Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long non-coding RNAs have age-dependent diurnal expression that correlates with age-related changes in genome-wide facultative heterochromatin (RNA-Seq data set)

ABSTRACT: The circadian rhythm controls timed choreography of gene expression to maintain normal cell physiology and metabolism. The predominant regulatory mechanism of the circadian rhythm is a transcriptional negative feedback loop that facilitates, and is facilitated by, circadian-regulated facultative heterochromatin. The long-term consequence of disrupted diurnal rhythm, or mutations in core clock genes, cause accelerated aging and an increased incidence in age-related diseases. To understand chromatin dynamics underlying age-related changes to circadian transcription, we performed a combined RNA-seq and ChIP-seq at two diurnal time-points for three different age groups. Our analysis focused on uncovering relationships between long non-coding RNA (lncRNA) and age-related changes to heterochromatin. We determined that the core clock genes maintain rhythmic expression regardless of age, but circadian output, including numerous lncRNAs, changes dramatically with age. In addition, there is both diurnal and age-related changes in Histone H3 lysine 9 tri-methylation (H3K9me3) that correlate with the changes in gene expression. Collectively, the data suggest a model where age-related changes in diurnal gene expression occur, in part, due to age-related redistribution of rhythmic facultative heterochromatin. Alterations in heterochromatin appear to be mediated by changes in diurnal lncRNA expression creating an interlocked circadian-chromatin regulatory network that undergoes age-dependent metamorphosis.

ORGANISM(S): Danio rerio

PROVIDER: GSE109855 | GEO | 2018/01/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Long non-coding RNAs have age-dependent diurnal expression that correlates with age-related changes in genome-wide facultative heterochromatin (ChIP-Seq data set)

Project description:The circadian rhythm controls timed choreography of gene expression to maintain normal cell physiology and metabolism. The predominant regulatory mechanism of the circadian rhythm is a transcriptional negative feedback loop that facilitates, and is facilitated by, circadian-regulated facultative heterochromatin. The long-term consequence of disrupted diurnal rhythm, or mutations in core clock genes, cause accelerated aging and an increased incidence in age-related diseases. To understand chromatin dynamics underlying age-related changes to circadian transcription, we performed a combined RNA-seq and ChIP-seq at two diurnal time-points for three different age groups. Our analysis focused on uncovering relationships between long non-coding RNA (lncRNA) and age-related changes to heterochromatin. We determined that the core clock genes maintain rhythmic expression regardless of age, but circadian output, including numerous lncRNAs, changes dramatically with age. In addition, there is both diurnal and age-related changes in Histone H3 lysine 9 tri-methylation (H3K9me3) that correlate with the changes in gene expression. Collectively, the data suggest a model where age-related changes in diurnal gene expression occur, in part, due to age-related redistribution of rhythmic facultative heterochromatin. Alterations in heterochromatin appear to be mediated by changes in diurnal lncRNA expression creating an interlocked circadian-chromatin regulatory network that undergoes age-dependent metamorphosis.

2018-01-30 | GSE109854 | GEO

The glomerular circadian clock temporally regulates basement membrane dynamics and glucocorticoid response

Project description:Kidney physiology has diurnal variation and abnormal circadian rhythm is associated with kidney disease. However, it is not known whether glomeruli, the filtering units in the kidney, are under circadian control. We therefore investigated core circadian clock components in glomeruli, together with their rhythmic targets and modes of regulation.

2024-09-20 | E-MTAB-13457 | biostudies-arrayexpress

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [RNA-Seq]

Project description:Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same ?transcriptional factory? and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2021-12-23 | GSE143718 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [BiSulfite-seq]

Project description:Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same “transcriptional factory” and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2021-12-24 | GSE166613 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIP-Seq]

2021-12-24 | GSE143719 | GEO

Control of bladder peripheral clock and diurnal micturition pattern by glucocorticoids

Project description:Peripheral clocks function to regulate each organ and are synchronized though various molecular and behavioral signals. However, signals that entrain the bladder clock remain elusive. Here, we show that glucocorticoids are a key cue for the bladder clock in vitro and in vivo. A pBmal1-dLuc human urothelial cell line showed significant shifts in gene expression after cortisol treatment while, in vivo, rhythmic bladder clock gene expression was not influenced by bilateral-adrenalectomy (ADx) but shifted 4 hours forward by corticosterone administration at the inactive phase (CORT). Moreover, the bladder clock shifted 8-12 hours in ADx+CORT mice. These mice saw decreases in the diurnal rhythm of volume voided per micturition, while maintaining diurnal activity rhythm. These results indicate that the diurnal rhythm of glucocorticoid signaling is a zeitgeber that overcomes other entrainment factors for the bladder clock and coordinates the diurnal rhythm of volume voided per micturition. (145 words)

2022-06-16 | GSE205971 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [HiC]

Project description:Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. Target genes and associated cis-binding motifs of transcription factors enrichment points to the existence of subnuclear organization hub enriched around the TFs. RNAPII-associated chromatin interaction domains (CIDs) are under circadian control, and static CIDs with common node genes but changed connecting genes along the circadian cycle, reveal they may function as distinct clock components in the interconnected circuits between morning and evening. Core circadian clock genes related chromatin connectivity networks reveal a compact and highly connected chromatin architecture serving to coordinate gene expression in the morning, whereas a scattered, loose chromatin architecture coordinates PM gene expression. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal the distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

2022-12-23 | GSE221374 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [FAIRE-seq]

2021-12-23 | GSE143723 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [DAP-seq]

2021-12-24 | GSE143722 | GEO

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIA-PET]

2021-12-24 | GSE143721 | GEO