from WT and 2 independent DREB2G OE lines. RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) for Illumina according to the manufacturer’s instruction and sequenced with Novaseq-6000 (Illumina) using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.
Project description:RNA-sequencing from RWPE-Ctrl (empty vector control), RWPE-1-AR (transduced with androgen receptor cDNA), LNCaP-pcDNA3.1 (empty vector control), and LNCaP-ARhi (transfected with androgen receptor cDNA) cells treated with 0, 1, 10, or 100 nM DHT for 4 hours before RNA extraction. Biological triplicate samples from each cell line in all conditions were collected. Aim of the experiment was to study androgen regulated gene expression in nonmalignant and cancer cells.
Project description:Lsd1 ablation triggers metabolic reprogramming of brown adipose tissue. Lsd1 protein complexes were purified from mouse adipose tissue and analyzed by label-free LC-MS/MS. Mice were kept under different conditions prior complex isolation.