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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 03, 2020 |
| Title |
Temporal profiles of hepatic gene expression in PAR bZip triple knockout mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. Mouse knockout models of different parts of the circadian clock network (Bmal1, Cry1/2, and Hlf/Dbp/Tef) exposed to controlled feeding regimens (ad libitum, night restricted feeding) were generated and analyzed for their temporal hepatic transcriptome. A genetical ablation of core loop elements altered feeding patterns that were restored by night restricted feeding. Mainly genes with a high amplitude were driven by the circadian clock but natural feeding patterns equally contributed to rhythmic gene expression with lower amplitude. We observed that Bmal1 and Cry1/2 KOs differed in rhythmic gene expression and identified differences in mean expression levels as a predictor for rhythmic gene expression. In Hlf/Dbp/Tef KO, mRNA levels of Hlf/Dbp/Tef target genes were decreased, albeit rhythmicity was overall preserved potentially due to the activity of the D-Box binding repressor NFIL3. Genes that lost rhythmicity in Hlf/Dbp/Tef KOs were identified to be no direct targets of PARbZip factors and presumably lost rhythmicity due to indirect effects. Collectively, our findings provide unprecedent insights into the diurnal transcriptome in mouse liver and defines the contribution of subloops of the circadian clock network and natural feeding cycles. The developed algorithm and a webapp to browse the outcomes of the study are publicly available to serve as a resource for the scientific community.
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| Overall design |
RNA-Seq from mRNA of mouse liver across the course of a day. Time-series include mRNA profiles of PARbZip proficient (Hlf+/+/Dbp+/+/Tef+/+) and deficient (Hlf-/-/Dbp-/-/Tef-/-) mice under an ad libitum feeding regimen.
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| Contributor(s) |
Weger BD, Gobet C, Martin E, Gachon F, Naef F |
| Citation(s) |
33452134 |
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| Submission date |
Aug 15, 2019 |
| Last update date |
Jul 12, 2022 |
| Contact name |
Benjamin D Weger |
| Organization name |
EPFL
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| Department |
SV
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| Lab |
Naef Lab
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| Street address |
Station 15
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| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
76344 |
| Country |
Germany |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (24)
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| GSM4036990 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT04 (S31) |
| GSM4036991 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT04 (S13) |
| GSM4036992 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT08 (S32) |
| GSM4036993 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT08 (S14) |
| GSM4036994 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT12 (S33) |
| GSM4036995 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT12 (S15) |
| GSM4036996 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT16 (S34) |
| GSM4036997 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT16 (S16) |
| GSM4036998 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT20 (S35) |
| GSM4036999 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT20 (S17) |
| GSM4037000 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT24 (S36) |
| GSM4037001 |
Liver, Hlf-/-/Dbp-/-/Tef-/-_AL_ZT24 (S18) |
| GSM4037002 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT04 (S25) |
| GSM4037003 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT04 (S1) |
| GSM4037004 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT08 (S26) |
| GSM4037005 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT08 (S2) |
| GSM4037006 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT12 (S27) |
| GSM4037007 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT12 (S3) |
| GSM4037008 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT16 (S28) |
| GSM4037009 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT16 (S4) |
| GSM4037010 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT20 (S29) |
| GSM4037011 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT20 (S5) |
| GSM4037012 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT24 (S30) |
| GSM4037013 |
Liver, Hlf+/+/Dbp+/+/Tef+/+_AL_ZT24 (S6) |
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| This SubSeries is part of SuperSeries: |
| GSE149698 |
Systematic analysis of differential rhythmic gene expression mediated by the circadian clock and feeding rhythms in mouse liver |
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| Relations |
| BioProject |
PRJNA560390 |
| SRA |
SRP218451 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135875_countData_tripleKO.txt.gz |
976.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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