Difference between revisions of "ENST00000608917.1"

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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.
+
''PACERR'', a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA), which 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 and activate the COX-2 gene, may function as an oncogene in osteosarcoma. <ref name="ref1" /><ref name="ref2" />
  
 
==Annotated Information==
 
==Annotated Information==
−
===Transcriptomic Nomeclature===
+
===Name===
−
PACER,PTGS2 antisense NFKB1 complex-mediated expression regulator RNA(HGNC nomenclature)
+
''PACERR'',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<ref name="ref1" />
 
"p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1<ref name="ref1" />
  
 
===Characteristics===
 
===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<ref name="ref1" />.
+
[[File:Identification of an antisense long non-coding RNA in the upstream region of the COX-2 gene.jpg|right|thumb|400px|'''Identification of an antisense long non-coding RNA in the upstream region of the COX-2 gene'''<ref name="ref1" />]]
 +
 
 +
''PACERR'',homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, was located in the upstream region of the human COX-2 gene<ref name="ref1" />.
  
 
===Celluar Localization===
 
===Celluar Localization===
−
PACER performs its functions in the nucleus<ref name="ref1" />.
+
PACERR performs its functions in the nucleus<ref name="ref1" />.
 +
 
 +
===Disease===
 +
inflammation and cancer
  
 
===Function===
 
===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<ref name="ref1" />.  
+
[[File:COX-2 is required to mediate PACER functions in osteosarcoma.jpg|right|thumb|500px|'''COX-2 is required to mediate PACER functions in osteosarcoma.'''<ref name="ref2" />]]
−
PACER directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter<ref name="ref1" />.
+
 
−
PACER belongs to a novel, unanticipated class of bona-fide transcriptional regulators<ref name="ref1" />.
+
PACERR 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<ref name="ref1" />.
 +
 +
PACERR directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter<ref name="ref1" />.
 +
 
 +
PACERR belongs to a novel, unanticipated class of bona-fide transcriptional regulators<ref name="ref1" />.
 +
 
 +
The upregulation of PACER contributes to the dysregulation of COX-2 in osteosarcoma and subsequently promotes the development of osteosarcoma.<ref name="ref2" />
  
 
===Regulation===
 
===Regulation===
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===Expression===
 
===Expression===
 +
[[File:Expression of PACER in osteosarcoma tissues and cells.gif|right|thumb|400px|'''Expression of ''PACER'' in osteosarcoma tissues and cells.'''<ref name="ref1" />]]
 +
 +
''PACER'' was overexpressed in osteosarcoma tissues and cell lines compared with normal tissues and osteoblasts, respectively. <ref name="ref1" />
 +
 +
''PACER'' was overexpressed in osteosarcoma tissues and two osteosarcoma cell lines compared with normal tissues and osteoblasts, respectively.<ref name="ref2" />
 +
 +
 
{|class='wikitable' style="text-align:center"
 
{|class='wikitable' style="text-align:center"
 
|-
 
|-
−
! | columnspan="3"|Primers used in RACE
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| | Primers used in RACE
−
|
 
−
|-
 
−
| |
 
 
| | initial
 
| | initial
 
| | nested
 
| | nested
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| | GTCTTTGCCCGAGCGCTTCCG
 
| | GTCTTTGCCCGAGCGCTTCCG
 
| | CCGCCGTGTCTGGTCTGTACGTC<ref name="ref1" />
 
| | CCGCCGTGTCTGGTCTGTACGTC<ref name="ref1" />
 +
|}
 +
{|class='wikitable' style="text-align:center"
 
|-
 
|-
−
! | Primers used for RNA quantitation|columnspan="3"
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| | Experiment
−
|-
+
| | Primer
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| | COX-2 mRNA
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| | Forward
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| | TCTGTACTGCGGGTGGAACA
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| | Reverse
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| | CAATTTGCCTGGTGAATGATTC<ref name="ref1" />
 
 
|-
 
|-
 +
| | RNA quantitation
 
| | PACER
 
| | PACER
 
| | TGTAAATAGTTAATGTGAGCTCCACG
 
| | TGTAAATAGTTAATGTGAGCTCCACG
 
| | GCAAATTCTGGCCATCGC<ref name="ref1" />
 
| | GCAAATTCTGGCCATCGC<ref name="ref1" />
 +
|}
 +
{|class='wikitable' style="text-align:center"
 
|-
 
|-
−
| | p50 mRNA
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| | Experiment
−
| | TTGCTGGTCCCACATAGTTG
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| | Primer
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| | ATGTATGTGAAGGCCCATCC<ref name="ref1" />
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| | Sequence
−
|-
 
