Difference between revisions of "NONHSAT096369"

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''DANCR'', an 855-base-pair lncRNA, suppressed differentiation.
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''DANCR'': A valuable cancer related long non-coding RNA for human cancers
  
 
==Annotated Information==
 
==Annotated Information==
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===Transcriptomic Nomeclature===
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===Name===
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''DANCR''，differentiation antagonizing non-protein coding RNA（HGNC nomenclature)
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Approved symbol: ''DANCR''
  
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"anti-differentiation ncRNA", "anti-differentiation noncoding RNA", lncRNA-ANCR<ref name="ref1" />
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Approved Name: ''DANCR'': Differentiation antagonizing non-protein coding RNA
  
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KIAA0114, "KIAA0114"<ref name="ref2" />
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Alias names: "anti-differentiation ncRNA",
 +
"anti-differentiation noncoding RNA",
 +
lncRNA-ANCR<ref name="ref1" />
 +
KIAA0114,"KIAA0114"<ref name="ref2" />
 +
"small nucleolar RNA host gene 13 (non-protein coding)", SNHG13 "adipogenesis up-regulated transcript 2", ''AGU2''<ref name="ref3" />
  
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"small nucleolar RNA host gene 13 (non-protein coding)", SNHG13 "adipogenesis up-regulated transcript 2", ''AGU2''<ref name="ref3" />
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LncBook transcript ID: HSALNT0288925
  
 
===Characteristics===
 
===Characteristics===
−
The ANCR gene is located on human chromosome 4, with the closest adjacent annotated genes located 54.8 kb upstream of (USP46) and 28.7 kb downstream from (ERVMER34-1) the ANCR locus. The ANCR locus consists of three exons and harbors a microRNA (MIR4449) and a snoRNA (SNORA26) in introns 1 and 2, respectively. These small RNAs are not coordinately expressed with ANCR and are not part of the mature ANCR transcript). <ref name="ref1" />
+
The ''DANCR'' gene is 855-base-pair long noncoding RNA located on human chromosome 4, with the closest adjacent annotated genes located 54.8 kb upstream of (USP46) and 28.7 kb downstream from (ERVMER34-1) the ''DANCR'' locus. The ''DANCR'' locus consists of three exons and harbors a microRNA (MIR4449) and a snoRNA (SNORA26) in introns 1 and 2, respectively. These small RNAs are not coordinately expressed with ''DANCR'' and are not part of the mature ''DANCR'' transcript. <ref name="ref1" />.
−
 
+
''DANCR'' contains another conserved GC-rich region in the first intron, which may be processed as a not-yet-annotated small functional RNA. This notion does, however, require more intensive analysis of the function of ''DANCR''. From an evolutionary perspective, it is of interest that transcription units of ''DANCR'' as well as AGD2 are shaped by retrotransposons. AGU2 contains a long terminal repeat (LTR)-like element, which provides its polyA signal.<ref name="ref3" />
−
It contains another conserved GC-rich region in the first intron, which may be processed as a not-yet-annotated small functional RNA. This notion does, however, require more intensive analysis of the function of DANCR. From an evolutionary perspective, it is of interest that transcription units of DANCR as well as AGD2 are shaped by retrotransposons. AGU2 contains a long terminal repeat (LTR)-like element, which provides its polyA signal.<ref name="ref3" />
 
  
 
===Function===
 
===Function===
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[[File: ANCR regulates a global gene expression program associated with epidermal differentiation..jpg|right|thumb|400px|'''ANCR regulates a global gene expression program associated with epidermal differentiation.''' <ref name="ref1" />.]]
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''DANCR'' suppresses a genetic program associated with epidermal differentiation. Depleting ''DANCR'' in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ''DANCR'' lncRNA is thus required to enforce the undifferentiated cell state within epidermis <ref name="ref1" />.
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''ANCR'' suppresses a genetic program associated with epidermal differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis<ref name="ref1" />
 
  
 
===Regulation===
 
===Regulation===
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''AGU2'' induction seen in adipogenesis might be due to cooperative stimulation by  Dex and IBMX.<ref name="ref3" />
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''AGU2'' induction conteol ''DANCR'' regulation<ref name="ref3" />.
 +
 
 +
===Disease===
 +
*Breast Cancer <ref name="ref4" />
 +
*Colorectal Cancer <ref name="ref4" />
 +
*Hepatocellular Cancer <ref name="ref4" />
 +
*Gastric Cancer <ref name="ref4" />
 +
*Glioma <ref name="ref4" />
 +
*Osteosarcoma <ref name="ref4" />
 +
*Prostate Cancer <ref name="ref4" />
  
