The Poly(C) Motif in the Proximal Promoter Region of the D Site-Binding Protein Gene (Dbp) Drives Its High-Amplitude Oscillation

REFERENCES

• Yang S, Van Dongen HPA, Wang K, Berrettini W, Bućan M. 2009. Assessment of circadian function in fibroblasts of patients with bipolar disorder. Mol Psychiatry 14:143–155. https://doi.org/10.1038/mp.2008.10.
   PubMed Web of Science ®Google Scholar
• Luo WY, Chen WF, Yue ZF, Chen DC, Sowcik M, Sehgal A, Zheng XZ. 2012. Old flies have a robust central oscillator but weaker behavioral rhythms that can be improved by genetic and environmental manipulations. Aging Cell 11:428–438. https://doi.org/10.1111/j.1474-9726.2012.00800.x.
   PubMed Web of Science ®Google Scholar
• Gloston GF, Yoo SH, Chen ZJ. 2017. Clock-enhancing small molecules and potential applications in chronic diseases and aging. Front Neurol 8:100. https://doi.org/10.3389/fneur.2017.00100.
   PubMed Web of Science ®Google Scholar
• Chen CY, Logan RW, Ma T, Lewis DA, Tseng GC, Sibille E, McClung CA. 2016. Effects of aging on circadian patterns of gene expression in the human prefrontal cortex. Proc Natl Acad Sci U S A 113:206–211. https://doi.org/10.1073/pnas.1508249112.
   PubMed Web of Science ®Google Scholar
• Wuarin J, Falvey E, Lavery D, Talbot D, Schmidt E, Ossipow V, Fonjallaz P, Schibler U. 1992. The role of the transcriptional activator protein DBP in circadian liver gene expression. J Cell Sci Suppl 16:123–127.
   PubMedGoogle Scholar
• Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M, Hashimoto S. 2005. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187–192. https://doi.org/10.1038/ng1504.
   PubMed Web of Science ®Google Scholar
• Mitsui S, Yamaguchi S, Matsuo T, Ishida Y, Okamura H. 2001. Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev 15:995–1006. https://doi.org/10.1101/gad.873501.
   PubMed Web of Science ®Google Scholar
• Falvey E, Marcacci L, Schibler U. 1996. DNA-binding specificity of PAR and C/EBP leucine zipper proteins: a single amino acid substitution in the C/EBP DNA-binding domain confers PAR-like specificity to C/EBP. Biol Chem 377:797–809.
   PubMed Web of Science ®Google Scholar
• Kumaki Y, Ukai-Tadenuma M, Uno KD, Nishio J, Masumoto KH, Nagano M, Komori T, Shigeyoshi Y, Hogenesch JB, Ueda HR. 2008. Analysis and synthesis of high-amplitude cis-elements in the mammalian circadian clock. Proc Natl Acad Sci U S A 105:14946–14951. https://doi.org/10.1073/pnas.0802636105.
   PubMed Web of Science ®Google Scholar
• Bozek K, Relogio A, Kielbasa SM, Heine M, Dame C, A K, Herzel H. 2009. Regulation of clock-controlled genes in mammals. PLoS One 4:e4882. https://doi.org/10.1371/journal.pone.0004882.
   PubMed Web of Science ®Google Scholar
• Ripperger JA, Shearman LP, Reppert SM, Schibler U. 2000. CLOCK, an essential pacemaker component, controls expression of the circadian transcription factor DBP. Genes Dev 14:679–689.
   PubMed Web of Science ®Google Scholar
• Ripperger JA, Schibler U. 2006. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet 38:369–374. https://doi.org/10.1038/ng1738.
   PubMed Web of Science ®Google Scholar
• Stratmann M, Suter DM, Molina N, Naef F, Schibler U. 2012. Circadian Dbp transcription relies on highly dynamic BMAL1-CLOCK interaction with E boxes and requires the proteasome. Mol Cell 48:277–287. https://doi.org/10.1016/j.molcel.2012.08.012.
