Difference between revisions of "ENST00000556013.2"

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''PTCSC3'',shorted for papillary thyroid carcinoma susceptibility candidate 3,is involved in Papillary thyroid carcinoma.
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''PTCSC3'', shorted for papillary thyroid carcinoma susceptibility candidate 3, is involved in Papillary thyroid carcinoma.
  
 
==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
−
''PTCSC3'':papillary thyroid carcinoma susceptibility candidate 3 (non-protein coding)(HGNC nomenclature)
+
''PTCSC3'': Papillary thyroid carcinoma susceptibility candidate 3 (HGNC nomenclature)
 +
 
 +
LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0209589 HSALNT0209589]
  
 
===Characteristics===
 
===Characteristics===
−
PTCSC3,a 1152 bp thyroid-specific lincRNA gene (PTCSC3), located in a linkage disequilibrium block with a GWAS-derived SNP (rs944289).
+
[[File:PTCSC3.jpg|right|thumb|400px|'''''PTCSC3'' structure with promoter region.''' PTCSC3 consists of four exons and the SNP rs944289 is located 3.2 kb upstream of exon 1; rs944289 is located within a C/EBPα and C/EBPβ transcription factor binding site, and the risk allele destroys it (in silico). It contains an ORF predicting a 95-amino acid peptide starting in exon 1 and ending in exon 4. The ORF is marked in green, and the polyA tail signal sequence (AATAAA) and polyA tail are marked in blue. <ref name="ref1" />]]
 +
''PTCSC3'' consists of 4 exons with a total length of 1152 bp, located on a human chromosome  14q13.3 and spanning more than 40 kb of genomic region in a linkage disequilibrium block with a GWAS-derived SNP (rs944289) <ref name="ref1" />.
 +
 
 
===Function===
 
===Function===
−
PTCSC3 expression is highly thyroid specific suggests that it is involved in thyroid function<ref name="ref1" />.
+
''PTCSC3'' regulate the expression of genes involved in DNA replication, recombination, repair, cellular movement, tumor morphology, and cell death especially the genes that are important for papillary thyroid carcinoma (PTC) development and progression such as ''S100A4'', ''RHOB'', ''MOAP1'', ''AKT'', ''CTSA'', ''MECP2'', ''FLNA'', ''C19orf33'', ''GDF15'', and others <ref name="ref1" /><ref name="ref4" />.
 +
 
 +
''PTCSC3'' expression is highly thyroid specific suggests that it is involved in thyroid function <ref name="ref1" />.  overexpression of PTCSC3 significantly downregulates miR-574-5p expression in thyroid cancer cells that are of papillary, follicular and anaplastic origin <ref name="ref2" />.  
 
   
 
   
−
PTCSC3 expression is significantly down-regulated in tumor compared with unaffected thyroid tissue, and the risk allele is associated with significantly stronger suppression of PTCSC3. The restoration of PTCSC3 expression in PTC cell line affects genes involved in thyroid tumorigenesis and inhibits cell growth<ref name="ref1" />.
+
''PTCSC3'' expression is significantly down-regulated in tumor compared with unaffected thyroid tissue, and the risk allele is associated with significantly stronger suppression of PTCSC3. The restoration of PTCSC3 expression in PTC cell line affects genes involved in thyroid tumorigenesis and inhibits cell growth <ref name="ref1" />.
  
 
rs944289 predisposes to PTC by dysregulating the expression of PTCSC3, which acts as a tumor suppressor<ref name="ref1" />.
 
rs944289 predisposes to PTC by dysregulating the expression of PTCSC3, which acts as a tumor suppressor<ref name="ref1" />.
  
−
===Diseases===
+
===Expression===
−
* Papillary thyroid carcinoma (PTC)<ref name="ref1" />
+
''PTCSC3'' is almost uniquely expressed in thyroid tissue with very low expression additionally in kidney tissue<ref name="ref1" />.
−
 
 
−
===PubmedID===
 
−
22586128
 
  
−
===Expression===
+
''PTCSC3'' significantly down-regulated in papillary thyroid carcinoma tissues compared to non-cancerous tissues <ref name="ref3" /><ref name="ref5" />.  
−
PTCSC3 is almost uniquely expressed in thyroid tissue with very low expression additionally in kidney tissue<ref name="ref1" />.
 