 
===Expression===
 
===Expression===
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{|class='wikitable' style="text-align:center"
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Long non-coding RNAs-''DANCR'' is a valuable cancer-related lncRNA that its dysregulated expression was found in a variety of malignancies, including hepatocellular carcinoma, breast cancer, glioma, colorectal cancer, gastric cancer, and lung cancer. The aberrant expressions of ''DANCR'' have been shown to contribute to proliferation, migration, and invasion of cancer cells <ref name="ref4" />
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|-
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===Sequence===
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| rowspan="1"| siControl(sense sequence)
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>gi|57291|ref|024031.2|Homo sapiens differentiation antagonizing non-protein coding RNA (DANCR), transcript variant 1, long non-coding RNA
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| | GUAGAUUCAUAUUGUAAGGUU<ref name="ref1" />
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<dnaseq>CCTCGCGACCCTCCTGCTTCCCTCCCCGCCCCGCGCCGCCTCTCTGGTTTGTGCGCCCGTCGCAGGTCGCAGGCCTCTTTGTCAGCTGGAGTTGCGCGGGCTGACGCGCCACTATGTAGCGGGTTTCGGGCGGGCCACGCGTGCGGGACAGGAACCCAACCCCAGCCGACCTTGAGCTCCAGGAGTTCGTCTCTTACGTCTGCGGAAGTGCAGCTGCCTCAGTTCTTAGCGCAGGTTGACAACTACAGGCACAAGCCATTGAAGCTGGAATGTCCTGTTGCTGGTATTTCAATTGACTTAAGCCAACTATCCCTTCAGTTACAATAGGAAAGTGCCTCTAATAAGGCCAAATATGCGTACTAACTTGTAGCAACCACGTGTCCGTGCAGTGCCACAGGAGCTAGAGCAGTGACAATGCTGGTGGCAACAGGGCAGTGTAGCAGGTGCTTCATGTTCACCTTTTCAACCTTTTCATTTAATTGTCACAACTCGGAGGTGGATTCTGTTAGGGACAGGCTGCCCCAGGACCACTCCGCCCCCGCTAACTCAATGCAGCTGACCCTTACCCTGAATACTCTGCAGCTGCATTCCTGAACCGTTATCTAGGCGCTATAGCAAGGTCACCAGACTTGCTACACCGAAGCCCTCTGGGTGGCACGGGGGAGGTCATGAGAAACGTGGATTACACCCCCTTGTAAATTCCTATTTTCACAAGATAATATATTGTAAGCCGGTCATGAGATTATATGTGGTAAAGTTAATTGACTAACAACCCCAGGGTCTCTCTCCCCCATATAAACCCCTCATTTTGTAAGCTCAGGGCTGCCACCTCCGACTGGTGGAGAAGCCTGGCAGGTTAATAAACTTACTTGGCCTGA</dnaseq>
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|-
 
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| rowspan="1"| siANCR(sense sequence)
 
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| | GCAGGTATGTTCCTAGCCT<ref name="ref1" />
 
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|-
 
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| rowspan="1"| shControl(sense sequence)
 
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| | GCTTCAATTCGCGCACCTA<ref name="ref1" />
 
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|-
 
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| rowspan="1"| shANCR (sense sequence)
 
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| |GCGTACTAACTTGTAGCAA.<ref name="ref1" />
 
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|}
 
−
 
 
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
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Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA<ref name="ref1" />
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*Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA.
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*Kazusa DNA Research Institute, Chiba, Japan
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Kazusa DNA Research Institute, Chiba, Japan<ref name="ref2" />
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*Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan China
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*Department of Pain Management, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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Center for Biological Resources and Informatics<ref name="ref3" />
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*Department of Radiology & Nuclear Medicine, Zhongnan Hospital of Wuhan University, Wuchang, Hubei Province, Wuhan, 430071, China
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==References==
 
==References==
Line 52: Line 51:
 
<ref name="ref2">Nagase T, Miyajima N, Tanaka A, Sazuka T, Seki N, Sato S, et al. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1[J]. DNA research : an international journal for rapid publication of reports on genes and genomes. 1995,2(1):37-43.</ref>(2）
 
<ref name="ref2">Nagase T, Miyajima N, Tanaka A, Sazuka T, Seki N, Sato S, et al. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1[J]. DNA research : an international journal for rapid publication of reports on genes and genomes. 1995,2(1):37-43.</ref>(2）
 
<ref name="ref3">Kikuchi K, Fukuda M, Ito T, Inoue M, Yokoi T, Chiku S, et al. Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation[J]. Nucleic acids research. 2009,37(15):4987-5000</ref>(3)
 
