Circadian Changes in the Pineal and Retina Transcriptomes of the Chicken as Revealed by RNA Sequencing

Here pineal gland and retina transcriptomes of chicken have been characterized using RNA-seq, with the goals of building a near complete data base of the thousands of transcripts in these tissues and promoting a better understanding of the genetic basis of their unique and overlapping functions. This effort has extended previous gene profiling efforts by the identification of thousands of transcripts not previously reported to exist in these tissues, hundreds of which exhibit daily rhythms in abundance. Gene expression appears to occur in four waves, peaking at distinct times during the 24 hour period. In this study animals were kept in constant darkness with the intention of identifying changes that occur as a function of the internal clock, not as a function of environmental lighting. Accordingly, the rhythmic changes identified are likely to be truly circadian in nature and to be either part of the biological clock or to be clock controlled genes. Ontological analysis of the tissue enriched transcripts and of the rhythmically expressed transcript revealed that many are linked to visual transduction, circadian clock function and melatonin synthesis. The findings of this report will be of significant value in future studies of the genetic basis of pineal and retinal function. Overall design: Three pineal glands or single retinas were collected in triplicate at circadian time 0, 4, 8, 12, 16, 20. Rhythmically expressed transcript were identified through RNA-seq based on these samples.

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