Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity

ABSTRACT: We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. Within K562 cells, scMPRA identified a subset of developmental promoters that are upregulated in the CD34+/CD38- sub-state, confirming this state as more “stem-like.” Finally, we deconvolved the intrinsic and extrinsic components of cell-to-cell variability and found that developmental promoters have a higher proportion of extrinsic noise compared to housekeeping promoters. We anticipate scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.

ORGANISM(S): Mus musculus Escherichia coli Homo sapiens

PROVIDER: GSE188639 | GEO | 2021/11/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genomic environments scale the activities of diverse core promoters

Project description:One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. We further show that core promoter scaling is a genome-wide phenomenon by testing six core promoters at thousands of locations across the genome. While the rank order of core promoters is preserved, the scaling of expression across the genome is non-linear and depends on the genomic location and the strength of the core promoter, but not on its class, suggesting that housekeeping and developmental promoters do not make different interactions with the surrounding genomic environment. Instead, our results support a modular genome in which genomic environments containing different enhancers and chromatin features scale the activities of core promoters in an independent, but non-linear manner.

2021-05-01 | GSE173678 | GEO

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.

2014-12-10 | E-GEOD-57876 | biostudies-arrayexpress

Transcription factor interactions explain the context-dependent activity of CRX binding sites

Project description:We assessed how the effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory sequence (CRS) depend on the local sequence context. We constructed a library of synthetic CRSs composed of TFBSs enriched in mouse photoreceptors and assayed them by massively parallel reporter assay in live mouse retina. We used the resulting data to train neural network-based models that predict CRS activity from sequence.

2023-03-05 | GSE225867 | GEO

Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

Project description:We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity. Reporter mRNA-seq from HepG2 and K562 cells transfected with a ~55,000-plex MPRA plasmid pool containing 5,418 mutated human enhancer sequences, each linked to 10 distinct 10-nt tags. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers.

2013-03-15 | E-GEOD-33367 | biostudies-arrayexpress

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 – 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 genes’ 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.

2014-12-10 | GSE57876 | GEO

Homo sapiens

Project description:HEK293 cell line - transposon reporter - raw sequence reads

| PRJNA291089 | ENA

Large-scale analysis of the integration of enhancer-enhancer signals by promoters

Project description:Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals approximately following a power-law, but the exponent of this response varies between promoters. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.

2023-08-10 | GSE240586 | GEO

Drosophila melanogaster

Project description:Clustering of Drosophila housekeeping promoters facilitates their expression

| PRJNA292609 | ENA

Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

2013-03-15 | GSE33367 | GEO

A systematic and scalable approach for dissecting the molecular 2 mechanisms of transcriptional regulation in bacteria

Project description:Gene regulation is one of the most ubiquitous processes in biology. And yet, while the catalogue of 15 bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in 16 these genomes are regulated. Characterizing the molecular mechanisms by which regulatory sequences 17 operate still requires focused efforts using low-throughput methods. Here we show how a combination of 18 massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used 19 to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both 20 well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all 21 cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including 22 previously unannotated ones, we can further extract quantitative biophysical models describing 23 input-output relationships. This method opens up the possibility of exhaustively dissecting the 24 mechanisms of promoter function in E. coli and a wide range of other bacteria.

2018-04-13 | PXD007892 | JPOST Repository

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data