TABLE 1.

Primers, DNA duplexes, and plasmids used in this study

Underlined and italic primer sequences represent LIC 5′-overhangs. Bold sequences indicate short Kozak consensus sequences. Bold and italic sequences indicate Rev-erbβ or THR core hexameric recognition sequences in DNA duplexes.

Primer, DNA duplex, or plasmid designation	Sequence or synopsis
Primers
FLRev-erbβ LIC forward	5′-TACTTCCAATCCAATGCTGAGGTGAATGCAGGAGGTGT-3′
FLRev-erbβ LIC reverse	5′-TTATCCACTTCCAATGTTAAGGGTGAACTTTAAAGGCCAAG-3′
KpnI-Kozak-Rev-erbβ forward	5′-GATCGGTACCATGGAGGTGAATGCAGGAGGTGTGATTGCCTATATCAGTT-3′
XhoI-Rev-erbβ reverse	5′-GATCCTCGAGTTAAGGGTGAACTTTAAAGGCCAAGAGCTCCTCAGAG-3′
KpnI-Kozak-Rev-erbα forward	5′-GATCGGTACCATGACGACCCTGGACTCCAACAACAACACAGGTGGCG-3′
NotI-Rev-erbα reverse	5′-GATCGCGGCCGCTCACTGGGCGTCCACCCGGAAGGACAGCAGCTTCTCG-3′
Rev-erbβ H21P forward	5′-CCAGCTCAGCCTCAAGCCCGGCCTCTTGTCACAGTGAG-3′
Rev-erbβ H21P reverse	5′-CTCACTGTGACAAGAGGCCGGGCTTGAGGCTGAGCTGG-3′
Rev-erbβ K282Q forward	5′-GAGAGCATGCAGCCGCAGAGAGGAGAACGG-3′
Rev-erbβ K282Q reverse	5′-CCGTTCTCCTCTCTGCGGCTGCATGCTCTC-3′
Rev-erbβ R288P forward	5′-GAGGAGAACGGATTCCGAAGAACATGGAGC-3′
Rev-erbβ R288P reverse	5′-GCTCCATGTTCTTCGGAATCCGTTCTCCTC-3′
Rev-erbβ H568F forward	5′-CGATCTTTAAACAACATGTTCTCTGAGGAGCTCTTGGCC-3′
Rev-erbβ H568F reverse	5′-GGCCAAGAGCTCCTCAGAGAACATGTTGTTTAAAGATCG-3′
Rev-erbβ C384A forward	5′-GGAAGAATGCATCTGGTTGCGCCAATGAGTAAGTCTCC-3′
Rev-erbβ C384A reverse	5′-GGAGACTTACTCATTGGCGCAACCAGATGCATTCTTCC-3′
Rev-erbα H602F forward	5′-CGGACCCTGAACAACATGTTCTCCGAGAAGCTGCTGTC-3′
Rev-erbα H602F reverse	5′-GACAGCAGCTTCTCGGAGAACATGTTGTTCAGGGTCCG-3′
NCoR540 LIC forward	5′-TACTTCCAATCCAATGCATCTGAGGCTGGGAAAGATAAAGGGCCTCCT-3′
NCoR540 LIC reverse	5′-TTATCCACTTCCAATGCTAGTCATCACTATCCGACAGGGTCTCGTACTG-3′
THRβ1 LIC forward	5′-TACTTCCAATCCAATGCAATGACTCCCAACAGTATGACAGAAAATGGC-3′
THRβ1 LIC reverse	5′-TTATCCACTTCCAATGCTAATCCTCGAACACTTCCAAGAACAAAGGGGG-3′
Fluorophore-labeled DNA duplexes
TR/FAM-Rev-DR2	TR/FAM-5′-CAACTAGGTCACTAGGTCAG-3′
	3′-GTTGATCCAGTGATCCAGTC-5′
FAM-BMal1-promoter	FAM-5′-CGGAAAGTAGGTTAGTGGTGCGACATTTAGGGAAGGCAGAAAGTAGGTCAGGG-3′
	3′-GCCTTTCATCCAATCACCACGCTGTAAATCCCTTCCGTCTTTCATCCAGTCCC-5′
FAM-hPL-promoter	FAM-5′-CAGGTGGGGTCAAGCAGGGAGAGAGAA-3′
	3′-GTCCACCCCAGTTCGTCCCTCTCTCTT-5′
Plasmids
pGB1-FLRev-erbβ-MGC	Rev-erbβ (NR1D2) ORF from the Mammalian Gene Collection cloned into a modified pMCSG7 vector resulting in a translational fusion between the His6-GB1 solubility tag and FLRev-erbβ with an internal TEV protease cleavage site for protein production in E. coli (this study).
pGB1-FLRev-erbβ-HGS	pGB1-FLRev-erbβ-MGC carrying H21P, K282Q, and R288P mutations reflecting the Human Genome Sequence; parent vector for H568F and H568F/C384A expression clones (this study).
pcDNA3.1(+)-FLRev-erbβ	The Rev-erbβ ORF from pGB1-FLRev-erbβ-HGS was subcloned into pcDNA3.1(+) using a forward primer containing a consensus Kozak sequence for expression in mammalian cells; parent vector for H568F, C384A, and H568F/C384A expression clones (this study).
pcDNA3.1(+)-Rev-erbα	The Rev-erbα ORF from mammalian gene collection vector 6190140 was subcloned into pcDNA3.1(+) for overexpression of Rev-erbα in mammalian cells; parent vector for the H602F expression clone (this study).
pMBP-NCoR1–540	DNA coding for the C-terminal 540 amino acids of NCoR1 was cloned into pMCSG9 resulting in a translational fusion between MBP and NCoR1–540 with an internal TEV protease cleavage site (this study).
pMBP-THRβ1	The THRβ1 ORF was cloned into pMCSG9 resulting in a translational fusion between MBP and THRβ1 with an internal TEV protease cleavage site (this study).
pCMV-βGal	Mammalian expression vector producing β-galactosidase for measuring transfection efficiency and normalizing luciferase activity (provided by Dr. Daniel Bochar, University of Michigan).
pGL3Basic-BMal1	Luciferase reporter vector driven by the core Bmal1 promoter (encompassing −422 to +108 bp with respect to the transcription start site) from M. musculus (71).