Difference between revisions of "PCAT6"

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(Created page with "==Annotated Information== ===Approved Symbol=== PCAT6 ===Approved Name=== prostate cancer associated transcript 6 (non-protein coding) ===Previous Symbols=== KDM5B-AS1 ===Syno...")
 
 
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''PCAT6'': prostate cancer associated transcript 6, promotes cellular proliferation and colony formation of prostate cancer.
 
==Annotated Information==
 
==Annotated Information==
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===Approved Symbol===
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===Name===
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PCAT6
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''PCAT6'': prostate cancer associated transcript 6 [https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:43714 (HGNC:43714)]
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===Approved Name===
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===Aliases===
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prostate cancer associated transcript 6 (non-protein coding)
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ncRNA-a2; PCAN-R1: prostate cancer-associated noncoding RNA 1; KDM5BAS1: KDM5B antisense RNA 1 (head to head); onco-lncRNA-96 [https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:43714 (HGNC:43714)]
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===Previous Symbols===
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KDM5B-AS1
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===Characteristics===
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===Synonyms===
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''PCAT6'' is a long non coding RNA gene located at chromosome 1q32.1, flanking the histone demethylase JARID1B/KDAM 5B. <ref name="ref1"/>
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ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
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===Chromosome===
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===Function===
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1q32.1
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[[File: ncRNA-a2.jpg|thumb|300px| ncRNA-a2 locus in HeLa cells. <ref name="ref1"/>]]
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===RefSeq ID===
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NR_046325
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''PCAT6'' promotes cellular proliferation and colony formation of prostate cancer. Molecular analysis revealed that ''PCAT6'' regulated the expression of two pivotal cancer-related proteins, c-Myc and p53, in lung cancer cells. <ref name="ref3"/>. Depletion of ncRNA-a2 (''PCAT6'') also results in significant reduction of ''KLHL12'', a gene known for negative regulation of the Wnt-beta catenin pathway <ref name="ref1" />.
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===OMIM ID===
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_
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===Expression===
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===Ensembl ID===
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Detectable expression of ncRNA-a2 (''PCAT6'') was confirmed in HeLa cells. <ref name="ref1" /> ''PCAN-R1'' or ''PCAT6'' showed positive correlation between gene expression and somatic copy number alteration (SCNA). <ref name="ref2" /> Knockdown of ''PCAN-R1'' resulted in substantial decrease in both cell growth and soft-agar colony formation in the androgen-dependent prostate cancer cell line LNCaP which was also later further confirmed in the androgen-independent prostate cancer cell line LNCaP-abl. The siRNA knockdown of ''PCAN-R1'' had no effect on the expression of its neighboring  protein-coding (PCG) gene ''KDM5B'' suggesting that the functional mechanism of ''PCAN-R1'' is not directly through its neighboring protein coding genes. In normal tissues, ''PCAN-R1'' and its neighboring PCG ''KDM5B'' showed the highest expression in testis <ref name="ref2" />
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ENSG00000228288
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===pubmed IDs===
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{| class='wikitable' style="text-align:center"
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20887892, 23728290
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|-
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! | Primer
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! | Forward primer
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! | Reverse primer
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|-
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| rowspan="1"|RT-PCR
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| | 5′-CAGGAACCCCCTCCTTACTC-3
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| | 5′-CTAGGGATGTGTCCGAAGGA-3′<ref name="ref2" />
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|-
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| rowspan="1"|RACE and northern blot analysis
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| | 5′-GACCTGGGCAACCCCAGCCTG-3′
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| |  5′-GATCACTAATACGACTCACTATAGGGCGCGAGGAGCGCCTCATCACC-3′<ref name="ref2" />
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|-
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| rowspan="2"|RNA interference
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| | siR1-1
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| | 5′-GGTGTCTCCATCCTCATTC-3′<ref name="ref2" />
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|-
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| | siR1-2
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| | 5′-CTCCCAGACCTCACGTCAA-3′<ref name="ref2" />
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|}
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===Diseases===
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* Lung Cancer <ref name="ref3" />
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* Prostate Cancer <ref name="ref2" />
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==Labs working on this lncRNA==
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* Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain <ref name="ref1" />
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* Center for Functional Cancer Epigeneitcs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA <ref name="ref2" />
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* Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China <ref name="ref3" />
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==References==
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<references>
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<ref name="ref1"> Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010,143(1):46-58.</ref>(1)
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<ref name="ref2"> Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer[J]. Nature structural & molecular biology. 2013,20(7):908-13.</ref>(2)
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<ref name="ref3"> Wan L, Zhang L, Fan K, Cheng Z-X, Sun Q-C & Wang J-J. Knockdown of Long Noncoding RNA PCAT6 Inhibits Proliferation and Invasion in Lung Cancer Cells[J]. Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics. 2016, 24(3):161-170.</ref>(3)
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</references>
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===Sequence===
 
