December 15, 2023
Database Expansion: 15 New Plant Species
TSSHub is pleased to announce a significant expansion of our plant species database. We have added TSS data for 15 important crops and model plants, including rice, wheat, and maize, providing valuable resources for plant molecular biology research.
Key Additions
- Major Crops: Rice (Oryza sativa), Wheat (Triticum aestivum), Maize (Zea mays), Soybean (Glycine max)
- Model Plants: Arabidopsis thaliana, Brachypodium distachyon
- Evolutionarily Significant Species: Marchantia polymorpha, Klebsormidium nitens
- Economic Crops: Cotton (Gossypium spp.), Grape (Vitis vinifera)
The new data is based on CAGE-seq, PRO-seq, and other TSS profiling technologies, covering various tissues, developmental stages, and environmental conditions. For each species, we provide:
- Precise TSS positions at single-nucleotide resolution
- Quantitative information on TSS usage across conditions
- Tissue/condition-specific TSS usage patterns
- Promoter sequence analysis
This expansion is part of our ongoing effort to create a comprehensive resource for studying gene expression regulation across the plant kingdom. The new data will enable comparative studies of transcriptional regulation between diverse plant species, providing insights into the evolution of gene regulation in plants and facilitating crop improvement efforts.
We thank our collaborators at various plant genomics institutes worldwide for contributing to this effort. The data is now available through our web interface and API.
November 28, 2023
New Feature: Comparative Genomics Analysis Tool
TSSHub is excited to announce the launch of our new Comparative Genomics Analysis module. This powerful tool enables researchers to perform cross-species comparisons of TSS usage patterns, helping to reveal evolutionary characteristics of gene expression regulation.
Key Features
- Multi-species TSS Alignment: Visualize and compare TSS positions across orthologous genes in multiple species
- Conservation Analysis: Quantify the degree of TSS conservation between species pairs or across evolutionary lineages
- Divergence Patterns: Identify species-specific or lineage-specific TSS usage patterns
- Regulatory Element Evolution: Track changes in promoter architecture and regulatory motifs
The new module integrates with our existing database and visualization tools, allowing seamless navigation between species-specific views and comparative analyses. Users can select species of interest, define orthologous gene sets, and perform various types of comparative analyses with an intuitive interface.
This tool is particularly valuable for researchers studying:
- Evolutionary conservation of gene regulatory mechanisms
- Lineage-specific adaptations in transcriptional regulation
- Impact of genome duplication events on gene expression
- Core regulatory principles shared across distant evolutionary lineages
The Comparative Genomics Analysis module has been developed in collaboration with computational biologists specializing in evolutionary genomics. We welcome feedback from the research community as we continue to refine and expand this functionality.
October 10, 2023
Research Highlight: Human Tissue-Specific TSS Atlas
TSSHub is proud to announce the release of a comprehensive Human Tissue-Specific TSS Atlas, based on the latest FANTOM6 data. This atlas provides high-resolution TSS usage maps across 50 human tissues and cell types, offering unprecedented insights into the complexity of human gene expression regulation.
Atlas Highlights
- Comprehensive Tissue Coverage: 50 distinct tissues and cell types, including brain regions, immune cells, and developmental stages
- High-Resolution Data: Single-nucleotide resolution TSS maps with quantitative usage information
- Alternative Promoter Analysis: Detailed annotation of alternative promoters and their tissue-specific usage
- Enhancer RNA Mapping: Identification of enhancer RNAs and their correlation with gene expression
This atlas reveals remarkable tissue specificity in promoter usage, with thousands of genes exhibiting alternative promoters with distinct tissue preferences. Such alternative promoters often lead to protein isoforms with different N-terminal domains, potentially affecting protein localization, activity, or stability.
Key findings from our analysis include:
- Over 60% of human genes use multiple promoters in a tissue-dependent manner
- Brain tissues show the highest diversity in promoter usage
- Tissue-specific promoters are often associated with distinct regulatory motifs
- Many disease-associated variants affect tissue-specific rather than constitutive promoters
This atlas provides a valuable resource for researchers studying human gene regulation, tissue-specific gene expression, and the impact of regulatory variation on disease. The data can be explored through our interactive browser and downloaded for further analysis.
We thank the FANTOM consortium for generating the original CAGE-seq data and making it publicly available. Our contribution has been to process, integrate, and provide user-friendly access to this rich dataset.