  
 
The cDNA of PTCSC3 was amplified by PCR,
 
The cDNA of PTCSC3 was amplified by PCR,
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|}
 
|}
  
 +
===Regulation===
 +
 +
C/EBPα and C/EBPβ regulate the transcriptional activity of the ''PTCSC3'' promoter <ref name="ref1" />.
 +
 +
===Diseases===
 +
* Papillary thyroid carcinoma (PTC) <ref name="ref1" />
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
−
* Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus<ref name="ref1" />.
+
* Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus.<ref name="ref1" />
 +
* Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia.<ref name="ref1" />
 +
* Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China.<ref name="ref2" />
 +
* Department of Geriatrics, Xiangya Second Hospital, Central South University, Changsha 410011, P.R. China.<ref name="ref2" />
 +
* Department of Endocrinology and Internal Medicine (J.J., K.S.), Medical University of Gdansk, Poland.<ref name="ref4" />
 +
* Department of Surgery, Yantai Yuhuangding Hospital, Affiliated with Medical College of Qingdao University, Yantai, China.<ref name="ref5" />
  
 
==References==
 
==References==
Line 66: Line 79:
 
<ref name="ref2"> Fan M, Li X, Jiang W, Huang Y, Li J & Wang Z. A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells[J]. Experimental and therapeutic medicine. 2013, 5(4):1143-1146.
 
<ref name="ref2"> Fan M, Li X, Jiang W, Huang Y, Li J & Wang Z. A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells[J]. Experimental and therapeutic medicine. 2013, 5(4):1143-1146.
 
</ref>(2)
 
</ref>(2)
 +
<ref name="ref3"> Yang Q-Q & Deng Y-F. Long non-coding RNAs as novel biomarkers and therapeutic targets in head and neck cancers[J]. International journal of clinical and experimental pathology. 2014, 7(4):1286.
 +
</ref>(3)
 +
<ref name="ref4"> Jendrzejewski J, Thomas A, Liyanarachchi S, Eiterman A, Tomsic J, He H et al. PTCSC3 is involved in papillary thyroid carcinoma development by modulating S100A4 gene expression[J]. The Journal of Clinical Endocrinology & Metabolism. 2015, 100(10):E1370-E1377.
 +
</ref>(4)
 +
<ref name="ref5"> Zheng H, Wang M, Jiang L, Chu H, Hu J, Ning J et al. BRAF-activated long noncoding RNA modulates papillary thyroid carcinoma cell proliferation through regulating thyroid stimulating hormone receptor[J]. Cancer research and treatment: official journal of Korean Cancer Association. 2016, 48(2):698.
 +
</ref>(5)
 
</references>
 
</references>
  
−
{{basic|
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===sequence===  
−
tID = ENST00000556013.2|
+
>gi|100886964|ref|NR_049735.2| Homo sapiens papillary thyroid carcinoma susceptibility candidate 3 (PTCSC3), long non-coding RNA
−
source = Gencode19|
+
<dnaseq>GAAAGAGGAAAAAAGTGATCTGGGACCTGTTGTTTTTCTTGCATCCCATTTCTACTCTGCCTGTGAGTGAAGACTGTTGTGGAAAAGTCAACTGGAGAGACCAGGTCAAAGGCCAAGCAGAAGAGGAATTAGGCTTAAGACTGCACTGAGAGGGAACACTAGACCATGGTGGCAAAATGGCCGAATAGGAGCAGCTCCAGTCTACAGCTCCCAGGGAGATTAATGCAAAAGATGGAGTCTCGACACGTTGCCCAAGCTGTTCTCAAACTCCAGGGCTTGAACAATCTTCCCACCTTGGCCTCCCAAGGCACTGGAATTACAGAGACAGTGCTCTGCAGGGAGTCTACCACTGTGATGGTTAATACTGAGTGTCAACTTGATTGGATTGAAGGATGCAAAGTATTGTTCCTGGGTGTGTCTGTGAGGGTGTTGCCAAAGGAGATTAACATTTGAGTCAGTGGGCTGGGAAAGGTAGACCCAGCCGTAATCTAGGTGGGCACCATCTAATCAGCTGCCAGCACAGCTAGAAGATAAAGTAGGCAGAAAAACATGAAAACATTAGACTGGCCTA</dnaseq>
−
same = ''PTCSC3'',|
 
−
classification = intergenic|
 
−
length = 571 nt|
 
−
location = chr14-:36605314..36645674|
 
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number = 4|
 
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exons = 36605314..36605562,36623010..36623100,36631830..36631889,36645504..36645674|
 
