Difference between revisions of "NONHSAT028508"

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Please input one-sentence summary here.
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HOTAIR epigenetically silence gene expression at many sites across the genome by recruitment of chromatin modifying complexes and the abnormal expression of HOTAIR is highly correlated with the development of many kinds of human cancers.
  
 
==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
HOTAIR: Hox antisense intergenic RNA
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Approved symbol: HOTAIR
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Approved name: HOX transcript antisense RNA
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HGNC ID: HGNC:33510
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Previous names: HOX transcript antisense RNA (non-protein coding)
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Alias symbols: HOXC-AS4; HOXC11-AS1; NCRNA00072
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Alias names: HOXC cluster antisense RNA 4 (non-protein coding); non-protein coding RNA 72
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RefSeq ID: NR_003716
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LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0289004 HSALNT0289004]
  
 
===Characteristics===
 
===Characteristics===
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Transcribed from the HOXC locus from a position intergenic and antisense to the flanking HOXC11 and HOXC12 genes <ref name="ref1" />.
 
Transcribed from the HOXC locus from a position intergenic and antisense to the flanking HOXC11 and HOXC12 genes <ref name="ref1" />.
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Some HOTAIR transcripts localise to the nucleus <ref name="ref4" />.
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Transcript found to be quite unstable with a half-life >4 hr in human Hela cells<ref name="ref6" />.
  
 
===Function===
 
===Function===
Originally identified as silencing the HoxD locus but has since been found to epigenetic silence gene expression at many sites across the genome by recruitment of PRC2 and LSD1/CoREST/REST repressive chromatin modifying complexes <ref name="ref1" />.<ref name="ref7" />.
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[[File: Hotair.png|thumb|550px| Changes in mRNA and occupancy of H3K4me2, H3K27me3, LSD1, and SUZ12 across HOXD locus after RNAi of HOTAIR in foreskin fibroblasts. Yellow boxes indicate regions of notable correlation between gain of H3K4me2 and concordant loss of LSD1, H3K27me3, and SUZ12. <ref name="ref7"/>]]
  
HOTAIR acts as a scaffold for protein complexes. A 5' domain binds PRC2 while a 3' domain binds LSD1<ref name="ref7" />.  
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Originally identified as silencing the HoxD locus<ref name="ref21" /> but has since been found to epigenetic silence gene expression at many sites across the genome by recruitment of PRC2 and LSD1/CoREST/REST repressive chromatin modifying complexes <ref name="ref1" /><ref name="ref7" />.  
  
Oncogene - regulates metastatic progression <ref name="ref2" />.<ref name="ref5" />.  
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HOTAIR has been suggested to function at the chromatin level by interacting with chromatin modifying protein complexes <ref name="ref9" />. It has been reported that HOTAIR expression is correlated with SUZ12 expression level and therefore may affect the epigenetic state of cancer tissues<ref name="ref11" />. HOTAIR acts as a scaffold for protein complexes. A 5' domain binds PRC2 while a 3' domain binds LSD1<ref name="ref7" />. Oncogenic effects of HOTAIR upregulation were dependent on PRC2 <ref name="ref2" />.  
  
HOTAIR dysregulated in breast cancer with frequent overexpression in metastases. Overexpression of HOTAIR leads to PRC2 re-targeting across the genome to a state similar to that in embryonic fibroblasts, promoting tumour invasion and metatasis. Oncogenic effects of HOTAIR upregulation were dependent on PRC2 <ref name="ref2" />.  
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Oncogene - regulates metastatic progression in many kinds of cancers <ref name="ref2" /><ref name="ref5" /><ref name="ref18" /><ref name="ref12" /><ref name="ref3" /><ref name="ref11" />. It is crucial for cell growth and viability and its knockdown induced apoptosis in breast cancer cells<ref name="ref10" />. There was a great upregulation of HOTAIR in Esophageal squamous cell carcinoma (ESCC) compared to their adjacent normal esophageal tissues. Meanwhile, patients with high HOTAIR expression have a significantly poorer prognosis than those with low expression. Moreover, HOTAIR was further validated to promote migration and invasion of ESCC cells in vitro<ref name="ref18" />. Knockdown of HOTAIR decreased prostate cancer (PCa) cell proliferation, migration and invasion and induced apoptosis and cell cycle arrest <ref name="ref12" />. High HOTAIR expression tightly correlated with the presence of liver metastasis and associated with poor prognosis <ref name="ref3" />. The aberrant expression of HOTAIR was associated with TNM staging and lymph node metastasis of gastric tumors<ref name="ref11" />. Reduced expression of HOTAIR in KATO III suppressed peritoneal dissemination suggest that HOTAIR plays a pivotal role in the development of gastric cancer<ref name="ref14" />.
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It is also highly correlated with malignant degree of cancer and the therapeutic effect <ref name="ref13" /><ref name="ref2" /><ref name="ref19" /><ref name="ref15" /><ref name="ref17" />.
  
