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

ABSTRACT: 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.

ORGANISM(S): Oryza sativa

PROVIDER: GSE143722 | GEO | 2021/12/24

REPOSITORIES: GEO

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

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.

2021-12-24 | GSE143721 | GEO

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

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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

OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

Project description:The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.

2018-05-10 | GSE114188 | GEO

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.

Project description:Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using stable isotope labeling by amino acids quantitative MS. To measure the daily accumulation of proteins, we designed an SILAC MS experiment, in which total protein extracts were harvested from C57BL/6J mice every 3 h for 2 d (eight samples per day). Relative protein abundance in each of 16 samples was quantified against a common reference sample labeled using the SILAC method. The generated mass spectra allowed the identification of a total of 5,827 distinct proteins, of which 70% yielded relative measurements in at least 8 of 16 samples. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors

2014-08-08 | PXD001211 | Pride

Diurnal expression data from developing barley caryopses

Project description:Caryopses of barley (Hordeum vulgare), like all other cereal seeds, are complex sink organs optimized for storage starch accumulation and embryo development. Their development from early stages after pollination to late stages of seed ripening has been studied in great detail. However, information on the caryopsesâ?? diurnal adaptation to changes in light, temperature and alterations in phloem-supplied carbon and nitrogen remained unknown. In this study, we applied the 22K Barley1 GeneChip microarray to investigate diurnal gene regulation events of barley caryopses at 11 to 12 days post anthesis. Developing barley caryopses were harvested at different time-points of a day (at 7:00 AM, 2:00 PM, 5:00 PM and 8:00 PM) including dark samples (6:00 AM and 10:00 PM). Pooled caryopses (form 3 Plants) from the respective time points were used for RNA extraction and hybridization on Affymetrix microarrays (Barley1 GeneChip; GEO accsession GPL1340). Biological replicates were performed.

2010-04-07 | E-GEOD-20034 | biostudies-arrayexpress

Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex

Project description:Rhythmic oscillations of physiological processes depend on integrating the circadian clock and diurnal environment. DNA methylation is epigenetically responsive to daily rhythms, as a subset of CpG dinucleotides in brain exhibit diurnal rhythmic methylation. A major genetic effect on rhythmic methylation was identified in a mouse Snord116 deletion model of the imprinted disorder Prader-Willi syndrome (PWS). > 23,000 diurnally rhythmic CpGs were identified in wild-type cortex, with nearly all lost or phase-shifted in PWS. Circadian dysregulation of a second imprinted Snord cluster at the Temple/Kagami-Ogata syndrome locus was observed at the level of methylation, transcription, and chromatin, providing mechanistic evidence of cross-talk. Genes identified by diurnal epigenetic changes in PWS mice overlapped rhythmic and PWS-specific genes in human brain and were enriched for PWS-relevant phenotypes and pathways. These results support the proposed evolutionary relationship between imprinting and sleep, and suggest possible chronotherapy in the treatment of PWS and related disorders.

2018-02-27 | GSE103249 | GEO

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