CircaDB: a database of mammalian circadian gene expression profiles

Pizarro, Angel; Hayer, Katharina E.; Lahens, Nicholas F.; Hogenesch, John B.

doi:10.1093/nar/gks1161

Cited by 288 publications

(316 citation statements)

References 34 publications

Supporting

Mentioning

288

Contrasting

Order By: Relevance

“…CircaDB, a database that compiles published transcriptome data of circadian time courses in different tissues and cellular systems, is a valuable resource for this purpose (49). We found that 176 out of 230 cyclically expressed genes in our data set also oscillate in at least one other cell or tissue type (76%) (see Fig.…”

Section: Identification Of Genes With Circadian Expression In Nih 3t3mentioning

confidence: 86%

“…However, if any of these factors plays a general role in the regulation of circadian rhythm, it should be cyclically expressed in most tissues. We therefore analyzed which of the 70 putative transcriptional regulators were also cyclically expressed in other tissues, again using the data sets provided by CircaDB (49). Indeed, we found all core clock components and well-established players in circadian rhythm to be cyclically expressed in nearly all investigated tissues ( For a more extensive characterization, we selected 2 candidates out of these 70 factors that had not been studied in detail with regard to circadian rhythm.…”

Section: Identification Of Genes With Circadian Expression In Nih 3t3mentioning

confidence: 99%

“…Tissue data were obtained from reference 7. Cyclical genes of these and other published tissue data sets, as well as cell line data sets, were obtained from CircaDB database (http://bioinf.itmat .upenn.edu/circa/) (49).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Identifying Novel Transcriptional Regulators with Circadian Expression

Schick

Becker

Thakurela

et al. 2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms.O rganisms adapt to the 24-h day-night cycle, which leads to oscillations in physiology and behavior. This is coordinated by an intrinsic molecular clock originating from the interplay of transcriptional-translational feedback loops (1). In mammals, the core loop consists of the transcriptional activators Clock and Bmal1 and the repressors Period (Per) and cryptochrome (Cry). In a second loop, retinoid-related orphan receptors (ROR) activate transcription while Rev-Erb factors (Nr1d1 and Nr1d2) repress transcription (2). These core clock components also regulate the expression of additional genes, possibly resulting in an oscillating transcription of these socalled clock-controlled genes and finally in the circadian phenotype.Recent genome-wide studies of circadian time courses in various mouse tissues indicated that each tissue expresses its own particular set of cyclical genes, which only partly overlap each other (3-7). Nearly half of all genes in the mouse genome show circadian oscillation in at least one tissue (7). The basic mechanisms causing transcriptional rhythms of the core clock components are similar among all tissues, but how tissue-specific circadian output is achieved remains unknown, although several mechanisms have been proposed (2). Among these are the use of tissue-specific transcription factors (TFs) or coregulators (6,8) and different temporal control of RNA polymerase II recruitment (9, 10), as well as defined rhythms in histone modifications accompanied by differential gene regulation (9-19).To gain further insight into the transcriptional control of the circadian rhythm, we aimed to identify novel factors, particularly transcription factors and epigenetic regula...

show abstract

Section: Identification Of Genes With Circadian Expression In Nih 3t3mentioning

confidence: 86%

Section: Identification Of Genes With Circadian Expression In Nih 3t3mentioning

confidence: 99%

See 1 more Smart Citation

Identifying Novel Transcriptional Regulators with Circadian Expression

Schick

Becker

Thakurela

et al. 2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…Another study to determine changes using samples collected every 2 hr for a period of 48 hours investigated variability in over 2300 genes [19], distinguishing between MyoD1 and Bmal1 [20]. However to date, variability in the Per2 gene induced by leucine has not been reported.…”

Section: Change In Per2 Gene Expressionmentioning

confidence: 99%

Effect of leucine uptake on hepatic and skeletal muscle gene expression in rats: a microarray analysis