 
Deletion of the HoxC cluster containing the cognate Hotair transcript in mouse showed little phenotypic effect, with little change in the expression on levels of H3K27me3 coverage in corresponding human HOTAIR Hoxd target genes <ref name="ref5" />.
 
Deletion of the HoxC cluster containing the cognate Hotair transcript in mouse showed little phenotypic effect, with little change in the expression on levels of H3K27me3 coverage in corresponding human HOTAIR Hoxd target genes <ref name="ref5" />.
  
Several species, such as the mammalian XIST or HOTAIR RNAs, have been suggested to function at the chromatin level by interacting with chromatin modifying protein complexes <ref name="ref9" />.HOTAIR methylation is not altered in cancer cells <ref name="ref9" />. HOTAIR coordinates with chromatin-modifying enzymes and regulates gene silencing. It is overexpressed in various carcinomas including breast cancer. Herein, we demonstrated that HOTAIR is crucial for cell growth and viability and its knockdown induced apoptosis in breast cancer cells<ref name="ref10" />.It has been reported that HOTAIR expression is correlated with SUZ12 expression level and therefore may affect the epigenetic state of cancer tissues<ref name="ref11" />.
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HOTAIR acts as an inducer of ubiquitin-mediated proteolysis on post-translational function<ref name="ref20" />. HOTAIR associates with E3 ubiquitin ligases bearing RNA-binding domains, Dzip3 and Mex3b, as well as with their respective ubiquitination substrates, Ataxin-1 and Snurportin-1. HOTAIR levels are highly upregulated in senescent cells, causing rapid decay of targets Ataxin-1 and Snurportin-1, and preventing premature senescence<ref name="ref20" />.
  
 
===Expression===
 
===Expression===
 
Expressed in posterior and distal fibroblasts <ref name="ref1" />.  
 
Expressed in posterior and distal fibroblasts <ref name="ref1" />.  
 
Expression level in cancer is an efficient predictor of metastasis and survival with high expression levels predictive of poor outcomes <ref name="ref2" />. Also in patients with stage IV colorectal cancer (CRC), HOTAIR expression levels were higher in cancerous tissues than in noncancerous tissues, with high HOTAIR expression tightly correlated with the presence of liver metastasis and associated with poor prognosis <ref name="ref3" />.
 
 
Some HOTAIR transcripts localise to the nucleus <ref name="ref4" />.
 
  
 
In situ hybridization analysis of the mouse cognate RNA (mHotair) showed expression similar to Hoxc11, with distinct levels in parts of the proximal hindlimbs, genital bud and tail in embryos at E11.5, as well as in in posterior part of the hindlimb and genital bud at E12.5 <ref name="ref5" />.
 
In situ hybridization analysis of the mouse cognate RNA (mHotair) showed expression similar to Hoxc11, with distinct levels in parts of the proximal hindlimbs, genital bud and tail in embryos at E11.5, as well as in in posterior part of the hindlimb and genital bud at E12.5 <ref name="ref5" />.
  
Transcript found to be quite unstable with a half-life >4 hr in human Hela cells<ref name="ref6" />.
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It is up-regulated in breast cancer <ref name="ref2" /><ref name="ref10" />, colorectal cancer (CRC) <ref name="ref3" />, Esophageal squamous cell carcinoma (ESCC) <ref name="ref18" />, ovarian cancer <ref name="ref13" />, gastric adenocarcinoma samples <ref name="ref11" />,Non-small-cell lung carcinoma (NSCLC) <ref name="ref19" />, laryngeal squamous cell cancer (LSCC) <ref name="ref15" />,cisplatin-resistant A549/DDP cells <ref name="ref16" />.
 
