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Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling

ABSTRACT: Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling

PROVIDER: PRJNA704824 | ENA |

REPOSITORIES: ENA

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Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

Project description:Aging changes global transcriptome including protein-coding and noncoding RNAs. Whether aging dependent lncRNAs undergo conserved regulation and function still remain unknown. We report aging dependent lncRNAs carry signature of evolutionary constraint and significantly enriched for targets of transcription factors and RNA binding proteins. Aging dependent lncRNAs is conservatively under NFκB pathway regulation. CRISPR screening for NFκB pathway found that aging dependent lncRNAs also extensively regulate NFκB pathway. The human NFKBMARL-1 is an evolutionary conserved lncRNA that can be traced to 29Mya before human. NFKBMARL-1 is induced during aging, inflammation and senescence through NFκB pathway. Reciprocally, NFKBMARL-1 directly regulates NFKBIZ in cis within same topological associated domain (TAD). NFKBMARL-1 binds to enhancer of NFKBIZ and recruits RELA to the NFKBIZ promoters and participates phase separation. These findings reveal that aging dependent lncRNAs are previously under-appreciated contributors to the evolutionary conservation and regulation of NFκB pathway.

2021-03-08 | GSE167504 | GEO

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

Project description:Aging changes global transcriptome including protein-coding and noncoding RNAs. Whether aging dependent lncRNAs undergo conserved regulation and function still remain unknown. We report aging dependent lncRNAs carry signature of evolutionary constraint and significantly enriched for targets of transcription factors and RNA binding proteins. Aging dependent lncRNAs is conservatively under NFκB pathway regulation. CRISPR screening for NFκB pathway found that aging dependent lncRNAs also extensively regulate NFκB pathway. The human LINC02085 is an evolutionary conserved lncRNA that can be traced to 29Mya before human. LINC02085 is induced during aging, inflammation and senescence through NFκB pathway. Reciprocally, LINC02085 directly regulates NFKBIZ in cis within same topological associated domain (TAD). LINC02085 binds to enhancer of NFKBIZ and recruits RELA to the NFKBIZ promoters and participates phase separation. These findings reveal that aging dependent lncRNAs are previously under-appreciated contributors to the evolutionary conservation and regulation of NFκB pathway.

2021-03-08 | GSE167510 | GEO

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

2021-03-08 | GSE167507 | GEO

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

| PRJNA704830 | ENA

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

| PRJNA704832 | ENA

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

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Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-03-08 | GSE167511 | GEO

Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

Project description:Functional studies of long noncoding RNAs (lncRNAs) have long been hindered by a lack of methods to assess their evolution. Here, we present lncHOME (lncRNA Homology Explorer), a computational pipeline that identifies a unique coPARSE-lncRNA class with conserved genomic locations and patterns of RNA binding protein (RBP) binding sites. Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects that were rescued by predicted zebrafish homologs. Knocking down the coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Moreover, we verified that human, mouse, and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved fuctions relying on specific RBP binding sites. Overall, our study demonstrates a comprehensive approach for studying functional conservation of lncRNAs and implicates numerous lncRNAs in regulating cellular physiology.

2024-01-26 | PXD046452 | Pride

NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_2

Project description:NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_2

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NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_4

Project description:NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation_4

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