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Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

ABSTRACT: After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that widespread evolutionary innovation has shaped the earliest stages of development. Here, we show that homologs of mammalian reprogramming factors OCT4 and SOX2 divergently regulate the two subgenomes of the allotetraploid Xenopus laevis, resulting in asymmetric activation of hundreds of homeologous gene pairs in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in enhancer architecture between the subgenomes, which likely arose after hybridization of X. laevis's diploid progenitors ~17 million years ago. However, comparison with diploid X. tropicalis shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the pluripotency transcriptional program, amidst genomic instability following hybridization.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE207026 | GEO | 2022/09/14

REPOSITORIES: GEO

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Hybridization led to a rewired pluripotency network in Xenopus laevis [ATAC-seq]

Project description:After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that widespread evolutionary innovation has shaped the earliest stages of development. Here, we show that homologs of mammalian reprogramming factors OCT4 and SOX2 divergently regulate the two subgenomes of the allotetraploid Xenopus laevis, resulting in asymmetric activation of hundreds of homeologous gene pairs in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in enhancer architecture between the subgenomes, which likely arose after hybridization of X. laevis's diploid progenitors ~17 million years ago. However, comparison with diploid X. tropicalis shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the pluripotency transcriptional program, amidst genomic instability following hybridization.

2022-09-14 | GSE207024 | GEO

Hybridization led to a rewired pluripotency network in Xenopus laevis [CUT&RUN]

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Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

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Hybridization led to a rewired pluripotency network in Xenopus laevis [CUT&RUN]

Project description:Hybridization led to a rewired pluripotency network in Xenopus laevis [CUT&RUN]

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Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

Project description:Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

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Hybridization led to a rewired pluripotency network in Xenopus laevis [ATAC-seq]

Project description:Hybridization led to a rewired pluripotency network in Xenopus laevis [ATAC-seq]

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Subgenome-dominant expression and alternative splicing in response to pathogen stress in polyploid Brassica napus and progenitors

Project description:Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids.

2023-02-04 | GSE201225 | GEO

Transcriptome Shock Invokes Disruption of Parental Expression-Conserved Genes in Tetraploid Wheat

Project description:Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner. We have 9 samples including two tissues, leaf and young-inflorescence, respectively. Each sample has three replicates. So we overall have 54 samples.

2016-02-12 | E-GEOD-65844 | biostudies-arrayexpress

Transcriptome Shock Invokes Disruption of Parental Expression-Conserved Genes in Tetraploid Wheat

2016-02-12 | GSE65844 | GEO

Transcriptome inheritance of a citrus somatic hybrid

Project description:The main objective of the present study was to analyze whether the novel phenotype of this complex three-way tetraploid interspecific hybrid, displaying mixed dominant, codominant and transgressive traits is associated with non additive expression of the two diploid parental genomes. Keywords: Comparative transcriptomic hybridization Three replicates for each sample category (C. reticulata Blanco, C. limon (L.) Burm.) and a allotetraploid somatic hybrid between both) were generated and compared by a reference design.

2010-06-21 | E-GEOD-18386 | biostudies-arrayexpress

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