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Profiling of AGO104-dependent gene expression in maize ovaries

ABSTRACT: Maize plants defective for the AGO104 protein show defects in chromatin condensation during meiosis, and subsequent failure to segregate chromosomes. AGO104 is a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob repeat DNA. Digital Gene Expression Tag Profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Thus, female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize.

ORGANISM(S): Zea mays

PROVIDER: GSE26859 | GEO | 2011/01/26

SECONDARY ACCESSION(S): PRJNA135985

REPOSITORIES: GEO

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Profiling of AGO104-dependent gene expression in maize ovaries

Project description:Maize plants defective for the AGO104 protein show defects in chromatin condensation during meiosis, and subsequent failure to segregate chromosomes. AGO104 is a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob repeat DNA. Digital Gene Expression Tag Profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Thus, female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize. Profiling of gene expression in mutant versus wilt type ovaries.

2011-01-26 | E-GEOD-26859 | biostudies-arrayexpress

Hypericum perforatum LCM-RNAseq

Project description:Hypericum perforatum L. (2n=4x=32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression variation in sexual and apomictic plants, by focusing on the ovule nucellus, which is the cellular domain primarily involved into the differentiation of meiocyte precursors and aposporous embryo sacs. Gene expression analysis performed by RNAseq identified 396 differentially expressed genes and 1834 transcripts displaying phenotype-specific expression. Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with the modulation of key genes involved in cell patterning, RNA splicing and RNA-directed DNA methylation.

2019-03-28 | GSE128923 | GEO

Hypoxia triggers meiotic fate acquisition in maize

Project description:Evidence from confocal microscopic reconstruction of maize anther development in fertile, mac1 (excess germ cells) and msca1 (no germ cells) flowers indicates that the male germ line is multiclonal and uses the MAC1 protein to organize the somatic niche. Furthermore, we identified redox status as a determinant of germ cell fate, defining a mechanism distinct from the animal germ cell lineage. Decreasing oxygen or H2O2 increases germ cell numbers, stimulates superficial germ cell formation, and rescues germinal differentiation in msca1 flowers. Conversly, oxidizing environments inhibit germ cell specification and cause ectopic differentiation in deeper tissues. We propose that hypoxia, arising naturally within growing anther tissue, acts as a positional cue to set germ cell fate. key words: anther development, maize, male-sterile Two replicates of laser microdissected pre-meiotic cells were compared to two replicates of whole anthers, which contains pre-meiotic cells and somatic cells, from the same developmental stage and individual wild type plants. In another experiment, laser microdissected pre-meiotic cells from wild type (mac1-heterozygous) anthers were compared to laser microdissected pre-meiotic cells from mac1 (mutant) anthers.

2012-07-04 | E-GEOD-39101 | biostudies-arrayexpress

Hypoxia triggers meiotic fate acquisition in maize

2012-07-05 | GSE39101 | GEO

Meiosis-associated argonaute (MAGO) proteins are necessary for meiosis in maize

Project description:Plants do not specify their germline until late in their life cycle. Hence, the plant germline is normally specified from terminally differentiated somatic cells, though the precise mechanism(s) are unknown. We have found that male gametogenesis in maize is associated with the accumulation of distinct 21-nt phased small-interfering RNAs (phasiRNAs) generated by meiosis-associated argonaute (MAGO) proteins. MAGO1 accumulates in the epidermis of pre-meiotic anthers while MAGO2 is found in developing meiocytes. We have found that MAGO proteins are required for meiocyte development as mutants display chromosomal defects and male infertility. Furthermore, we detect the heat stress-induced activation of a distinct class of Long terminal repeat retrotransposons in the male germline of MAGO mutants. Our data suggests that MAGO proteins and the reproductive phasiRNAs play important roles protecting the germline from transposable elements during environmental stress conditions.

2022-01-04 | PXD013891 | Pride

The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the caenorhabditis elegans germline.

Project description:Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes including Ash2 and Wdr5. While individual subunits contribute to complex activity, how they influence gene expression in a specific tissue remains largely unknown. In caenorhabditis elegans, SET-2/SET1, WDR-5.1 and ASH-2 are differentially required for germline H3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2 or wdr-5.1, we show that these subunits play unique and redundant functions to promote expression of germline genes and repress somatic genes. We further show that in set-2 and wdr-5.1 deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells, and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1 to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency, and underline the complexity of the cellular network regulating this process. Gene misregulation in SET1/set-2, wdr-5.1 and ash-2 defective germlines

2014-09-04 | E-GEOD-61094 | biostudies-arrayexpress

The RNA Polymerase II subunit RPB-9 directs transcriptional elongation at piRNA loci in C. elegans

Project description:PIWI-interacting RNAs (piRNAs) are genomically-encoded small RNAs that regulate germ cell development and guarantee germline integrity. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. To date, piRNA biogenesis mechanisms are still unclear. Here, we show that the RNA Polymerase II subunit RPB-9 is required to promote transcription elongation at piRNA loci. Through genetic and biochemical experiments, we demonstrate that rpb-9-mediated piRNA production is needed to repress two DNA transposon families and a subset of somatic genes in the C. elegans germline.

2020-12-07 | PXD018657 | Pride

The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the caenorhabditis elegans germline.

2014-09-04 | GSE61094 | GEO

Abiotic stress-response reprogramming events underlie successful initiation of apomixis

Project description:This experiment provides the gene expression data from seedlings of 2 different species from Boechera genus, (Boechera stricta - referred as Sex-1; Boechera gunnisoniana - referred as Apo-1 here). The main intent of the experiment is to identify expression changes in species which reproduce differently (Sexual vs apomixis) and at somatic stages (seedling) to identify mechanisms governing changes occurring in prior to reproduction stage as preparatory mechanism.

2017-05-01 | E-MTAB-4972 | biostudies-arrayexpress

Arabidopsis Argonaute4, Argonaute6 and Argonaute9 associated small RNAs

Project description:We sequenced the small RNA bound to AGO4, AGO6 and AGO9 and compared these sRNAs to other libraries isolated such as total sRNAs, ago4 mutant, drd3-1 mutant, an AGO4 D660A slicer mutant and AGO6 and AGO9 under the AGO4 promoter. Keywords: Epigenetics Illumina samples: There are 17 unique samples representing 2 biological replicates of AGO6IP, 2 biological replicates of AGO9 IP, 3 biological replicates of total floral small RNAs, 1 technical replicate of total floral small RNA. 454 samples: These samples comprise 3 biological replicates of FLAG AGO4 IP.

2010-02-21 | E-GEOD-16545 | biostudies-arrayexpress

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