−
context = <html><div align="center">
 
−
<iframe src="http://lncrna.big.ac.cn/view/?data=species/human&loc=chr14:36605314..36645674&tracklist=0&overview=0&tracks=DNA,RefGene,lncRNA" style=" border-width:0 " width="100%" height="250" scrolling="yes"></iframe>
 
−
</div></html>|
 
−
sequence = <dnaseq>GAAAGAGGAAAAAAGTGATCTGGGACCTGTTGTTTTTCTTGCATCCCATTTCTACTCTGCCTGTGAGTGAAGACTGTTGTGGAAAAGTCAACTGGAGAGACCAGGTCAAAGGCCAAGCAGAAGAGGAATTAGGCTTAAGACTGCACTGAGAGGGAACACTAGACCATGGTGGCAAAATGGCCGAATAGGAGCAGCTCCAGTCTACAGCTCCCAGGGAGATTAATGCAAAAGATGGAGTCTCGACACGTTGCCCAAGCTGTTCTCAAACTCCAGGGCTTGAACAATCTTCCCACCTTGGCCTCCCAAGGCACTGGAATTACAGAGACAGTGCTCTGCAGGGAGTCTACCACTGTGATGGTTAATACTGAGTGTCAACTTGATTGGATTGAAGGATGCAAAGTATTGTTCCTGGGTGTGTCTGTGAGGGTGTTGCCAAAGGAGATTAACATTTGAGTCAGTGGGCTGGGAAAGGTAGACCCAGCCGTAATCTAGGTGGGCACCATCTAATCAGCTGCCAGCACAGCTAGAAGATAAAGTAGGCAGAAAAACATGAAAACATTAGACTGGCCTA</dnaseq>|
 
−
}}
 
−
[[Category:Intergenic]][[Category:ENSG00000259104.2]][[Category:Transcripts]][[Category:Transcripts]]
 

Latest revision as of 10:52, 21 August 2019

PTCSC3, shorted for papillary thyroid carcinoma susceptibility candidate 3, is involved in Papillary thyroid carcinoma.

Annotated Information

Name

PTCSC3: Papillary thyroid carcinoma susceptibility candidate 3 (HGNC nomenclature)

LncBook ID: HSALNT0209589

Characteristics

PTCSC3 structure with promoter region. PTCSC3 consists of four exons and the SNP rs944289 is located 3.2 kb upstream of exon 1; rs944289 is located within a C/EBPα and C/EBPβ transcription factor binding site, and the risk allele destroys it (in silico). It contains an ORF predicting a 95-amino acid peptide starting in exon 1 and ending in exon 4. The ORF is marked in green, and the polyA tail signal sequence (AATAAA) and polyA tail are marked in blue. [1]

PTCSC3 consists of 4 exons with a total length of 1152 bp, located on a human chromosome 14q13.3 and spanning more than 40 kb of genomic region in a linkage disequilibrium block with a GWAS-derived SNP (rs944289) [1].

Function

PTCSC3 regulate the expression of genes involved in DNA replication, recombination, repair, cellular movement, tumor morphology, and cell death especially the genes that are important for papillary thyroid carcinoma (PTC) development and progression such as S100A4, RHOB, MOAP1, AKT, CTSA, MECP2, FLNA, C19orf33, GDF15, and others [1][2].

PTCSC3 expression is highly thyroid specific suggests that it is involved in thyroid function [1]. overexpression of PTCSC3 significantly downregulates miR-574-5p expression in thyroid cancer cells that are of papillary, follicular and anaplastic origin [3].

PTCSC3 expression is significantly down-regulated in tumor compared with unaffected thyroid tissue, and the risk allele is associated with significantly stronger suppression of PTCSC3. The restoration of PTCSC3 expression in PTC cell line affects genes involved in thyroid tumorigenesis and inhibits cell growth [1].

rs944289 predisposes to PTC by dysregulating the expression of PTCSC3, which acts as a tumor suppressor[1].

Expression

PTCSC3 is almost uniquely expressed in thyroid tissue with very low expression additionally in kidney tissue[1].

PTCSC3 significantly down-regulated in papillary thyroid carcinoma tissues compared to non-cancerous tissues [4][5].

