Lineage Landscape: a comprehensive database that records lineage commitment across species

Abstract

Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.

DNA methylation clocks for estimating biological age in Chinese cohorts

“…For example, CDKN2A , a canonical marker for cellular aging ( Krishnamurthy et al, 2004 ), is upregulated during aging and hypomethylated in the elderly ( Fig. 2E ), consistent with the results recorded in the Lineage Landscape ( Yan et al, 2023 ). Furthermore, the activated probe-gene pairs (decreased DNA methylation and increased expression) were enriched in pathways such as platelet activation, Ras protein signal transduction, while the repressed probe-gene pairs (increased DNA methylation and decreased expression) are associated with glycogen biosynthetic process and positive regulation of cold-induced thermogenesis, both of which were closely related to homeostasis ( Ngo and Steyn, 2015 ; Wang et al, 2022 ) ( Fig.…”

Biomarkers of aging

“…Changes in RNA expression levels both in single cells or bulk tissues during aging have been widely reported in various common model organisms across tissues, and a large number of data resources and databases have been developed (Aging Atlas, 2021;Kang et al, 2022;Ma et al, 2020;Sun et al, 2023;Tabula Muris, 2020;Yan et al, 2023). The association between genes with aging makes it possible to predict the rate of aging or lifespan based on transcriptome data.…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…The popular returning CellMarker ( 72 ), for human and mouse, reports significantly expanded content, both in terms of number and type of marker but also encompassing new sequencing technologies; while the new Cell Taxonomy database ( 73 ) covers thousands of curated cell types across 34 species. Another new database TEDD ( 74 ) looks at temporal (co-) expression and chromatin accessibility during development in model organisms while Lineage Landscape ( 75 ) explores similar themes, additionally covering epigenomics data. Finally, interesting perspectives on genome evolution are offered by the returning HGTree ( 76 ), now covering horizontal gene transfer in eight times as many prokaryotic species, and the new DupScan ( 77 ) which provides detailed insights into whole genome duplications in vertebrates.…”