===Sequence===
 
>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA
 
>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA
 
<dnaseq>GACGCCCCAGAGGCCGGACCTGGGCAACCCCAGCCTGGAGGTGCCGGGGCCGGAGCTCCCAGAGGGCTGGGTGCGAGGCCTAGGCGGGGTCAGGTTCGGGTTCCTAGGCCATAGCGGAGCTGCAGCCCAGGCGGCCGGAGCGGAACCCAGCCCCGCTCCGAGTGCCACGTCTCCAGGAACCCCCTCCTTACTCTTGGACAACACTCCGCCCCCGCCCGGGCCTCCGTCCCCCAAACCGCCCTCATTTGTGCAGCGCCAGATCCTTCGGACACATCCCTAGGTGTCTCCATCCTCATTCGGTCCATCCAACTCCCAGACCTCACGTCAACCGGCTGCACCCCACTTTCCAGCCTGCGCCCCAGATCTGCAGCCTTCGCCCCTAGATACACCCGCCTGGTGATGAGGCGCTCCTCGCGTTCCTTCCGGGCTCCAGGTGTCCGTGAGCCTCCCTTCCGCCCTGGCCTCCGGTCTCTGCCTTGCTCGTGCTTCTACCACCACCCTTCCCCTCCCAACCCGGTGGATCCTCTCGTCTCCCCCAGTCTCCAGTGCACCGGCTTTCCCTCGTCCTCTGCGCAGTCCATCTCAGCTCATCTCTCCAATTCAATGCCATCATCTCTCCTCACCATCTCTCGGTGCCCTGGAATGTTTGCTGTCAGATGTCCCCTGTGAAACCCACAAACGCTTGCGATTTGGCCTCCTTGTTTTATTTTGTGTAGTCCTACAACGTCTTGTTACTACCCCCTATTACAACACTTATAACTCAG</dnaseq>
 
<dnaseq>GACGCCCCAGAGGCCGGACCTGGGCAACCCCAGCCTGGAGGTGCCGGGGCCGGAGCTCCCAGAGGGCTGGGTGCGAGGCCTAGGCGGGGTCAGGTTCGGGTTCCTAGGCCATAGCGGAGCTGCAGCCCAGGCGGCCGGAGCGGAACCCAGCCCCGCTCCGAGTGCCACGTCTCCAGGAACCCCCTCCTTACTCTTGGACAACACTCCGCCCCCGCCCGGGCCTCCGTCCCCCAAACCGCCCTCATTTGTGCAGCGCCAGATCCTTCGGACACATCCCTAGGTGTCTCCATCCTCATTCGGTCCATCCAACTCCCAGACCTCACGTCAACCGGCTGCACCCCACTTTCCAGCCTGCGCCCCAGATCTGCAGCCTTCGCCCCTAGATACACCCGCCTGGTGATGAGGCGCTCCTCGCGTTCCTTCCGGGCTCCAGGTGTCCGTGAGCCTCCCTTCCGCCCTGGCCTCCGGTCTCTGCCTTGCTCGTGCTTCTACCACCACCCTTCCCCTCCCAACCCGGTGGATCCTCTCGTCTCCCCCAGTCTCCAGTGCACCGGCTTTCCCTCGTCCTCTGCGCAGTCCATCTCAGCTCATCTCTCCAATTCAATGCCATCATCTCTCCTCACCATCTCTCGGTGCCCTGGAATGTTTGCTGTCAGATGTCCCCTGTGAAACCCACAAACGCTTGCGATTTGGCCTCCTTGTTTTATTTTGTGTAGTCCTACAACGTCTTGTTACTACCCCCTATTACAACACTTATAACTCAG</dnaseq>

Latest revision as of 05:23, 22 November 2018

PCAT6: prostate cancer associated transcript 6, promotes cellular proliferation and colony formation of prostate cancer.

