Ontology highlight
ABSTRACT:
PROVIDER: PRJNA799647 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17709722_1.fastq.gz | Fastqsanger.gz | |||
| SRR17709722_2.fastq.gz | Fastqsanger.gz | |||
| SRR17709723_1.fastq.gz | Fastqsanger.gz | |||
| SRR17709723_2.fastq.gz | Fastqsanger.gz | |||
| SRR17709724_1.fastq.gz | Fastqsanger.gz |
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Project description:Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. This strategy, which directly delineates the expression profiles of individual promoters and was designed to offer optimal sample multiplexing capabilities, represents an advantageous alternative to standard RNA-Seq for a wide range of transcriptome profiling applications. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposons harbor TSSs driving the expression of hundreds of annotated genes, and they often impart their own expression specificity upon the genes they regulate. Detailed analysis of particular transposons identified sequence elements encoding these regulatory properties. Our results show that transposable elements contribute significantly to the generation of standing variation and to the evolution of gene regulatory networks, by distributing stereotyped regulatory modules throughout the genome.
2012-08-30 | GSE36212 | GEO
Project description:Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs.
2023-04-13 | GSE200769 | GEO
Project description:Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs.
2023-04-13 | GSE200768 | GEO
Project description:Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs.
2023-04-13 | GSE200767 | GEO
Project description:Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. This strategy, which directly delineates the expression profiles of individual promoters and was designed to offer optimal sample multiplexing capabilities, represents an advantageous alternative to standard RNA-Seq for a wide range of transcriptome profiling applications. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposons harbor TSSs driving the expression of hundreds of annotated genes, and they often impart their own expression specificity upon the genes they regulate. Detailed analysis of particular transposons identified sequence elements encoding these regulatory properties. Our results show that transposable elements contribute significantly to the generation of standing variation and to the evolution of gene regulatory networks, by distributing stereotyped regulatory modules throughout the genome. This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression throughout 36 stages of the life cycle of Drosophila melanogaster. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. Embryos, larvae, pupae and adult flies were collected at specific stages of development, and RAMPAGE profiles were established for pools of whole organisms. The data was analyzed using custom scripts and algorithms that are all available upon request. Supplementary files: Dmel_Combined_+.bw: bigWig coverage by cDNA 5' ends (+ strand). Dmel_Combined_-.bw: bigWig coverage by cDNA 5' ends (- strand). Dmel_All_RAMPAGE_peaks.bed: BED file describing all RAMPAGE peaks. Dmel_GeneTSS_RAMPAGE_peaks.bed: BED file describing all peaks attributed to annotated genes. GeneTSS_expression_RAMPAGE_RPM.txt: Expression matrix for all genic peaks (RPM: reads per million). Transposon_expression_RAMPAGE_RPM.txt: Expression matrix for all RepeatMasker-annotated transposon classes (RPM: reads per million). Genome build: dm3
2012-08-30 | E-GEOD-36212 | biostudies-arrayexpress
Project description:In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species. Determination of H3K4me1- and H3K4me3-binding sites in the zebrafish genome.
2011-02-25 | E-GEOD-20600 | biostudies-arrayexpress
Project description:The zebrafish has been widely used for the study of human disease and development, as ~70% of the protein-coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome, however, has lagged behind that of other model systems such as mouse and Drosophila. Based on multi-omics approaches taken in the ENCODE and Roadmap Epigenomics projects, we performed RNA-seq, ATAC-seq, ChIP-seq and Hi-C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall, we have identified 235,596 cis-regulatory elements, which potentially shape the tissue-specific and developmental-stage-specific gene expression in zebrafish. A comparison of zebrafish, human, and mouse regulatory elements allowed us to identify both evolutionarily conserved and species-specific regulatory sequences. Furthermore, through the analysis of Hi-C data in zebrafish brain and muscle, we observed different levels of 3D genome organization, including compartment, topological associating domains (TADs), and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization.
2020-09-04 | GSE134055 | GEO
Project description:The placenta is a fast-evolving organ that displays large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here were assessed the contribution of transposable elements to human trophoblast gene expression by acting as enhancers or promoters. Using epigenomic data from primary trophoblast and human stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential trophoblast expression. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as expression enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting trophoblast migration and secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.
2022-04-15 | GSE200759 | GEO
Project description:The placenta is a fast-evolving organ that displays large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here were assessed the contribution of transposable elements to human trophoblast gene expression by acting as enhancers or promoters. Using epigenomic data from primary trophoblast and human stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential trophoblast expression. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as expression enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting trophoblast migration and secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.
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Project description:The placenta is a fast-evolving organ that displays large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here were assessed the contribution of transposable elements to human trophoblast gene expression by acting as enhancers or promoters. Using epigenomic data from primary trophoblast and human stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential trophoblast expression. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as expression enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting trophoblast migration and secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.
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