The cDNA of PTCSC3 was amplified by PCR,

Primer Experiment Forward Reverse
PTCSC3 PCR 5'-GTACGGTACCCTCCTTCAGACTTCTCAGTACTC-3' 5'-CGACTCGAGATTGCTACTGTGAGCATAACCTAC-3'[3]
PTCSC3 RT-PCR 5'-TCAAACTCCAGGGCTTGAAC-3' 5'-ATTACGGCTGGGTCTACCT-3'[3]
PTCSC3 Quantitative RT-PCR 5'-TCAAACTCCAGGGCTTGAAC-3' 5'-ATTACGGCTGGGTCTACCT-3'[3]
PTCSC3 PCR 5'-gtacggtaccCTCCTTCAGACTTCTCAGTACTC-3' 5'-tcgactcgagATTGCTACTGTGAGCATAACCTAC-3'[1]
rs944289 PCR 5'-atcaggtaccGGCAATTGAAGTTCCCAAAA-3' 5'-atcactcgagGCCTCCAGACTTGGACTGAG-3'[1]

Regulation

C/EBPα and C/EBPβ regulate the transcriptional activity of the PTCSC3 promoter [1].

Diseases

  • Papillary thyroid carcinoma (PTC) [1]

Labs working on this lncRNA

  • Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus.[1]
  • Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia.[1]
  • Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China.[3]
  • Department of Geriatrics, Xiangya Second Hospital, Central South University, Changsha 410011, P.R. China.[3]
  • Department of Endocrinology and Internal Medicine (J.J., K.S.), Medical University of Gdansk, Poland.[2]
  • Department of Surgery, Yantai Yuhuangding Hospital, Affiliated with Medical College of Qingdao University, Yantai, China.[5]

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 Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, et al. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type[J]. Proceedings of the National Academy of Sciences of the United States of America. 2012,109(22):8646-51.
  2. ↑ 2.0 2.1 Jendrzejewski J, Thomas A, Liyanarachchi S, Eiterman A, Tomsic J, He H et al. PTCSC3 is involved in papillary thyroid carcinoma development by modulating S100A4 gene expression[J]. The Journal of Clinical Endocrinology & Metabolism. 2015, 100(10):E1370-E1377.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Fan M, Li X, Jiang W, Huang Y, Li J & Wang Z. A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells[J]. Experimental and therapeutic medicine. 2013, 5(4):1143-1146.
  4. ↑ Yang Q-Q & Deng Y-F. Long non-coding RNAs as novel biomarkers and therapeutic targets in head and neck cancers[J]. International journal of clinical and experimental pathology. 2014, 7(4):1286.
  5. ↑ 5.0 5.1 Zheng H, Wang M, Jiang L, Chu H, Hu J, Ning J et al. BRAF-activated long noncoding RNA modulates papillary thyroid carcinoma cell proliferation through regulating thyroid stimulating hormone receptor[J]. Cancer research and treatment: official journal of Korean Cancer Association. 2016, 48(2):698.

sequence

>gi|100886964|ref|NR_049735.2| Homo sapiens papillary thyroid carcinoma susceptibility candidate 3 (PTCSC3), long non-coding RNA

000001 GAAAGAGGAA AAAAGTGATC TGGGACCTGT TGTTTTTCTT GCATCCCATT TCTACTCTGC CTGTGAGTGA AGACTGTTGT 000080
000081 GGAAAAGTCA ACTGGAGAGA CCAGGTCAAA GGCCAAGCAG AAGAGGAATT AGGCTTAAGA CTGCACTGAG AGGGAACACT 000160
000161 AGACCATGGT GGCAAAATGG CCGAATAGGA GCAGCTCCAG TCTACAGCTC CCAGGGAGAT TAATGCAAAA GATGGAGTCT 000240
000241 CGACACGTTG CCCAAGCTGT TCTCAAACTC CAGGGCTTGA ACAATCTTCC CACCTTGGCC TCCCAAGGCA CTGGAATTAC 000320
000321 AGAGACAGTG CTCTGCAGGG AGTCTACCAC TGTGATGGTT AATACTGAGT GTCAACTTGA TTGGATTGAA GGATGCAAAG 000400
000401 TATTGTTCCT GGGTGTGTCT GTGAGGGTGT TGCCAAAGGA GATTAACATT TGAGTCAGTG GGCTGGGAAA GGTAGACCCA 000480
000481 GCCGTAATCT AGGTGGGCAC CATCTAATCA GCTGCCAGCA CAGCTAGAAG ATAAAGTAGG CAGAAAAACA TGAAAACATT 000560
000561 AGACTGGCCT A
Retrieved from "https://ngdc.cncb.ac.cn/lncrnawiki1/index.php?title=ENST00000556013.2&oldid=1276516"