Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked. Recently CTCF anchored loops have been described as major features of chromatin organisation. However, the dynamics and role for these structures in differentiation is unknown. We used Tethered Chromatin Conformation Capture (TCC) to assess for the dynamics of CTCF-anchor loop formation upon differentiation of mouse embryonic stem cells (ESC) and neural stem cells (NSC).
Project description:Wheat is one of the most significant crops in terms of human consumption in the world. In a climate change scenario, extreme weather event such as heatwaves will be more frequent especially during the grain-filling (GF) stage and could affect grain weight and quality of crops. Molecular mechanisms underlying the response to short heat stress (HS) have been widely reported for the hexaploid wheat (Triticum aestivum) but the regulatory heat stress mechanisms in tetraploid durum wheat (Triticum turgidum ssp. durum) remain partially understood. In this work, we performed a transcriptomic analysis of durum wheat grains to HS during early GF to identify key HS response genes and their predicted regulatory networks under glasshouse conditions.
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.
Project description:To determine 3D chromosomal structure in differentating ectoderm of the frog Xenopus laevis, we performed tethered conformation capture (TCC) (PMID: 22198700) on wild-type dissected ectoderm and ectoderm injected with multicilin. We used these data to investigate possible differences between these conditions (we found very few) and also to determine the positions of topologically-associated domains (TADs). These data were also used to facilitate chromosome-level assembly of the X. laevis genome.
Project description:To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer T47D cells and Tamoxifen resistant breast cancer T47D cells.
Project description:To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer MCF7 cells and Tamoxifen resistant breast cancer MCF7 cells.
Project description:Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of durum variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. Overall, we provide a valuable resource for studying endosperm development in this increasingly important crop species.
Project description:Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. turgidum developing grains, under single and combined water-deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNA (DEMs) specific to genotypes, stress types and different reproductive time-points are provided. The first degradome-seq report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome-seq profiled 53,146 T. turgidum genes, with differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development and hormone transduction pathways. miRNA-mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed, based on integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.
