Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Circadian temporal profiling of MMH-D3 hepatocytes


ABSTRACT: The circadian clock generates daily rhythms in mammalian liver processes, such as glucose and lipid homeostasis, xenobiotic metabolism, and regeneration. The mechanisms governing these rhythms are not well understood, particularly the distinct contributions of the cell-autonomous clock and central pacemaker to rhythmic liver physiology. Through microarray expression profiling in MMH-D3 hepatocytes, we identified over 1,000 transcripts that exhibit circadian oscillations, demonstrating that many rhythms can be driven by the cell-autonomous clock and that MMH-D3 is a valid circadian model system. The genes represented by these circadian transcripts displayed both co-phasic and anti-phasic organization within a protein-protein interaction network, suggesting the existence of competition for binding sites or partners by genes of disparate transcriptional phases. Multiple pathways displayed enrichment in MMH-D3 circadian transcripts, including the polyamine synthesis module of the glutathione metabolic pathway. The polyamine synthesis module, which is highly associated with cell proliferation and whose products are required for initiation of liver regeneration, includes enzymes whose transcripts exhibit circadian oscillations, such as ornithine decarboxylase (Odc1) and spermidine synthase (Srm). Metabolic profiling revealed that the enzymatic product of SRM, spermidine, cycles as well. Thus, the cell-autonomous hepatocyte clock can drive a significant amount of transcriptional rhythms and orchestrate physiologically relevant modules such as polyamine synthesis. Samples were collected every 2 hours for a duration of 46 hours from differentiated MMH-D3 hepatocytes synchronized via serum shock. Cells were synchronized by serum shock and incubated for 12 hours, and then samples were collected every 2 hours from 12 hours post-serum shock to 58 hours post-serum shock, for a total of 24 samples.

ORGANISM(S): Mus musculus

SUBMITTER: Susanna Wang 

PROVIDER: E-GEOD-31049 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis.

Atwood Ann A   DeConde Robert R   Wang Susanna S SS   Mockler Todd C TC   Sabir Jamal S M JS   Ideker Trey T   Kay Steve A SA  

Proceedings of the National Academy of Sciences of the United States of America 20111031 45


The circadian clock generates daily rhythms in mammalian liver processes, such as glucose and lipid homeostasis, xenobiotic metabolism, and regeneration. The mechanisms governing these rhythms are not well understood, particularly the distinct contributions of the cell-autonomous clock and central pacemaker to rhythmic liver physiology. Through microarray expression profiling in Met murine hepatocytes (MMH)-D3, we identified over 1,000 transcripts that exhibit circadian oscillations, demonstrati  ...[more]

Similar Datasets

2011-11-03 | GSE31049 | GEO
2017-04-05 | MTBLS292 | MetaboLights
2022-04-22 | PXD025179 | Pride
2015-11-04 | E-GEOD-69853 | biostudies-arrayexpress
2013-08-30 | GSE34442 | GEO
2013-08-30 | E-GEOD-34443 | biostudies-arrayexpress
2013-08-30 | E-GEOD-34442 | biostudies-arrayexpress
2015-11-04 | GSE69853 | GEO
2013-08-30 | GSE34443 | GEO
2020-07-30 | GSE143526 | GEO