   PubMed Web of Science ®Google Scholar
• Stratmann M, Stadler F, Tamanini F, van der Horst GT, Ripperger JA. 2010. Flexible phase adjustment of circadian albumin D site-binding protein (DBP) gene expression by CRYPTOCHROME1. Genes Dev 24:1317–1328. https://doi.org/10.1101/gad.578810.
   PubMed Web of Science ®Google Scholar
• Wuarin J, Schibler U. 1990. Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63:1257–1266. https://doi.org/10.1016/0092-8674(90)90421-A.
   PubMed Web of Science ®Google Scholar
• Mueller CR, Maire P, Schibler U. 1990. DBP, a liver-enriched transcriptional activator, is expressed late in ontogeny and its tissue specificity is determined posttranscriptionally. Cell 61:279–291. https://doi.org/10.1016/0092-8674(90)90808-R.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–8. https://doi.org/10.1093/nar/gkp335.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36.
   PubMedGoogle Scholar
• Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. 2013. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8:2281–2308. https://doi.org/10.1038/nprot.2013.143.
   PubMed Web of Science ®Google Scholar
• Kiyohara YB, Nishii K, Ukai-Tadenuma M, Ueda HR, Uchiyama Y, Yagita K. 2008. Detection of a circadian enhancer in the mDbp promoter using prokaryotic transposon vector-based strategy. Nucleic Acids Res 36:e23. https://doi.org/10.1093/nar/gkn018.
   PubMed Web of Science ®Google Scholar
• Bennett MK, Erondu NE, Kennedy MB. 1983. Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain. J Biol Chem 258:12735–12744.
   PubMedGoogle Scholar
• Ohno T, Onishi Y, Ishida N. 2006. A novel E4BP4 element drives circadian expression of mPeriod2. Nucleic Acids Res 35:648–655. https://doi.org/10.1093/nar/gkl868.
   PubMed Web of Science ®Google Scholar
• Yamajuku D, Shibata Y, Kitazawa M, Katakura T, Urata H, Kojima T, Nakata O, Hashimoto S. 2010. Identification of functional clock-controlled elements involved in differential timing of Per1 and Per2 transcription. Nucleic Acids Res 38:7964–7973. https://doi.org/10.1093/nar/gkq678.
   PubMed Web of Science ®Google Scholar
• Lee KH, Woo KC, Kim DY, Kim TD, Shin J, Park SM, Jang SK, Kim KT. 2012. Rhythmic interaction between Period1 mRNA and hnRNP Q leads to circadian time-dependent translation. Mol Cell Biol 32:717–728. https://doi.org/10.1128/MCB.06177-11.
   PubMed Web of Science ®Google Scholar
• Boden M, Bailey TL. 2008. Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Res 36:4108–4117. https://doi.org/10.1093/nar/gkn374.
   PubMed Web of Science ®Google Scholar
• Buske FA, Boden M, Bauer DC, Bailey TL. 2010. Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics 26:860–866. https://doi.org/10.1093/bioinformatics/btq049.
   PubMed Web of Science ®Google Scholar
• Lee KH, Kim SH, Kim HJ, Kim W, Lee HR, Jung Y, Choi JH, Hong KY, Jang SK, Kim KT. 2014. AUF1 contributes to Cryptochrome1 mRNA degradation and rhythmic translation. Nucleic Acids Res 42:3590–3606. https://doi.org/10.1093/nar/gkt1379.
   PubMed Web of Science ®Google Scholar
• Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. 2017. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14:959–962. https://doi.org/10.1038/nmeth.4396.
   PubMed Web of Science ®Google Scholar
• Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10:1213–1218. https://doi.org/10.1038/nmeth.2688.
   PubMed Web of Science ®Google Scholar
• Choi HS, Hwang CK, Song KY, Law P-Y, Wei L-N, Loh HH. 2009. Poly(C)-binding proteins as transcriptional regulators of gene expression. Biochem Biophys Res Commun 380:431–436. https://doi.org/10.1016/j.bbrc.2009.01.136.
   PubMed Web of Science ®Google Scholar