The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
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ABSTRACT:
PROVIDER: PRJNA532621 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10466062_1.fastq.gz | Fastqsanger.gz | |||
| SRR10466062_2.fastq.gz | Fastqsanger.gz | |||
| SRR10466063_1.fastq.gz | Fastqsanger.gz | |||
| SRR10466063_2.fastq.gz | Fastqsanger.gz | |||
| SRR10466064_1.fastq.gz | Fastqsanger.gz |
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Project description:MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
2019-12-03 | GSE129744 | GEO
Project description:MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
| S-EPMC6914339 | biostudies-literature
Project description:MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules, and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS genes underpin the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.
| S-EPMC8788222 | biostudies-literature
Project description:Effects of loss-of-function of AtMIKC* MADS-box genes on the mature Arabidopsis pollen transcriptome.
2007-12-04 | E-MEXP-1138 | biostudies-arrayexpress
Project description:The mads-box mutant line showed an abscisic acid (ABA)-insensitive phenotype. The AGAMOUS-LIKE 67 (AT1G77950) gene encodes a transcription factor that is nuclear-localized, as observed by transiently transformed epidermal onion cells, specifically expressed in seeds and involved in an ABA signaling pathway during seed germination (Fernández-Arbaizar et al. 2012). SALK_050367 seeds were obtained from the Arabidopsis Biological Resource Center, ABRC.
2019-12-31 | GSE25451 | GEO
Project description:MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. Our findings revealed that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number, cell production rate, fully elongated cell size, but only the overexpression of SOC1 affects distal root stem cell differentiation. Additionally, these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.
2023-11-13 | GSE247158 | GEO
Project description:Litchi possesses unique flower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower organ development remains largely unknown. MADS-box genes are promise candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes, and can be divided into type I and type II genes. Fifty type I MADS-box genes are sub-divided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC*-type genes. Both two types of LcMADS genes mainly contain ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveals that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes including LcMADS42/46/47/75/93/100 play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS75 (LcAP1) and LcMADS51 (LcSTK). However, JA probably plays a negative role in litchi flower development.
2021-10-27 | GSE182444 | GEO
Project description:Litchi possesses unique flower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower organ development remains largely unknown. MADS-box genes are promise candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes, and can be divided into type I and type II genes. Fifty type I MADS-box genes are sub-divided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC*-type genes. Both two types of LcMADS genes mainly contain ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveals that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes including LcMADS42/46/47/75/93/100 play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS75 (LcAP1) and LcMADS51 (LcSTK). However, JA probably plays a negative role in litchi flower development.
2021-10-27 | GSE182439 | GEO
Project description:Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter seed size. Specifically, paternal-excess crosses (2 × 4) delay endosperm cellularization (EC) and produce larger seeds, whereas maternal-excess crosses (4 × 2) promote precocious EC and produce smaller seeds. The mechanisms for responding to the parental genome dosage imbalance and for gene expression changes in endosperm are unknown. In plants, RNA polymerase IV (PolIV or p4) encoded by NRPD1a is required for biogenesis of a major class of 24-nt small interfering RNAs (also known as p4-siRNAs), which are predominately expressed in developing endosperm. Here we show that p4-siRNA accumulation depends on the maternal genome dosage, and maternal p4-siRNAs target transposable elements (TEs) and TE-associated genes (TAGs) in seeds. The p4-siRNAs correlate negatively with expression levels of AGAMOUS-LIKE (AGL) genes in endosperm of interploidy crosses. Moreover, disruption of maternal NRPD1a expression is associated with p4-siRNA reduction and AGL up-regulation in endosperm of reciprocal crosses. This is unique genetic evidence for maternal siRNAs in response to parental genome imbalance and in control of transposons and gene expression during endosperm development.
2011-11-11 | GSE25280 | GEO
Project description:The identification of a number of cis-elements which direct gene expression in maize endosperm, and the characterization of corresponding DNA binding proteins, point to the interaction of different classes of transcription factors in this tissue. To assess whether MADS box genes are also involved in maize endosperm development, cDNA and genomic MADS box clones have been isolated. The three cDNA clones ZEM1, ZEM2 and ZEM3 were cloned from a maize endosperm cDNA library using a probe based on sequences conserved in plant MADS box genes. Further transcripts were cloned by RT-PCR experiments and designated ZEM4 and ZEM5. Analysis of the corresponding genomic clones led to the identification of the ZEM2 MADS box gene family, three members of which were characterized sharing 97% sequence identity in corresponding domains. 100% sequence identities between cDNA and one of the genomic clones, conserved exon-intron boundaries and the demonstration of in vivo splicing in a maize endosperm transient expression system, show that the transcripts ZEM1-5 are derived by alternative splicing of ZEMa, one ZEM2 member. The ZEMa transcripts are present in almost all maize tissues, but specific differentially spliced forms accumulate preferentially in maturing endosperm and leaf. The function of the ZEMa gene is discussed in the light of similarities in the expression pattern with members of the human MEF2/RSRF gene family.
| S-EPMC307004 | biostudies-other