Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster - PubMed (original) (raw)

Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster

Yiing Lin et al. Proc Natl Acad Sci U S A. 2002.

Abstract

We measured daily gene expression in heads of control and period mutant Drosophila by using oligonucleotide microarrays. In control flies, 72 genes showed diurnal rhythms in light-dark cycles; 22 of these also oscillated in free-running conditions. The period gene significantly influenced the expression levels of over 600 nonoscillating transcripts. Expression levels of several hundred genes also differed significantly between control flies kept in light-dark versus constant darkness but differed minimally between per(01) flies kept in the same two conditions. Thus, the period-dependent circadian clock regulates only a limited set of rhythmically expressed transcripts. Unexpectedly, period regulates basal and light-regulated gene expression to a very broad extent.

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Figures

Figure 1

(A) Overall experimental design. Numbers in boxes refer to hours of collection for control (y w) and_per_01 flies; gold numbers indicate times of lights on. (B) Venn-diagram summary of results from control flies. Based on two cycles, 377 circadianly expressed genes were identified in LD, and 447 were identified in DD. Based on three cycles in LD, a subset of 72 genes were identified as diurnally expressed. Twenty-two of these genes were found also to be rhythmic in DD flies.

Figure 2

(A) Phase-ordered expression patterns of the 72 genes identified as diurnally expressed in control flies. The positions of five known rhythmic genes of the circadian system are denoted on the_Left_. Tick marks show the positions of those diurnally expressed genes also found to be rhythmic in control flies kept in DD (B), _per_01 flies kept in LD 12:12 (C), and _per_01 flies kept in DD (D).

Figure 3

Representative circadian expression patterns found in control flies under three cycles in LD (Right) and two cycles in DD (Left).

Figure 4

Basal gene expression is modulated by period and light. “Heat-plot” rank profiles of expression levels of genes exhibiting significant change in basal expression differences between experimental conditions (P < 0.0001, Mann–Whitney_U_ test) are shown. From left to right, entire cycles (6 or 8 time points, in LD or DD) are grouped. (A) Expression levels of 650 genes from DD conditions on each of a total of 32 microarrays (y w, 20;_per_01, 12). (Upper) Those 330 genes with expression levels significantly higher in control flies (_y w_-Hi). (Lower) Those 320 genes with expression levels significantly higher in per_01(per_-Hi). Pseudocolor indicates relative rank order in expression (yellow, highest; blue, lowest). (B) Comparison of control flies kept in LD versus DD. Those 178 genes that exhibit significant differences in expression between LD (17 measurements) and DD (20 measurements) are shown. LD-Hi, higher average expression in LD; DD-Hi, higher average expression in DD. (C) Comparison of_per_01 flies between LD versus DD (12 measurements each). Other markings are as described for_B. (B and C) Data for the same 178 genes, displayed in register. (D) Representative expression levels of individual genes from_B and C, as denoted by numbers in parenthesis. Microarray intensity values of control LD (17 points), control DD (20 points), _per_01flies in LD (12 points), and_per_01 flies in DD (12 points) conditions are shown as means (+SE).

Figure 5

Confirming the influence of period on basal gene expression. (A) Reverse transcription–PCR was performed on total RNA extracted from control and_per_01 flies pooled from multiple time points in DD. RP49, control; MW, molecular weight markers. (B) Reverse transcription–PCR performed on total RNA from pooled time points of other clock mutant flies (tim, Clk, and cyc) kept in DD conditions.

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Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster - PubMed (original) (raw)