Dataset Information

Characterization of Transcriptionally Active Clock Complexes in Time and Space Using Quantitative Proteomics

ABSTRACT: Circadian gene expression in mammals relies on the oscillatory activity of the BMAL1/CLOCK transcription factor complex, rhythmically binds to DNA. Despite the conserved presence of BMAL1/CLOCK in all tissues, circadian transcriptional outputs minimally overlap between tissues. Revision for the project PXD062751

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Lung, Liver, Kidney

SUBMITTER: Fatih Aygenli

LAB HEAD: Maria Robles

PROVIDER: PXD077567 | Pride | 2026-06-24

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20260305_SA_FA_ChIP_Liv10_IgG_1.raw	Raw
	20260305_SA_FA_ChIP_Liv10_IgG_2.raw	Raw
	20260305_SA_FA_ChIP_Liv10_IgG_3.raw	Raw
	20260305_SA_FA_ChIP_Liv10_IgG_4.raw	Raw
	20260305_SA_FA_ChIP_Liv10_PROX1_1.raw	Raw

Items per page:

1 - 5 of 70

Similar Datasets

Project description:Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control. Based predominantly on the transcription feedback loops important for core circadian timekeeping, it is commonly assumed that this widespread mRNA cycling reflects circadian transcriptional cycling. To address this issue, we directly measured dynamic changes in mouse liver transcription using Nascent-Seq. Many genes are rhythmically transcribed over the 24h day, which include precursors of several non-coding RNAs as well as the expected set of core clock genes. Surprisingly however, nascent RNA rhythms overlap poorly with mRNA abundance rhythms assayed by RNA-seq. This is because most mouse liver genes with rhythmic mRNA expression manifest poor transcriptional rhythms, indicating a prominent role of post-transcriptional regulation in setting mRNA cycling amplitude. To gain further insight into circadian transcriptional regulation, we also characterized the rhythmic transcription of liver genes targeted by the transcription factors CLOCK and BMAL1; they directly target other core clock genes and sit at the top of the molecular circadian clock hierarchy in mammals. CLK:BMAL1 rhythmically bind at the same discrete phase of the circadian cycle to all target genes, which not surprisingly have a much higher percentage of rhythmic transcription than the genome as a whole. However, there is a surprisingly heterogeneous set of cycling transcription phases of direct target genes, which even include core clock genes. This indicates a disconnect between rhythmic DNA binding and the peak of transcription, which is likely due to other transcription factors that collaborate with CLK:BMAL1. In summary, the application of Nascent-Seq to a mammalian tissue provides surprising insights into the rhythmic control of gene expression and should have broad applications beyond the analysis of circadian rhythms. CLK and BMAL1 DNA binding profile in the mouse liver at ZT8, sequenced along an Input sample using GAII (ChIP-Seq) Supplementary file ChIPSeq_Mouse_Liver_Processed_data_Table1.txt represents annotated CLK and BMAL1 peaks.

Dataset Information

Characterization of Transcriptionally Active Clock Complexes in Time and Space Using Quantitative Proteomics

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets