Abstract
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells. However, the genome-wide transcriptional activities that guide divergence of apical and basal cell development remain unknown. Here, we present a comprehensive transcriptome analysis of apical and basal cell lineages, uncovering distinct molecular pathways during cell lineage specification. Selective deletion of inherited transcripts and specific de novo transcription contribute to the establishment of cell lineage-specific pathways for cell fate specification. Embryo-related pathways have been specifically activated in apical cell lineage since 1-cell embryo stage, but quick transcriptome remodeling toward suspensor-specific pathways are found in basal cell lineage. Furthermore, long noncoding RNAs and alternative splicing isoforms may be involved in cell lineage specification. This work also provides a valuable lineage-specific transcriptome resource to elucidate the molecular pathways for divergence of apical and basal cell lineages at genome-wide scale.
Highlights
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells
We demonstrate that AC lineage (ACL) and basal cell lineage (BCL) specification occurs immediately after asymmetric zygote division and identify previously unknown lineage-specific transcripts, including protein-coding genes, long noncoding RNAs, and alternative splicing isoforms, associated with lineage specification
To investigate spatial and temporal gene expression during ACL and BCL specification in Arabidopsis, based on our previous study[12], we performed a comparative analysis of 2-cell proembryos and 32-cell embryos
Summary
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells. Various methods of isolating cells, such as laser capture microdissection, fluorescence-activated cell sorting, isolation of nuclei tagged in specific cell types have been used to isolate embryo proper and suspensor of globular embryos for cellular or nuclear transcriptome analysis[8,9,10] These pioneer studies provided valuable data for understanding the mechanism underlying cell type establishment, but deep transcriptome studies of the apical and basal cell lineages have been challenging due to technical difficulties in isolating living early proembryos and dissecting the ACL and BCL. We developed a reliable method for isolating live apical and basal cells and their descendants, which enables cell lineage-specific transcriptome profiling[11] We apply this technique to generate a transcriptional map of the ACL and BCL of early proembryos at 1-cell and 32-cell embryo stage. Our data provide insight into the progression of cell lineage specification during early embryogenesis
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