Allele specific effects of a Drosophila hybrid incompatibility gene
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ABSTRACT:
PROVIDER: PRJNA485119 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using Drosophila SL2 cells we induced overxpression of the HMR protein and generated genome-wide binding profiles by performing ChIP-Seq with anti-HMR antibody.
2019-01-01 | GSE118291 | GEO
Project description:Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces which shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genome-wide in female adult heads of D. melanogaster, D. simulans and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.
2009-08-05 | GSE17453 | GEO
Project description:We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome, of which nearly 68% were represented in R9308 versus Xieqingzao B by CT and GA SNPs. This may indicate that DNA methylation, a heritable epigenetic mark, exists in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during at least one stage, suggesting that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed allelic expression biases towards the R9308 allele at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed allele expression biases towards the R9308 allele. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play an important role in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study would provide valuable information for further understanding molecular mechanisms of heterosis. Root mRNA profiles of a super-hybrid rice Xieyou 9308 and its parents at tillering and heading stages were generated by deep sequencing, in duplicate, on Illumina Hiseq 2000 platform.
2014-05-16 | E-GEOD-43727 | biostudies-arrayexpress
Project description:We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome, of which nearly 68% were represented in R9308 versus Xieqingzao B by CT and GA SNPs. This may indicate that DNA methylation, a heritable epigenetic mark, exists in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during at least one stage, suggesting that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed allelic expression biases towards the R9308 allele at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed allele expression biases towards the R9308 allele. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play an important role in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study would provide valuable information for further understanding molecular mechanisms of heterosis.
2014-05-16 | GSE43727 | GEO
Project description:We used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL×93-11 and GL×TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.
2015-09-30 | GSE66537 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNA polymerase II phosphorylated at serine 5 (PolII-S5p; the transcription initiation form) in female mouse cultured hybrid cells and female hybrid brain derived from mouse systems with skewed X inactivation based on crosses between C57BL/6J (BL6) and M. spretus. In these systems, alleles can be differentiated by frequent SNPs between mouse species, and the active X (Xa) compared to the haploid set of autosomes from the same species. To examine PolII-S5p occupancy in vivo, ChIP-seq was done in brain from an adult female F1 mouse in which the BL6 X is always active and the spretus X inactive. Uniquely mapped reads containing informative SNPs were assigned to each haploid chromosome set (BL6 or spretus) and were counted to establish allele-specific PolII-S5p occupancy profiles. We found that PolII-S5p allele-specific occupancy with or without normalization by input genomic DNA sequencing data showed that expressed genes on the Xa (>1RPKM) had 30% higher PolII-S5p peak levels at their promoters compared to autosomal genes from the same species (BL6). This result was confirmed by performing an independent allele-specific ChIP-seq analysis on fibroblasts derived from embryonic kidney (Patski cell line) that have the opposite X inactivation pattern from the brain sample, i.e. an Xa from M. spretus and an Xi from BL6. These findings suggest that transcription initiation of X-linked genes is enhanced to contribute to X upregulation in cell lines and in vivo. Examination of allele-specific PolII-S5p occupancy in mouse hybrid cells and brain.
2013-02-15 | E-GEOD-44255 | biostudies-arrayexpress
Project description:Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.
2023-08-31 | GSE240784 | GEO
Project description:Determine allele level expression in hybrid mice of different ages
2017-02-28 | GSE93787 | GEO
Project description:Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences.
2011-12-21 | GSE34591 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNA polymerase II phosphorylated at serine 5 (PolII-S5p; the transcription initiation form) in female mouse cultured hybrid cells and female hybrid brain derived from mouse systems with skewed X inactivation based on crosses between C57BL/6J (BL6) and M. spretus. In these systems, alleles can be differentiated by frequent SNPs between mouse species, and the active X (Xa) compared to the haploid set of autosomes from the same species. To examine PolII-S5p occupancy in vivo, ChIP-seq was done in brain from an adult female F1 mouse in which the BL6 X is always active and the spretus X inactive. Uniquely mapped reads containing informative SNPs were assigned to each haploid chromosome set (BL6 or spretus) and were counted to establish allele-specific PolII-S5p occupancy profiles. We found that PolII-S5p allele-specific occupancy with or without normalization by input genomic DNA sequencing data showed that expressed genes on the Xa (>1RPKM) had 30% higher PolII-S5p peak levels at their promoters compared to autosomal genes from the same species (BL6). This result was confirmed by performing an independent allele-specific ChIP-seq analysis on fibroblasts derived from embryonic kidney (Patski cell line) that have the opposite X inactivation pattern from the brain sample, i.e. an Xa from M. spretus and an Xi from BL6. These findings suggest that transcription initiation of X-linked genes is enhanced to contribute to X upregulation in cell lines and in vivo.
2013-02-15 | GSE44255 | GEO