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Series GSE256533 Query DataSets for GSE256533
Status Public on Mar 05, 2024
Title Clock-dependent chromatin accessibility rhythms regulate circadian transcription
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. We observed significant oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
 
Overall design Transposase-accessible chromatin sequencing (ATAC-seq) of Drosophila melanogaster clock neurons. Cells were isolated by fluorescence-activated cell sorting (FACS) using Clk-GAL4>UAS-GFP-NLS line developed in the lab. GFP-positive and DAPI-negative cells were sorted to be clock neurons and each sample consist 1~2 thousand cells. GFP-negative and DAPI-negative cells were sorted to be non-clock cell controls.
Web link https://pubmed.ncbi.nlm.nih.gov/38805552/
 
Contributor(s) Yuan Y, Brovkina M, Clowney EJ, Yadlapalli S
Citation(s) 38805552
Submission date Feb 24, 2024
Last update date Jun 04, 2024
Contact name Swathi Yadlapalli
E-mail(s) swathi@umich.edu
Organization name University of Michigan
Street address 109 Zina Pitcher Pl
City Ann Arbor
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
Samples (33)
GSM8105694 adult brain, wildtype ZT0 repeat-1
GSM8105695 adult brain, wildtype ZT12 repeat-1
GSM8105696 adult brain, wildtype ZT control-1
Relations
BioProject PRJNA1079999

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Supplementary file Size Download File type/resource
GSE256533_RAW.tar 162.9 Mb (http)(custom) TAR (of BW, NARROWPEAK)
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Raw data are available in SRA
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