Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway

Abstract

*Background* It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. *Results* We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different regions within the 3’ end of the last exon. We demonstrate that in murine brown adipose tissue two downstream 3’ probe sets experience circadian baseline oscillation in counter-phase to the upstream probe set. Such differences in expression patterns are a telltale sign of alternative splicing within the last exon of SOCS3. In contrast, all three probe sets oscillated in a common phase in murine liver and white adipose tissue. This suggests that the regulation of SOCS3 expression in brown fat is tissue specific. Another component of the signaling pathway, Janus kinase (JAK), is directly regulated by SOCS and has alternative transcript probe sets oscillating in counter-phase in a white adipose tissue specific manner. *Conclusion*We hypothesize that differential oscillation of alternative transcripts may provide a mechanism to maintain steady levels of expression in spite of circadian baseline variation.

Regulation of Clock-Controlled Genes in Mammals

“…The REV-ERBα matrix is not included in the TRANSFAC database (version 10.4), nevertheless its closely related nuclear receptor RORα is overrepresented. Moreover, the recently described additional regulators HSF [10] , STAT3 [11] , SP1 [12] as well as PPARγ, GR, ERRα, RXR, TR, SREBP-1 [13] belong to our predictions. Tables 1 and 2 represent about 22% of all vertebrate binding motifs in TRANSFAC (version 10.4), and the fact that essentially all known circadian regulators are in the tables strongly supports our bioinformatic approach.…”

“…Several other E-box-like motifs such as c-MYC∶MAX, USF, STRA13 (DEC1), MyoD or SREBP-1 are overrepresented as well. Additionally, the recently discovered circadian regulators STAT3 [11] , HSF1 [10] , SP1 [12] and nuclear factors (LXR/RXR, GR, ERRα, PPARγ, HNF-4, T3R) [13] , [28] occur in several lists of overrepresented sites. These examples support the conclusion that our bioinformatic analysis identifies known clock-related regulatory elements as overrepresented in promoter regions of CCGs.…”

“…Indeed, recent experiments show that e.g. heat-shock factor HSF1 [10] , the transcription activator STAT3 [11] , the transcription factor SP1 [12] or hormone receptors such as the glucocorticoid receptor (GR), thyroid receptor (TR) or estrogen receptor (ER) [13] , [14] are involved in circadian gene regulation.…”

Alternative splicing at the right time

“…there are several examples of alternative spliced genes which are involved in the modulation of circadian outputs. Among them, we mentioned the case of Suppressor of Cytokine Signaling 3 (SoCS3) in M. musculus, 47 Pigment Dispersing factor (PDf) in C. elegans, 48 and Glycine-Rich RNA-Binding Protein 7, 49 and Rubisco Activase 30,50 sequence. Notably, this effect could be comparable to the role of temperature in regulating the AS of D. melanogaster per gene (dmpi8), which affects recognition of suboptimal 5'SS and 3'SS.…”