−
! | Custom siRNA|columnspan="3"
 
 
|-
 
|-
 +
| rowspan="2"|Knokdown
 
| | siPACER-753
 
| | siPACER-753
 
| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
 
| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
−
| |
 
 
|-
 
|-
 
| | siPACER-870
 
| | siPACER-870
 
| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
 
| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
−
| |
 
−
|-
 
−
! | shRNA
 
−
|-
 
−
| | PACER ‘870’ shRNA
 
−
| | 5’ - gatcc GGACAAAGGAAGCGGCGAT cttcctgtcaga ATCGCCGCTTCCTTTGTCC tttttg
 
−
| | 3’ -    g CCTGTTTCCTTCGCCGCTA GAAGGACAGTCT TAGCGGCGAAGGAAACAGG aaaaacttaa<ref name="ref1" />
 
 
|}
 
|}
 +
 +
===Disease===
 +
''PACER'' may be regarded as a therapeutic target in human osteosarcoma.<ref name="ref2" />
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
−
Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
+
* Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States<ref name="ref1" />
 +
*Spine Tumor Center, Changzheng Hospital, Second Military Medical University, Fengyang Rd 415#, Huangpu District, Shanghai, China.<ref name="ref2" />
 +
==References==
 +
<references>
 +
<ref name="ref1">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.</ref>(1)
 +
<ref name="ref2">Qian M, Yang X, Li Z, Jiang C, Song D, Yan W, et al. P50-associated COX-2 extragenic RNA (PACER) overexpression promotes proliferation and metastasis of osteosarcoma cells by activating COX-2 gene[J]. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine. 2016,37(3):3879-86.</ref>(2)
 +
</references>
  
−
==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|
 
{{basic|
 
tID = ENST00000608917.1|
 
tID = ENST00000608917.1|

Latest revision as of 13:27, 1 July 2016

PACERR, a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA), which 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 and activate the COX-2 gene, may function as an oncogene in osteosarcoma. [1][2]

Annotated Information

Name

PACERR,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[1]

Characteristics

Identification of an antisense long non-coding RNA in the upstream region of the COX-2 gene[1]

PACERR,homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, was located in the upstream region of the human COX-2 gene[1].

Celluar Localization

PACERR performs its functions in the nucleus[1].

Disease

inflammation and cancer

Function

COX-2 is required to mediate PACER functions in osteosarcoma.[2]

PACERR 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[1].

PACERR directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter[1].

PACERR belongs to a novel, unanticipated class of bona-fide transcriptional regulators[1].

The upregulation of PACER contributes to the dysregulation of COX-2 in osteosarcoma and subsequently promotes the development of osteosarcoma.[2]

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[1].

Expression

Expression of PACER in osteosarcoma tissues and cells.[1]

PACER was overexpressed in osteosarcoma tissues and cell lines compared with normal tissues and osteoblasts, respectively. [1]

PACER was overexpressed in osteosarcoma tissues and two osteosarcoma cell lines compared with normal tissues and osteoblasts, respectively.[2]


Primers used in RACE initial nested
5'RACE TATGTATGTATGTGCTGCATATAG ATGTCAGCCTTTCTTAACCTTAC[1]
3'RACE GTCTTTGCCCGAGCGCTTCCG CCGCCGTGTCTGGTCTGTACGTC[1]
Experiment Primer Forward Reverse
RNA quantitation PACER TGTAAATAGTTAATGTGAGCTCCACG GCAAATTCTGGCCATCGC[1]
Experiment Primer Sequence
Knokdown siPACER-753 TGGAAAGAGAGGCGGGAAA[1]
siPACER-870 TGGAAAGAGAGGCGGGAAA[1]

Disease

PACER may be regarded as a therapeutic target in human osteosarcoma.[2]

Labs working on this lncRNA

  • Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States[1]
  • Spine Tumor Center, Changzheng Hospital, Second Military Medical University, Fengyang Rd 415#, Huangpu District, Shanghai, China.[2]

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 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.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Qian M, Yang X, Li Z, Jiang C, Song D, Yan W, et al. P50-associated COX-2 extragenic RNA (PACER) overexpression promotes proliferation and metastasis of osteosarcoma cells by activating COX-2 gene[J]. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine. 2016,37(3):3879-86.

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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Predicted Small Protein

Name ENST00000608917.1_smProtein_95:226
Length 44
Molecular weight 4914.4025
Aromaticity 0.116279069767
Instability index 79.0720930233
Isoelectric point 4.59381103516
Runs 5
Runs residual 0.0410243010191
Runs probability 0.0137078254725
Amino acid sequence MSFLLRSLCPSASESQFWTDRLGWDTGGGQKDTWLPLQESERP
Secondary structure LLEEELLLLLLLLLLLLHHHHLLLLLLLLLLLLLLLLLLLLLL
PRMN -
PiMo -
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