<ref name="ref3">Kikuchi K, Fukuda M, Ito T, Inoue M, Yokoi T, Chiku S, et al. Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation[J]. Nucleic acids research. 2009,37(15):4987-5000</ref>(3)
 +
<ref name="ref4">Thin KZ, Liu X, Feng X, Raveendran S & Tu JC. LncRNA-DANCR: A valuable cancer related long non-coding RNA for human cancers[J]. Pathology-Research and Practice. 2018
 +
</ref>(4)
 
</references>
 
</references>
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{{basic|
 
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tID = NONHSAT096369|
 
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source = NONCODE4.0|
 
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same = ''DANCR'',''ANCR'',"anti-differentiation ncRNA", "anti-differentiation noncoding RNA", lncRNA-ANCR,KIAA0114, "KIAA0114","small nucleolar RNA host gene 13 (non-protein coding)", ''SNHG13'' "adipogenesis up-regulated transcript 2", ''AGU2''|
 
−
classification = intergenic|
 
−
length = 878 nt|
 
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location = chr4+:53578425..53580478|
 
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number = 3|
 
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exons = 53578425..53578694,53578991..53579126,53579661..53580478|
 
−
context = <html><div align="center">
 
−
<iframe src="http://lncrna.big.ac.cn/view/?data=species/human&loc=chr4:53578425..53580478&tracklist=0&overview=0&tracks=DNA,RefGene,lncRNA" style=" border-width:0 " width="100%" height="250" scrolling="yes"></iframe>
 
−
</div></html>|
 
−
sequence = <dnaseq>CCTCGCGACCCTCCTGCTTCCCTCCCCGCCCCGCGCCGCCTCTCTGGTTTGTGCGCCCGTCGCAGGTCGCAGGCCTCTTTGTCAGCTGGAGTTGCGCGGGCTGACGCGCCACTATGTAGCGGGTTTCGGGCGGGCCACGCGTGCGGGACAGGAACCCAACCCCAGCCGACCTTGAGCTCCAGGAGTTCGTCTCTTACGTCTGCGGAAGTGCAGCTGCCTCAGTTCTTAGCGCAGGTTGACAACTACAGGCACAAGCCATTGAAGCTGGAATGTCCTGTTGCTGGTATTTCAATTGACTTAAGCCAACTATCCCTTCAGTTACAATAGGAAAGTGCCTCTAATAAGGCCAAATATGCGTACTAACTTGTAGCAACCACGTGTCCGTGCAGTGCCACAGGAGCTAGAGCAGTGACAATGCTGGTGGCAACAGGGCAGTGTAGCAGGTGCTTCATGTTCACCTTTTCAACCTTTTCATTTAATTGTCACAACTCGGAGGTGGATTCTGTTAGGGACAGGCTGCCCCAGGACCACTCCGCCCCCGCTAACTCAATGCAGCTGACCCTTACCCTGAATACTCTGCAGCTGCATTCCTGAACCGTTATCTAGGCGCTATAGCAAGGTCACCAGACTTGCTACACCGAAGCCCTCTGGGTGGCACGGGGGAGGTCATGAGAAACGTGGATTACACCCCCTTGTAAATTCCTATTTTCACAAGATAATATATTGTAAGCCGGTCATGAGATTATATGTGGTAAAGTTAATTGACTAACAACCCCAGGGTCTCTCTCCCCCATATAAACCCCTCATTTTGTAAGCTCAGGGCTGCCACCTCCGACTGGTGGAGAAGCCTGGCAGGTTAATAAACTTACTTGGCCTGA</dnaseq>|
 
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}}
 
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[[Category:Intergenic]][[Category:NONHSAG037936]][[Category:Transcripts]]
 

Latest revision as of 02:44, 13 August 2019

DANCR: A valuable cancer related long non-coding RNA for human cancers

Annotated Information

Name

Approved symbol: DANCR

Approved Name: DANCR: Differentiation antagonizing non-protein coding RNA

Alias names: "anti-differentiation ncRNA", "anti-differentiation noncoding RNA", lncRNA-ANCR[1] KIAA0114,"KIAA0114"[2] "small nucleolar RNA host gene 13 (non-protein coding)", SNHG13 "adipogenesis up-regulated transcript 2", AGU2[3]

LncBook transcript ID: HSALNT0288925

Characteristics

The DANCR gene is 855-base-pair long noncoding RNA located on human chromosome 4, with the closest adjacent annotated genes located 54.8 kb upstream of (USP46) and 28.7 kb downstream from (ERVMER34-1) the DANCR locus. The DANCR locus consists of three exons and harbors a microRNA (MIR4449) and a snoRNA (SNORA26) in introns 1 and 2, respectively. These small RNAs are not coordinately expressed with DANCR and are not part of the mature DANCR transcript. [1]. DANCR contains another conserved GC-rich region in the first intron, which may be processed as a not-yet-annotated small functional RNA. This notion does, however, require more intensive analysis of the function of DANCR. From an evolutionary perspective, it is of interest that transcription units of DANCR as well as AGD2 are shaped by retrotransposons. AGU2 contains a long terminal repeat (LTR)-like element, which provides its polyA signal.[3]

Function

DANCR suppresses a genetic program associated with epidermal differentiation. Depleting DANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The DANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis [1].

