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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

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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.

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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.

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

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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

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

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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.

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