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High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

ABSTRACT: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

PROVIDER: PRJNA482608 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7586710.fastq.gz	Fastqsanger.gz
	SRR7586720.fastq.gz	Fastqsanger.gz
	SRR7586730.fastq.gz	Fastqsanger.gz
	SRR7586740.fastq.gz	Fastqsanger.gz
	SRR7586711.fastq.gz	Fastqsanger.gz

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High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

Project description:Bidirectional transcription initiates at both coding and non-coding genomic elements, including mRNA and long non-coding RNA (lncRNA) promoters and enhancer RNAs (eRNAs). However, each class has different tissue-specific expression profiles with lncRNAs and eRNAs being the most tissue-specific. How these complex differences in expression profiles and tissue-specificities are encoded in a single DNA sequence, however, remains an open question. Here, we address this question using multiple computational and experimental approaches, including massively parallel reporter assays (MPRA). As most transcription factors (TFs) are enriched near the transcription start sites (TSSs) of both promoters and enhancers, we focus our analyses on these core promoter regions. We find that divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than non-divergent lncRNA and mRNA core promoters, respectively. Conversely, lincRNAs and eRNAs are more tissue-specific than divergent genes. This higher tissue-specificity is strongly associated with having less complex TF motif profiles at the core promoter. We confirm these findings using single-nucleotide deletions in MPRA and we identify specific TFs regulating a set of disease-related lncRNAs. Finally, we assess the effects of genetic variation at core promoters and find that 22% of common single nucleotide polymorphisms show significant regulatory effects. Collectively, our findings characterize the important role of core promoter sequences in determining expression levels across both coding and non-coding gene classes and highlight an unexpected role of TF motif architecture in explaining the more restricted expression patterns of lncRNAs and eRNAs.

2019-01-08 | GSE117594 | GEO

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity.

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Project description:De novo methylation of CpG islands is seen in many tumors, but the general rules governing this process are not known. By analyzing DNA from tumors, as well as normal tissues, and by utilizing a wide range of published data, we have been able to identify a well-defined set of tumor targets, each of which has its own M-bM-^@M-^\coefficientM-bM-^@M-^] of methylation that is largely determined by its inherent relative ability to recruit the polycomb complex. This pattern is initially formed by a slow process of de novo methylation that occurs during aging and then undergoes expansion early in tumorigenesis, where it may play a role as an inhibitor of development-associated gene activation. We also demonstrate that DNA methylation patterns can be used to diagnose the primary tissue source of tumor metastases. CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

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Project description:De novo methylation of CpG islands is seen in many tumors, but the general rules governing this process are not known. By analyzing DNA from tumors, as well as normal tissues, and by utilizing a wide range of published data, we have been able to identify a well-defined set of tumor targets, each of which has its own “coefficient” of methylation that is largely determined by its inherent relative ability to recruit the polycomb complex. This pattern is initially formed by a slow process of de novo methylation that occurs during aging and then undergoes expansion early in tumorigenesis, where it may play a role as an inhibitor of development-associated gene activation. We also demonstrate that DNA methylation patterns can be used to diagnose the primary tissue source of tumor metastases.

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Enhancer-core promoter specificity separates developmental and housekeeping regulation

Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters M-bM-^@M-^S one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genesM-bM-^@M-^Y core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.

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