Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Role of Lsd1 in HOTAIR function

ABSTRACT: HOTAIR is a scafold long non-coding RNA tethering PRC2 and Lsd1/REST/coREST complexes to gene promoters to repress transcription of genes involved in epithelial to mesenchymal transition (EMT). To decipher a role of the Lsd1 in HOTAIR function we generated epithelial cell lines expressing full length and truncated versions of HOTAIR missing first 5'-300 (Epi-HOTΔP) and last 3'-500 bp (Epi-HOTΔL) interacting with HOTAIR partners. These cell lines were further used to determine Lsd1 binding sites using chromatin immunoprecipitation approach.

ORGANISM(S): Homo sapiens

PROVIDER: GSE106262 | GEO | 2021/04/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification and functional characterization of long non-coding RNAs associated with epithelial-to-mesenchymal transition

Project description:In the last decade, new high-throughput sequencing techniques have revealed the complexity of the human transcriptome, allowing the characterization of long non-coding (lnc)RNAs. Since their expression has been reported as very specific to tissue, developmental stage and pathological variations, some lncRNAs have been proposed as biomarkers for diagnosis as well as prognosis of tumors. In this project, we aime in identification of lncRNAs associated with the epithelial-to-mesenchymal transition (EMT), a biological process that promotes metastasis. This was performed on an in vitro model (Castro Vega et al, 2015) in which primary HEK cells naturally undergo EMT. Cells were immortalized prior and after EMT, therefore giving rise to the Epi (HA5-Early) and Mes (HA5-Late) cell-lines, which respectively display epithelial and mesenchymal phenotypes. HOTAIR is one the lcnRNAs functionning as a scaffold to tether PRC2 and Lsd1/REST/coREST complexes to gene promoter to epigenetically repress transcription. Its high expression is associated with poor-prognosis cancer and promotes EMT. To decipher a role of PRC2 and Lsd1 interacting domains in HOTAIR function we generated Epi cell lines expressing full length and truncated versions of HOTAIR missing first 5'-300 bp and last 3'-500 bp interacting with HOTAIR partners. Total RNA form these cell lines was extracted and sequenced to reveal HOTAIR targets dependent of its intercation with PRC2 and/or Lsd1.

2021-04-22 | GSE106516 | GEO

Profiling of Lsd1 and chromatin marks in epithelial cells overexpressing HOTAIR variants

Project description:Epithelial-to-mesenchymal transitions (EMT) underlie a loss of epithelial traits by normal cells during development and neoplastic cells during cancer metastasis. The long noncoding RNA HOTAIR triggers EMT, in part by serving as a scaffold for Polycomb Repressive Complex 2 (PRC2) and thus promoting repressive histone H3 Lys27 methylation. In addition to PRC2, HOTAIR interacts with the Lsd1 lysine demethylase, an epigenetic regulator of cell fate during development and differentiation. Here, we showed that HOTAIR requires the Lsd1-interacting domain, but not the PRC2-interacting domain, to promote migration of epithelial cells. Our results suggest that the HOTAIR-Lsd1 asociation redistributes Lsd1 on chromatin and hence reprograms the epithelial transcriptome.

2021-04-22 | GSE162937 | GEO

ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays

Project description:Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes. LSD1 and SUZ12 co-occupied on 721 genes in human foreskin fibroblasts. Coordinate loss of SUZ12 and LSD1 occupancy was caused by HOTAIR knockdown. Comparison occupancy of LSD1 and SUZ12 of siGFP and siHOTAIR foreskin fibroblasts on human HG18 promoter arrays. Human foreskin fibroblasts were transfected with siGFP or siHOTAIR. The cells were harvested and ChIP analysis with anti-LSD1 and anti-SUZ12 antibodies was performed.

2010-07-07 | E-GEOD-22344 | biostudies-arrayexpress

ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-H3K4me2, anti-LSD1 or anti-SUZ12 antibodies on HOX tiling array

Project description:Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes. Coordinate loss of SUZ12 and LSD1 occupancy caused by HOTAIR knockdown were concentrated in proximal promoters of HOXD genes. These regions correspondingly lost H3K27me3 and gained H3K4me2, the respective histone methylation products of PRC2 and LSD1 complexes. Comparison occupancy of LSD1 and SUZ12 of siGFP and siHOTAIR foreskin fibroblasts on HOX tiling array. Human foreskin fibroblasts were transfected with siGFP or siHOTAIR. The cells were harvested and ChIP analysis with anti-H3K4me2, anti-LSD1 and anti-SUZ12 antibodies was performed.

2010-07-08 | E-GEOD-22343 | biostudies-arrayexpress

Role of Lsd1 in HOTAIR function

Project description:Role of Lsd1 in HOTAIR function

| PRJNA416065 | ENA

ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays

2010-07-08 | GSE22344 | GEO

ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-H3K4me2, anti-LSD1 or anti-SUZ12 antibodies on HOX tiling array

Project description:Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes. Coordinate loss of SUZ12 and LSD1 occupancy caused by HOTAIR knockdown were concentrated in proximal promoters of HOXD genes. These regions correspondingly lost H3K27me3 and gained H3K4me2, the respective histone methylation products of PRC2 and LSD1 complexes.

2010-07-08 | GSE22343 | GEO

SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [RNA-Seq]

Project description:SFMBT1 is a poorly characterized mammalian MBT domain-containing protein homologous to Drosophila SFMBT, a Polycomb group protein involved in epigenetic regulation of gene expression. Here, we show that SFMBT1 regulates transcription in somatic cells and during spermatogenesis through the formation of a stable complex with LSD1 and CoREST. When bound to its gene targets, SFMBT1 recruits its associated proteins and causes chromatin compaction and transcriptional repression. SFMBT1, LSD1, and CoREST share a large fraction of target genes including those encoding replication-dependent histones. Simultaneous occupancy of histone genes by SFMBT1, LSD1, and CoREST is regulated during the cell cycle and correlates with the loss of RNA polymerase II at these promoters during G2, M, and G1. The interplay between the repressive SFMBT1M-bM-^@M-^SLSD1M-bM-^@M-^SCoREST complex and RNA polymerase II contributes to the timely transcriptional regulation of histone genes in human cells. SFMBT1, LSD1, and CoREST also form a stable complex in germ cells and their chromatin binding activity is regulated during spermatogenesis. RNA-seq in HeLaS3 cells ctrl compared to triple knockdown for SFMBT1, CoREST, and LSD1

2013-03-26 | E-GEOD-45442 | biostudies-arrayexpress

ChIRP-MS of long non-coding RNA HOTAIR

Project description:Accumulating evidence highlights the role of long non-coding RNAs (lncRNA) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, an unbiased and comprehensive method to map its interactome has not yet been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting HOTAIR has functions independent of its (post-)transcriptional mode-of-action.

2022-02-15 | PXD029057 | Pride

Profiling of Lsd1 and chromatin marks in epithelial cells overexpressing HOTAIR variants

Project description:Profiling of Lsd1 and chromatin marks in epithelial cells overexpressing HOTAIR variants

| PRJNA683879 | ENA