Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of AGAMOUS-LIKE36

Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin–specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin–dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds

Characteristics of de novo structural changes in the human genome

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (120 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations

Reproductive cross-talk: seed development in flowering plants

Flowering plants have evolved to be a predominant life form on earth. A common principle of flowering plants and probably one of the main reasons for their evolutionary success is the rapid development of an embryo next to a supporting tissue called the endosperm. The embryo and the endosperm are protected by surrounding maternal tissues, the integuments, and the trinity of integuments, embryo and endosperm comprise the plant seed. For proper seed development, these three structures have to develop in a highly controlled and co-ordinated manner, representing a paradigm for cell-cell communication during development. Communication pathways between the endosperm and the seed coat are now beginning to be unravelled. Moreover, recently isolated mutants affecting plant reproduction have allowed a genetic dissection of seed development, and revealed that the embryo plays a previously unrecognized yet important role in co-ordinating seed development

Natural Variation in the Degree of Autonomous Endosperm Formation Reveals Independence and Constraints of Embryo Growth During Seed Development in Arabidopsis thaliana

Seed development in flowering plants is a paradigm for the coordination of different tissues during organ growth. It requires a tight interplay between the two typically sexually produced structures: the embryo, developing from the fertilized egg cell, and the endosperm, originating from a fertilized central cell, along with the surrounding maternal tissues. Little is known about the presumptive signal transduction pathways administering and coordinating these different tissues during seed growth and development. Recently, a new signal has been identified emanating from the fertilization of the egg cell that triggers central cell proliferation without prior fertilization. Here, we demonstrate that there exists a large natural genetic variation with respect to the outcome of this signaling process in the model plant Arabidopsis thaliana. By using a recombinant inbred line population between the two Arabidopsis accessions Bayreuth-0 and Shahdara, we have identified two genetic components that influence the development of unfertilized endosperm. Exploiting this natural variation, we could further dissect the interdependence of embryo and endosperm growth during early seed development. Our data show an unexpectedly large degree of independence in embryo growth, but also reveal the embryo's developmental restrictions with respect to endosperm size. This work provides a genetic framework for dissection of the interplay between embryo and endosperm during seed growth in plants

Characteristics of de novo structural changes in the human genome

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (120 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations

Characteristics of de novo structural changes in the human genome

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (120 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations