TY  - GEN
A1  - Stefanski, Julia
AV  - public
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/15475/
N2  - The circadian clock is a tightly regulated mechanism that has evolved in most organisms to enable them to anticipate daily reoccurring changes in the environment. Expression
analysis in mouse suggests that about 10% of the mammalian transcriptome may be under circadian control, however the overlap between different tissues is very small [1]. Mechanisms determining this cell type specificity of clock controlled genes are not yet understood. The human osteosarcoma cell line U2OS expresses a functional circadian clock and has been used in many circadian studies [2, 3, 4], yet, except for components of the core clock machinery, no genes have been found to be rhythmically
expressed in this cell line in a microarray analysis [3] whereas about 3000 rhythmic transcripts have been identified in mouse liver [3, 5, 6]. 

This work shows ChIP-sequencing data of BMAL1, CLOCK, and CRY1 that indicates that the circadian transcription regulators bind in sequence-specific manner to several thousand sites in the genome of U2OS, comparable to the number found in mouse liver [5]. However, time course microarray experiments carried out to verify functionality of these sites, found only 58 rhythmic genes harboring a binding site, suggesting a high amount of opportunistic binding that cannot be linked to transcription. Even most genes with high-scoring binding sites in their promoter were apparently arrhythmic. U2OS cell lines stably expressing luciferase reporter constructs under control of representative promoters were generated and revealed that BMAL1 and CLOCK functionally act on these, but rhythmic expression appears to be superimposed by a high basal transcription. The data indicates that high amplitude transcription rhythms are masked by constitutive transcription that overwrites the rhythmic contribution of the circadian clock, resulting in apparent arrhythmicity due to low amplitude oscillations. This work suggests that the cell-type specific circadian transcriptome is not determined on the level of BMAL1-CLOCK binding and rhythmic activation of transcription by these circadian regulators, but rather by the cell-type specific ratio of circadian versus genespecific or general transcription regulators.

Bibliography:
[1] Satchidananda Panda, Marina P. Antoch, Brooke H. Miller, Andrew I. Su, Andrew B. Schook, Marty Straume, Peter G. Schultz, Steve A. Kay, Joseph S. Takahashi, and John B. Hogenesch. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell, 109(3):307?20, May 2002.
[2] Christopher Vollmers, Satchidananda Panda, and Luciano DiTacchio. A high-throughput assay for siRNA-based circadian screens in human U2OS cells. PloS ONE, 3(10):e3457, January 2008.
[3] Michael E. Hughes, Luciano DiTacchio, Kevin R. Hayes, Christopher Vollmers, S. Pulivarthy, Julie E. Baggs, Satchidananda Panda, and John B. Hogenesch. Harmonics of circadian gene transcription in mammals. PLoS Genetics, 5(4):e1000442, April 2009.
[4] Bert Maier, Sabrina Wendt, Jens T. Vanselow, Thomas Wallach, Silke Reischl, Stefanie Oehmke, Andreas Schlosser, and Achim Kramer. A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock. Genes & Development, 23(6):708?18, March 2009.
[5] Guillaume Rey, François Cesbron, Jacques Rougemont, Hans Reinke, Michael Brunner, and Felix Naef. Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver. PLoS Biology, 9(2):e1000595, February 2011.
[6] Nobuya Koike, Seung-Hee Yoo, Hung-Chung Huang, Vivek Kumar, Choogon Lee, Tae-Kyung Kim, and Joseph S. Takahashi. Transcriptional Architecture and Chromatin Landscape of the
Core Circadian Clock in Mammals. Science, 338(6105):349?54, August 2012.

ID  - heidok15475
TI  - Binding of Circadian Transcription Regulators and Rhythmic Gene Expression in Human Cells
Y1  - 2013///
ER  -