ZFIN ID: ZDB-FIG-160824-21
Huang et al., 2016 - The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbα and indirectly via Cebpb/(C/ebpβ) in zebrafish. Autophagy   12(8):1292-309 Full text @ Autophagy
ADDITIONAL FIGURES
EXPRESSION / LABELING:
Genes:
Fish:
Condition:
Anatomical Term:
Stage Range: Day 4 to Day 5
PHENOTYPE:
Fish:
Condition:
Observed In:
Stage Range: Day 4 to Day 5

Fig. 8

Transcriptome analysis and a model for circadian regulation of autophagy. (A) Numbers of differentially expressed genes (DEGs) in nr1d1 mutant fish at CT2 and CT12, revealed by transcriptome analysis. (B) Histogram of 523 DEGs in nr1d1 mutant fish shared between CT12 and CT2. Red colors represent upregulation, green colors downregulation. (C) List of genes with significant fold-changes, revealed by transcriptome analysis. The fold-changes were calculated by values of WT vs. nr1d1/rev-erbα. Genes with positive values were downregulated in the nr1d1 mutant, and those with negative values upregulated. (D) Upregulated genes atg10, ucp3, slc5a1, rbp4, wdr3, exosc3, gbgt1l4, fn1b and ddx46 and downregulated genes urod, gria3a and gsk3b, revealed by transcriptome analysis, are reconfirmed by independent qRT-PCR analysis. Three independent experiments were performed. Data represent mean ± s.d. (E) JC-1 staining assays. Mitochondria with low membrane potential are in green and mitochondria with high membrane potential in red. (F) Relative Red/Green ratio was quantified by ImageJ. Data represent mean±s.d. of the 3 independent experiments. **, P ≤ 0 .01. The Student t test was applied. (G) qRT-PCR analysis of ppargc1a in nr1d1 mutants under DD condition. The mRNA expression pattern was analysis by JTK-CYCLE method. ADJ.P for adjusted minimal P-values (*, P ≤ 0 .05), AMP for amplitude. Two-way ANOVA with the Tukey post hoc test was conducted (***, P ≤ 0 .001). (H) A model for circadian regulation of autophagy in zebrafish. Transcription factor cebpb is regulated by the Clock-Arntl/Bmal heterodimer and induces autophagy rhythms in zebrafish and mice, while Nr1d1 directly controls autophagy genes through RORE. Further, nutritional signals can affect both autophagy and circadian rhythms in zebrafish.

Gene Expression Details
Gene Antibody Fish Conditions Stage Anatomy Assay
atg10 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
ddx46 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
exosc3 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
fn1b nr1d1sus010/sus010 control Day 5 whole organism RTPCR
gbgt1l4 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
gria3a nr1d1sus010/sus010 control Day 5 whole organism RTPCR
gsk3ba nr1d1sus010/sus010 control Day 5 whole organism RTPCR
ppargc1a nr1d1sus010/sus010 constant dark Day 4 to Day 5 whole organism RTPCR
rbp4 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
slc5a1 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
ucp3 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
urod nr1d1sus010/sus010 control Day 5 whole organism RTPCR
wdr3 nr1d1sus010/sus010 control Day 5 whole organism RTPCR
Antibody Labeling Details No data available
Phenotype Details
Fish Conditions Stage Phenotype
nr1d1sus010/sus010 control Day 5 whole organism urod expression decreased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism gria3a expression decreased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism gsk3ba expression decreased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism gbgt1l4 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism exosc3 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism atg10 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism ddx46 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism ucp3 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism slc5a1 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism rbp4 expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism fn1b expression increased amount, abnormal
nr1d1sus010/sus010 control Day 5 whole organism wdr3 expression increased amount, abnormal
nr1d1sus010/sus010 constant dark Day 4 - Day 5 whole organism ppargc1a expression decreased amount, abnormal
Acknowledgments:
ZFIN wishes to thank the journal Autophagy for permission to reproduce figures from this article. Please note that this material may be protected by copyright. Full text @ Autophagy