ENST00000608917.1

PACER, a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA) is expressed in the upstream region of COX-2 and functions to directly sequester the repressive NF-κB p50 subunit from the COX-2 promoter.

Annotated Information

Transcriptomic Nomeclature

PACER,PTGS2 antisense NFKB1 complex-mediated expression regulator RNA(HGNC nomenclature)

"p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1

Characteristics

PACER,homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, with 793 bp, was located in the upstream region of the human COX-2 gene.

Celluar Localization

PACER performs its functions in the nucleus.

Function

PACER facilitates assembly of RNA Polymerase II pre-initiation complexes, through recruitment of the histone acetyltransferase p300 to catalyze histone acetylation at the COX-2 locus upon stimulus-induction. PACER directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter. PACER belongs to a novel, unanticipated class of bona-fide transcriptional regulators.

Regulation

CTCF regulates the COX-2 locus by establishing and maintaining an open chromatin domain demarcated by two CTCF/cohesin complexes that is characterized by decreased H4K20 trimethylation, increased H3K4 di- and tri- methylation and increased histone acetylation.

Expression

Primers used in RACE|columnspan="3"
	initial	nested
5'RACE	TATGTATGTATGTGCTGCATATAG	ATGTCAGCCTTTCTTAACCTTAC
3'RACE	GTCTTTGCCCGAGCGCTTCCG	CCGCCGTGTCTGGTCTGTACGTC
Primers used for RNA quantitation|columnspan="3"
COX-2 mRNA	TCTGTACTGCGGGTGGAACA	CAATTTGCCTGGTGAATGATTC
PACER	TGTAAATAGTTAATGTGAGCTCCACG	GCAAATTCTGGCCATCGC
p50 mRNA	TTGCTGGTCCCACATAGTTG	ATGTATGTGAAGGCCCATCC
Custom siRNA|columnspan="3"
siPACER-753	TGGAAAGAGAGGCGGGAAA
siPACER-870	TGGAAAGAGAGGCGGGAAA
shRNA
PACER ‘870’ shRNA	5’ - gatcc GGACAAAGGAAGCGGCGAT cttcctgtcaga ATCGCCGCTTCCTTTGTCC tttttg	3’ - g CCTGTTTCCTTCGCCGCTA GAAGGACAGTCT TAGCGGCGAAGGAAACAGG aaaaacttaa

Labs working on this lncRNA

Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States

References

Krawczyk M, Emerson BM. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes[J]. eLife. 2014,3:e01776.

Basic Information

Transcript ID	ENST00000608917.1
Source	Gencode19
Same with	PACER ,PTGS2-AS1
Classification	antisense
Length	825 nt
Genomic location	chr1+:186649754..186650578
Exon number	1
Exons	186649754..186650578
Genome context
Sequence	000001 AATTTGGGAG CAGAGGGGGT AGTCCCCACT CTCCTGTCTG ATCCCTCCCT CTCCTCCCCG AGTTCCACCG CCCCAGGCGC 000080 000081 ACAGGTTTCC GCCAGATGTC TTTTCTTCTT CGCAGTCTTT GCCCGAGCGC TTCCGAGAGC CAGTTCTGGA CTGATCGCCT 000160 000161 TGGATGGGAT ACCGGGGGAG GGCAGAAGGA CACTTGGCTT CCTCTCCAGG AATCTGAGCG GCCCTGAGGT CCGGGGGCGC 000240 000241 AGGGAATCCC CTCTCCCGCC GCCGCCGCCG TGTCTGGTCT GTACGTCTTT AGAGGGTCGA GGAAGTCACG TCGGGACAGA 000320 000321 CTGGGGCGAG TAAGGTTAAG AAAGGCTGAC ATGTTTTATG TTTTAGTGAC GACGCTTAAT AGGCTGTATA TCTGCTCTAT 000400 000401 ATGCAGCACA TACATACATA GCTTTTTAAA AAACTCTTAT TTTGTGGAAT GAAATAGCTA CCTTCAGTGT ACATAGCTGT 000480 000481 AATTTATCTT TGTAGCTAAG TTGCTTTCAA CAGAAGAAAT ACTGTTCTCC GTACCTTCAC CCCCTCCTTG TTTCTTGGAA 000560 000561 AGAGAGGCGG GAAAGGTAAA TTCTCCTCAT AATACTGGTC CTAAGCAGTT ACCCTGTAAA TAGTTAATGT GAGCTCCACG 000640 000641 GGTCACCAAT ATAAAGTTTC CTGCCTTCTG ATGGACAAAG GAAGCGGCGA TGGCCAGAAT TTGCAGGGAC GCTAAATGTC 000720 000721 CAAAACGTAT GCCTTAAGGC ATTTCTCTCC CTGATGCGTG GATTATTTTG GTTACTAGCC CTTCATAGGA GATACTGGTA 000800 000801 AAATAAATTC GAGTTTTAAA GTTCA

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