SUMMARY The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. LincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types.

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DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types.

Stem cell niche and root meristem size are maintained by intercellular interactions and signaling networks of a peptide hormone, Root Meristem Growth Factor 1 (RGF1). How RGF1 regulates root meristem development is an essential question to understand stem cell function. Although five receptors of RGF1 have been identified, the downstream signaling mechanism remains unknown. Here, we report a series of signaling events following RGF1 action. The RGF1-receptor pathway controls the distribution of reactive oxygen species (ROS) along the developmental zones of the Arabidopsis root. We identify a novel transcription factor, RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 ( RITF1) that plays a central role in mediating RGF1 signaling. Manipulating RITF1 expression leads to redistribution of ROS along the root developmental zones. Changes in ROS distribution, in turn, enhance the stability of the PLETHORA2 (PLT2) protein, a master regulator of root stem cells. Our study, thus, clearly depicts a signaling cascade initiated by RGF1, linking the RGF1 peptide to ROS regulatory mechanisms.Roots encounter various environmental conditions and respond by altering their growth. Root growth arises through controlled cell division in the meristematic zone, equivalent to the transit amplifying zone in animals. After division, most cells increase their size in the elongation zone and mature in the differentiation zone. The size of these developmental zones is determined by intrinsic and extrinsic signals. Reactive oxygen species (ROS) are an intrinsic signal for establishing the size of the meristematic zone. Superoxide (O 2 − ) primarily accumulates in the meristematic zone, while hydrogen peroxide (H 2 O 2 ) mainly accumulates in the differentiation zone 1,2 . The balance between O 2 − and H 2 O 2 modulates the transition from proliferation to differentiation 2 .