PVT1

Species: Homo sapiens

Position: chr8: 127794532-128101253

Known as: PVT1 , ENSG00000249859

Transcript: NR_003367 , ENST00000513868 , ENST00000521951

Sequence: Download

Description:

The PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.



sgRNAs

sgRNA_ID Sequence Position (Chr) Position (Lnc) Length PAM Type Validity Cell line Note Ref.
sgRNA1 CGGGTTGCCCGTGACGTCA 127794501-127794519(-) up stream 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA2 CCTCCGGGCAGAGCGCGTG 127794532-127794550(+) gene body (near 5') 19 TGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA3 CCGGGCAGAGCGCGTGTGG 127794535-127794553(+) gene body (near 5') 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA4 GTGTGGCGGCCGAGCACAT 127794548-127794566(+) gene body (near 5') 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA5 GGCCGAGCACATGGGCCCG 127794555-127794573(+) gene body (near 5') 19 CGG CRISPRi;CRISPRedit Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA6 CGAGACTTGGCCCTGAGTA 127794774-127794792(+) gene body (near 5') 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA7 CACAGCGCATCCCTACTCA 127794787-127794805(-) gene body (near 5') 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA8 GGGATGCGCTGTGAGTAGT 127794793-127794811(+) gene body (near 5') 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA9 GTAGTCGGACGGAGGAAAG 127794807-127794825(+) gene body (near 5') 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA10 CCGAATGGCCGGTGCATAG 127794937-127794955(+) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA11 ATTAGGAGAAAAACCTTCC 127795899-127795917(+) gene body (near 5') 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA12 CCTTCCCGGAAGCTGCAGA 127795912-127795930(+) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA13 AAATACAGAATCCGTGTCT 127795936-127795954(+) gene body (near 5') 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA14 GTGTCTGGGAGAAACCTCG 127795949-127795967(+) gene body (near 5') 19 TGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA15 TGGGAGAAACCTCGTGGCC 127795954-127795972(+) gene body (near 5') 19 TGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA16 TAATGGAGACCAGGCCACG 127795966-127795984(-) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA17 ATCTCAAATAATGGAGACC 127795974-127795992(-) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA18 GCCGAAGCTTTAGACCACG 127796023-127796041(-) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA19 GAATAAGCCACTCTTAACC 127796149-127796167(-) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA20 TCTGCACTCAAGATAGATG 127796177-127796195(-) gene body (near 5') 19 AGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA21 GCGAGCCGCCGTGACGTCA 127794489-127794507(+) up stream 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA22 CGTCACGGCGGCTCGCGCT 127794486-127794504(-) up stream 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA23 CGGCTCGCGCTCGGGCCTC 127794479-127794497(-) up stream 19 GGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA24 GAGGACGCACGCGGCGGGC 127794431-127794449(+) up stream 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA25 GGCCCGCCGCGTGCGTCCT 127794432-127794450(-) up stream 19 CGG CRISPRi Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA26 GGACCGAGGACGCACGCGGC 127794426-127794445(+) up stream 20 GGG CRISPRa Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA27 GCCGGGACCGAGGACGCACG 127794422-127794441(+) up stream 20 CGG CRISPRa Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA28 GCCTGCTTCCCGGCAGCGC 127794355-127794373(-) up stream 19 AGG CRISPRa Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA29 GGGCGACTGCGGCCGCCAA 127794290-127794308(-) up stream 19 GGG CRISPRa Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA30 GCCGCCACACGCGCTCTGCC 127794538-127794557(-) gene body (near 5') 20 CGG CRISPRedit Experimental validated MDA-MB-231;MCF-7 NA [1]
sgRNA32 TCTCCAGAAGGACAGAATAA 128096511-128096530(+) gene body (near 3') 20 CGG CRISPRi Experimental validated T24;5637 NA [2]
sgRNA33 AAAAGAATTTAATAGACACG 128101227-128101246(-) gene body (near 3') 20 AGG CRISPRi Experimental validated T24;5637 NA [2]
sgRNA34 TTGGTGGGGCTTGTGAATC 128096540-128096559(-) gene body (near 3') 19 TGG CRISPRi Experimental validated T24;5637 NA [2]
sgRNA35 ACGAGGCCGGCCACGCCACG 128101210-128101229(-) gene body (near 3') 20 TGG CRISPRi Experimental validated T24;5637 NA [2]
sgRNA36 GATTCACAAGCCCCACCAAG 128096541-128096560(+) gene body (near 3') 20 AGG CRISPRi Experimental validated T24;5637 NA [2]

GBrowser


Links

lncRNA Function:

sgRNA Design Tool:

Reference

1. Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, et al. (2018). Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell 173(6): 1398-1412.e22.

2. Peng L, Pan P, Chen J, Yu X, Wu J, et al. (2018). A tetracycline-inducible CRISPR/Cas9 system, targeting two long non-coding RNAs, suppresses the malignant behavior of bladder cancer cells. Oncol Lett 16(4): 4309-4316.