Regulation

AGU2 induction conteol DANCR regulation[3].

Disease

  • Breast Cancer [4]
  • Colorectal Cancer [4]
  • Hepatocellular Cancer [4]
  • Gastric Cancer [4]
  • Glioma [4]
  • Osteosarcoma [4]
  • Prostate Cancer [4]

Expression

Long non-coding RNAs-DANCR is a valuable cancer-related lncRNA that its dysregulated expression was found in a variety of malignancies, including hepatocellular carcinoma, breast cancer, glioma, colorectal cancer, gastric cancer, and lung cancer. The aberrant expressions of DANCR have been shown to contribute to proliferation, migration, and invasion of cancer cells [4]

Sequence

>gi|57291|ref|024031.2|Homo sapiens differentiation antagonizing non-protein coding RNA (DANCR), transcript variant 1, long non-coding RNA

000001 CCTCGCGACC CTCCTGCTTC CCTCCCCGCC CCGCGCCGCC TCTCTGGTTT GTGCGCCCGT CGCAGGTCGC AGGCCTCTTT 000080
000081 GTCAGCTGGA GTTGCGCGGG CTGACGCGCC ACTATGTAGC GGGTTTCGGG CGGGCCACGC GTGCGGGACA GGAACCCAAC 000160
000161 CCCAGCCGAC CTTGAGCTCC AGGAGTTCGT CTCTTACGTC TGCGGAAGTG CAGCTGCCTC AGTTCTTAGC GCAGGTTGAC 000240
000241 AACTACAGGC ACAAGCCATT GAAGCTGGAA TGTCCTGTTG CTGGTATTTC AATTGACTTA AGCCAACTAT CCCTTCAGTT 000320
000321 ACAATAGGAA AGTGCCTCTA ATAAGGCCAA ATATGCGTAC TAACTTGTAG CAACCACGTG TCCGTGCAGT GCCACAGGAG 000400
000401 CTAGAGCAGT GACAATGCTG GTGGCAACAG GGCAGTGTAG CAGGTGCTTC ATGTTCACCT TTTCAACCTT TTCATTTAAT 000480
000481 TGTCACAACT CGGAGGTGGA TTCTGTTAGG GACAGGCTGC CCCAGGACCA CTCCGCCCCC GCTAACTCAA TGCAGCTGAC 000560
000561 CCTTACCCTG AATACTCTGC AGCTGCATTC CTGAACCGTT ATCTAGGCGC TATAGCAAGG TCACCAGACT TGCTACACCG 000640
000641 AAGCCCTCTG GGTGGCACGG GGGAGGTCAT GAGAAACGTG GATTACACCC CCTTGTAAAT TCCTATTTTC ACAAGATAAT 000720
000721 ATATTGTAAG CCGGTCATGA GATTATATGT GGTAAAGTTA ATTGACTAAC AACCCCAGGG TCTCTCTCCC CCATATAAAC 000800
000801 CCCTCATTTT GTAAGCTCAG GGCTGCCACC TCCGACTGGT GGAGAAGCCT GGCAGGTTAA TAAACTTACT TGGCCTGA

Labs working on this lncRNA

  • Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA.
  • Kazusa DNA Research Institute, Chiba, Japan
  • Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan China
  • Department of Pain Management, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
  • Department of Radiology & Nuclear Medicine, Zhongnan Hospital of Wuhan University, Wuchang, Hubei Province, Wuhan, 430071, China

References

  1. ↑ 1.0 1.1 1.2 Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, et al. Suppression of progenitor differentiation requires the long noncoding RNA ANCR[J]. Genes & development. 2012,26(4):338-43.
  2. ↑ Nagase T, Miyajima N, Tanaka A, Sazuka T, Seki N, Sato S, et al. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1[J]. DNA research : an international journal for rapid publication of reports on genes and genomes. 1995,2(1):37-43.
  3. ↑ 3.0 3.1 3.2 Kikuchi K, Fukuda M, Ito T, Inoue M, Yokoi T, Chiku S, et al. Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation[J]. Nucleic acids research. 2009,37(15):4987-5000
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 Thin KZ, Liu X, Feng X, Raveendran S & Tu JC. LncRNA-DANCR: A valuable cancer related long non-coding RNA for human cancers[J]. Pathology-Research and Practice. 2018
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