Seed development in Arabidopsis thaliana undergoes an initial phase of endosperm proliferation followed by a second phase in which the embryo grows at the expense of the endosperm. As mature seed size is largely attained during the initial phase, seed size is coordinately determined by the growth of the maternal ovule, endosperm, and embryo. Here, we identify SHORT HYPOCOTYL UNDER BLUE1 (SHB1) as a positive regulator of Arabidopsis seed development that affects both cell size and cell number. shb1-D, a gain-of-function overexpression allele, increases seed size, and shb1, a loss-of-function allele, reduces seed size. SHB1 is transmitted zygotically. The increase in shb1-D seed size is associated with endosperm cellurization, chalazal endosperm enlargement, and embryo development. SHB1 is required for the proper expression of two other genes that affect endosperm development, MINISEED3 (MINI3) and HAIKU2 (IKU2), a WRKY transcription factor gene and a leucine-rich repeat receptor kinase gene. SHB1 associates with both MINI3 and IKU2 promoters in vivo. SHB1 may act with other proteins that bind to MINI3 and IKU2 promoters to promote a large seed cavity and endosperm growth in the early phase of seed development. In the second phase, SHB1 enhances embryo cell proliferation and expansion through a yet unknown IKU2-independent pathway. INTRODUCTIONIn angiosperms, double fertilization leads to the formation of a diploid embryo and a triploid endosperm, as the endosperm arises from the central cell that contains two identical haploid genomes. The endosperm constitutes the major volume of the mature seed in monocots and some dicots. In Arabidopsis thaliana and many other dicots, seed development is marked by two distinct phases (Sundaresan, 2005). In an initial phase, rapid growth and proliferation of the endosperm results in a large increase in size (Boisnard-Lorig et al., 2001). Then, embryo growth takes place at the expense of endosperm during the second phase. At maturity, the seed contains only a single layer of endosperm cells, and the maternal integument ultimately becomes the seed coat (Scott et al., 1998;Garcia et al., 2003). Seed coat formation and endosperm growth precede embryo growth in Arabidopsis, and the seed reaches almost its final size before the enlargement of the embryo. Therefore, seed size is determined by the coordinated growth of the diploid embryo, the triploid endosperm, and the diploid maternal ovule.Both maternal and nonmaternal factors are involved in seed size regulation (Garcia et al., 2005). In Arabidopsis, an increased dosage of the paternal genome in the endosperm increases seed size, whereas an increased dosage of the maternal genome reduces seed size, with delayed cellularization of the peripheral endosperm and hypertrophy of the chalazal endosperm and associated nodules (Scott et al., 1998). Mutations in DNA METHYLTRANSFERASE1 (MET1) and DECREASE IN DNA METHYLATION1 (DDM1) dramatically reduce DNA methylation and cause parent-of-origin effects on F1 seed size (Xiao et al., 2006). Poll...

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 3 Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.

Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer. However, practical tools for studying the signatures of copy number alterations are still lacking. Here, a user-friendly open source bioinformatics tool “sigminer” has been constructed for copy number signature extraction, analysis and visualization. This tool has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations. Five copy number signatures are identified from human PC genome with this tool. The underlying mutational processes for each copy number signature have been illustrated. Sample clustering based on copy number signature exposure reveals considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. This copy number signature analysis in PC provides distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.