Cheon

2015

J. Exerc. Nutr, Biochem.

View full text Add to dashboard Cite

Wookwang Cheon. Effect of leucine uptake on hepatic and skeletal muscle gene expression in rats: a microarray analysis. JENB., Vol. 19, No. 2, pp.139-146, 2015 [Purpose] This study was performed to explore the physiological functions of leucine by exploring genes with leucine-dependent variability using DNA microarray.[Methods] Sprague-Dawley rats (n = 20) were separated into a HPD (30% High Protein Diet, n = 10) group and a NPD (0% Non Protein Diet, n = 10) group and fed a protein diet for 2 weeks. At the end of the 2-week period, the rats were fasted for 12-16 hours, further separated into subgroups within the HPD (Saline, n = 5, Leucine, n = 5) and NPD (Saline, n = 5, Leucine, n = 5) groups and administered with a leucine solution. The liver and muscles were harvested after 2 hours for RNA extraction. RNA purification from the isolated muscles and target gene identification using DNA chip were performed. The target gene was determined based on the results of the DNA chip experiment, and mRNA expression of the target gene was analyzed using Real-Time PCR.[Results] In the skeletal muscle, 27 genes were upregulated while 52 genes were down regulated after leucine administration in the NPD group. In the liver, 160 genes were up-regulated while 126 were down-regulated. The per2 gene was one of the genes with leucine-dependent induction in muscles and liver.[Conclusion] This study was performed to explore the physiological functions of leucine, however, a large number of genes showed variability. Therefore, it was difficult to definitively identify the genes linked with a particular physiological function. Various nutritional effects of leucine were observed. High variability in cytokines, receptors, and various membrane proteins were observed, which suggests that leucine functions as more than a nutrient. The interpretation may depend on investigators' perspectives, therefore, discussion with relevant experts and the BCAA (Branched-Chain Amino Acids) society may be needed for effective utilization of this data.

show abstract

“…Dr. Schibler's group published an important article in 1990 describing their discovery of a new transcription factor, D-site albumin-binding protein (DBP) (9). DBP is a master regulator of metabolic pathways in a number of tissues, including the kidney, where it exhibits dramatic circadian oscillations (11). This early work was led by Dr. Mueller, a "night owl," who performed his animal experiments late in the day (9).…”

mentioning

confidence: 99%

Taking into account circadian rhythm when conducting experiments on animals

Gumz

2016

American Journal of Physiology-Renal Physiology

View full text Add to dashboard Cite

Gumz ML. Taking into account circadian rhythm when conducting experiments on animals. Am J Physiol Renal Physiol 310: F454-F455, 2016. First published December 30, 2015 doi:10.1152/ajprenal.00549.2015.-Do your kidneys know what time it is? Mounting evidence from human studies and animal models strongly suggests that the answer to this question is yes. The time has come to start reporting the time of day at which renal physiology studies are performed. circadian rhythm; physiology; reproducibility; rigor DO YOUR KIDNEYS KNOW what time it is? Mounting evidence from human studies and animal models strongly suggests that the answer to this question is yes. Human studies dating back several decades have consistently demonstrated time-of-daydependent changes in glomerular filtration rate, renal electrolyte excretion, renal blood flow, and circulating levels of several hormones that act directly on the kidney, including aldosterone ( Fig. 1) (for review see Refs. 14 and 19). A new report suggests that these rhythms are evident in children and teenagers, in addition to adults (6). Animal data from several laboratories have established a role for the molecular clock in the regulation of blood pressure, renal electrolyte handling, fetal kidney development, glomerular filtration rate, and renal metabolism (reviewed in Refs. 2 and 13). Importantly, unbiased global transcriptomic studies also support a role for circadian rhythms in renal function; the kidney is second only to the liver in terms of the absolute number of mRNAs that oscillate with a significant circadian rhythm (20). Collectively, these studies support the concept that time is an important aspect of renal function. A logical consequence of this finding is that researchers should consider the time of day in experimental design and, subsequently, should report the time of day at which experiments are conducted.The timing of physiological function is controlled by the circadian clock. On a basic level, the core molecular clock comprises several transcription factors, including BMAL1, CLOCK, PER, and CRY, that regulate gene expression [for details on this mechanism, see an excellent review (10)]. These clock proteins are expressed in nearly every cell type and tissue that has been tested, and this mechanism underlying circadian rhythms is conserved from bread mold to humans (4). The term "circadian" comes from the Latin circa dia, meaning "about a day." Franz Halberg first coined this term in the 1950s to describe rhythmic physiological functions exhibiting a period of ϳ24 h (5). Together with Frederic Bartter and their colleagues, Halberg established that adrenocortical hormones, including cortisol and aldosterone, were produced with a circadian pattern (3, 7). Importantly, they demonstrated that these rhythms persisted, even under constant conditions, the defining characteristic for a process to be considered truly "circadian."The time of day at which physiological parameters are measured can affect the results of an experiment. One of the best examples of this...

show abstract

CircaDB: a database of mammalian circadian gene expression profiles

Cited by 288 publications

References 34 publications

Identifying Novel Transcriptional Regulators with Circadian Expression

Identifying Novel Transcriptional Regulators with Circadian Expression

Effect of leucine uptake on hepatic and skeletal muscle gene expression in rats: a microarray analysis

Taking into account circadian rhythm when conducting experiments on animals

Contact Info

Product

Resources

About