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

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

PROVIDER: PRJNA704832 | ENA |

REPOSITORIES: ENA

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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 [ChIRP]

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

| PRJNA704835 | ENA

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]

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 | GSE167507 | GEO

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 are evolutionarily conserved and participate in NFκB signaling

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

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High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

Project description:Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.

2020-10-12 | GSE137348 | GEO

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