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5 protocols using pgl4.11 vector

1

Transcriptional Regulation of Mouse Spib and Sox8

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The coding sequences of mouse Spib and Sox8 were amplified from RANKL-stimulated, organoid–derived cDNA and subcloned into pcDNA3.1 vector (Life Technologies). The Gp2 promoter region (0 to –2,494 nucleotides) was amplified from genomic DNA of C57BL/6 mouse and subcloned into pCRII-Blunt-TOPO vector (Life Technologies), and then into pGL4.11 vector (Promega). PCR primers for cloning are summarized in Table S1. HEK293T and CMT93 cells were cultured in a 24-well plate and transfected with the combination of expression plasmids using Lipofectamine 3000 (Life Technologies). After 24-h incubation, luciferase activity was measured using the Dual-Luciferase Reporter Assay System (Promega).
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2

Cloning and Bioinformatic Analysis of Periostin Promoter

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For the reporter constructs, the periostin promoter regions (−4000 to +50 bp) were amplified from human genomic DNA (Zyagen, CA) by PCR using iProof High-Fidelity DNA Polymerase (Bio-Rad, CA). The PCR products were subcloned into the pGL4.11 vector (Promega, WI) upstream of a luciferase gene using the KpnI/EcoRV restriction sites. Computational analysis to identify promoter-bound transcription factors was done using the Transcription Element Search System (TESS) (http://www.cbil.upenn.edu/cgi-bin/tess/tess).
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3

BCL2 Promoter Cloning and Deletion

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A DNA fragment of human BCL2 promoter (–1670/+16) was PCR amplified and cloned into the pGL4.11 vector (Promega). Deletion of the predicted KLF-binding site (–1125/–1099) within the cloned BCL2 promoter fragment (–1670/+16) was performed using the In-Fusion HD Cloning Plus Kit (TaKara Bio, 638910). All PCR products were validated by DNA-Seq.
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4

Constructing Luciferase Reporter Vectors with Diverse Regulatory Elements

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To construct p4xCRE-3xSRE-TATA-Luc2P, four tandem repeats of the cAMP-response element (5′-AGCCTGACGTCAGAG-3′)42 (link),43 (link), three tandem repeats of the serum-response element (5′-AGGATGTCCATATTAGGACATCT-3′)44 (link),45 (link) derived from the human c-fos gene, and an adenovirus E1b TATA sequence (5′-AGGGTATATAATG-3′)46 (link),47 (link) were subsequently inserted into a pGL4.11 vector (Promega, Madison, WI, USA). Similarly, p4xCRE-TATA-Luc2P and p3xSRE-TATA-Luc2P were constructed. To construct p2xSRF-TATA-Luc2P, two tandem repeats of serum-response factor-response element (5′-TCGACTGTACTGTATGTCCATATTAGGACATCTG-3′)48 (link),49 (link) derived from the human c-fos gene and the TATA sequence were inserted into a pGL4.11 vector. The NFAT luciferase reporter vector was obtained from Addgene (#10959)50 (link). To construct the GPCR expression vectors, we utilized the Gateway system and subcloned 258 full-length human GPCR cDNAs from pDONR201 vectors51 (link) into pcDNA3.2/V5-DEST vectors (Thermo Fisher Scientific). Mutant GPR55 expression vectors were constructed by site-directed mutagenesis with Tks Gflex DNA polymerase (Takara Bio, Shiga, Japan) using primers (Supplementary Table 1).
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5

Promoter Activity Assay of TRF, RAD50, VEGF

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The promoter regions of TRF1, TRF2, RAD50, and VEGF (1 000 bp upstream from the transcription start site (TSS)) in Supplementary Table S2 were synthesized (Tsingke Biotechnology, China) and constructed into the pGL4.11 vector (Promega, USA, Cat. No. E6661). The pGL4.11 constructs (150 ng) and internal control vector pRL-TK (30 ng, Promega, USA, Cat. No. E2241) were co-transfected into mouse fibroblasts using Lipofectamine 2000 (Thermo Fisher, USA). At 48 h post transfection, luminescence was measured using a Dual-Luciferase Reporter Assay System (Promega, USA, Cat. No. E1960) and Luminoskan Ascent instrument (Thermo Fisher, USA).
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