Annotated Information

Name

PCAT6: prostate cancer associated transcript 6 (HGNC:43714)

Aliases

ncRNA-a2; PCAN-R1: prostate cancer-associated noncoding RNA 1; KDM5BAS1: KDM5B antisense RNA 1 (head to head); onco-lncRNA-96 (HGNC:43714)

Characteristics

PCAT6 is a long non coding RNA gene located at chromosome 1q32.1, flanking the histone demethylase JARID1B/KDAM 5B. [1]

Function

ncRNA-a2 locus in HeLa cells. [1]

PCAT6 promotes cellular proliferation and colony formation of prostate cancer. Molecular analysis revealed that PCAT6 regulated the expression of two pivotal cancer-related proteins, c-Myc and p53, in lung cancer cells. [2]. Depletion of ncRNA-a2 (PCAT6) also results in significant reduction of KLHL12, a gene known for negative regulation of the Wnt-beta catenin pathway [1].

Expression

Detectable expression of ncRNA-a2 (PCAT6) was confirmed in HeLa cells. [1] PCAN-R1 or PCAT6 showed positive correlation between gene expression and somatic copy number alteration (SCNA). [3] Knockdown of PCAN-R1 resulted in substantial decrease in both cell growth and soft-agar colony formation in the androgen-dependent prostate cancer cell line LNCaP which was also later further confirmed in the androgen-independent prostate cancer cell line LNCaP-abl. The siRNA knockdown of PCAN-R1 had no effect on the expression of its neighboring protein-coding (PCG) gene KDM5B suggesting that the functional mechanism of PCAN-R1 is not directly through its neighboring protein coding genes. In normal tissues, PCAN-R1 and its neighboring PCG KDM5B showed the highest expression in testis [3]

Primer Forward primer Reverse primer
RT-PCR 5′-CAGGAACCCCCTCCTTACTC-3 5′-CTAGGGATGTGTCCGAAGGA-3′[3]
RACE and northern blot analysis 5′-GACCTGGGCAACCCCAGCCTG-3′ 5′-GATCACTAATACGACTCACTATAGGGCGCGAGGAGCGCCTCATCACC-3′[3]
RNA interference siR1-1 5′-GGTGTCTCCATCCTCATTC-3′[3]
siR1-2 5′-CTCCCAGACCTCACGTCAA-3′[3]

Diseases

  • Lung Cancer [2]
  • Prostate Cancer [3]

Labs working on this lncRNA

  • Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain [1]
  • Center for Functional Cancer Epigeneitcs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA [3]
  • Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China [2]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010,143(1):46-58.
  2. ↑ 2.0 2.1 2.2 Wan L, Zhang L, Fan K, Cheng Z-X, Sun Q-C & Wang J-J. Knockdown of Long Noncoding RNA PCAT6 Inhibits Proliferation and Invasion in Lung Cancer Cells[J]. Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics. 2016, 24(3):161-170.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer[J]. Nature structural & molecular biology. 2013,20(7):908-13.

Sequence

>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA

000001 GACGCCCCAG AGGCCGGACC TGGGCAACCC CAGCCTGGAG GTGCCGGGGC CGGAGCTCCC AGAGGGCTGG GTGCGAGGCC 000080
000081 TAGGCGGGGT CAGGTTCGGG TTCCTAGGCC ATAGCGGAGC TGCAGCCCAG GCGGCCGGAG CGGAACCCAG CCCCGCTCCG 000160
000161 AGTGCCACGT CTCCAGGAAC CCCCTCCTTA CTCTTGGACA ACACTCCGCC CCCGCCCGGG CCTCCGTCCC CCAAACCGCC 000240
000241 CTCATTTGTG CAGCGCCAGA TCCTTCGGAC ACATCCCTAG GTGTCTCCAT CCTCATTCGG TCCATCCAAC TCCCAGACCT 000320
000321 CACGTCAACC GGCTGCACCC CACTTTCCAG CCTGCGCCCC AGATCTGCAG CCTTCGCCCC TAGATACACC CGCCTGGTGA 000400
000401 TGAGGCGCTC CTCGCGTTCC TTCCGGGCTC CAGGTGTCCG TGAGCCTCCC TTCCGCCCTG GCCTCCGGTC TCTGCCTTGC 000480
000481 TCGTGCTTCT ACCACCACCC TTCCCCTCCC AACCCGGTGG ATCCTCTCGT CTCCCCCAGT CTCCAGTGCA CCGGCTTTCC 000560
000561 CTCGTCCTCT GCGCAGTCCA TCTCAGCTCA TCTCTCCAAT TCAATGCCAT CATCTCTCCT CACCATCTCT CGGTGCCCTG 000640
000641 GAATGTTTGC TGTCAGATGT CCCCTGTGAA ACCCACAAAC GCTTGCGATT TGGCCTCCTT GTTTTATTTT GTGTAGTCCT 000720
000721 ACAACGTCTT GTTACTACCC CCTATTACAA CACTTATAAC TCAG
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