 
There is site-specific cytosine methylation in the lncRNA HOTAIR. Methylation of C1683 is widespread in different cell types and it is not limited by the abundance of HOTAIR RNA levels. Furthermore, the degree of methylation of C1683 appears to be remarkably high, suggesting that it might be important for the function of HOTAIR. In this respect, it is interesting to note that C1683 is located in the vicinty of the region that has previously been shown to interact with the LSD1 complex.It is therefore tempting to speculate thatmethylation of this cytosine may affect the ability of HOTAIR to interact with LSD1<ref name="ref9" />.LncRNA profiling showed that HOTAIR was highly regulated by genistein and its expression was higher in castration-resistant PCa cell lines than in normal prostate cells. Knockdown (siRNA) of HOTAIR decreased PCa cell proliferation, migration and invasion and induced apoptosis and cell cycle arrest. miR-34a was also up-regulated by genistein and may directly target HOTAIR in both PC3 and DU145 PCa cells<ref name="ref12" />.RNA HOTAIR expressions were higher in ovarian cancer; it may play a role in ovarian cancer, and become a biomarker for malignant degree of ovarian cancer and may provide a novel therapeutic target for ovarian cancer<ref name="ref13" />. Reduced expression of HOTAIR in KATO III suppressed peritoneal dissemination suggest that HOTAIR plays a pivotal role in the development of gastric cancer<ref name="ref14" />. HOTAIR plays an oncogenic role in human laryngeal squamous cell cancer (LSCC),HOTAIR levels were significantly higher in LSCC than in corresponding adjacent non-neoplastic tissues,HOTAIR is an independent prognostic factor of LSCC<ref name="ref15" />. HOTAIR expression was significantly upregulated in cisplatin-resistant A549/DDP cells compared with in parental A549 cells. Knockdown of HOTAIR by RNA interference could resensitize the responses of A549/DDP cells to cisplatin both in vitro and in vivo. In contrast, overexpression of HOTAIR could decrease the sensitivity of A549 and SPC-A1 cells to cisplatin. We also found that the siRNA/HOTAIR1-mediated chemosensivity enhancement was associated with inhibition of cell proliferation, induction of G0/G1 cell-cycle arrest and apoptosis enhancement through regulation of p21(WAF1/CIP1) (p21) expression. Also, pcDNA/p21or siRNA/p21 could mimic the effects of siRNA/HOTAIR1 or pcDNA/HOTAIR on the sensitivity of LAD cells to cisplatin. Importantly, siRNA/p21 or pcDNA/p21 could partially rescue the effects of siRNA/HOTAIR1 or pcDNA/HOTAIR on both p21 expression and cisplatin sensitivity in LAD cells. Further, HOTAIR was observed to be significantly downregulated in cisplatin-responding LAD tissues, and its expression was inversely correlated with p21 mRNA expression. Taken together, our findings suggest that upregulation of HOTAIR contributes to the cisplatin resistance of LAD cells, at least in part, through the regulation of p21 expression <ref name="ref16" />.HOTAIR is a potential biomarker for ESCC prognosis, and the dysregulation of HOTAIR may play an important role in ESCC progression<ref name="ref17" />.
 
  
 
===Conservation===
 
===Conservation===
HOTAIR exists in mammals but with poor sequence conservation <ref name="ref1" />.<ref name="ref8" />. A 239 bp domain in HOTAIR exon 6 is especially conserved in mammals <ref name="ref8" />.  
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HOTAIR exists in mammals but with poor sequence conservation <ref name="ref1" /><ref name="ref8" />. A 239 bp domain in HOTAIR exon 6 is especially conserved in mammals <ref name="ref8" />.  
  
 
The mouse EST (AK035706) homologous to human HOTAIR is comprised of two exons only, with the second half of the first exon showing similarity to exon 4 of HOTAIR, whereas the second exon is homologous to exon 6 of HOTAIR <ref name="ref5" />. This may underlie differences in function since the first three exons of HOTAIR (absent from mHotair) contain binding sites for EZH2, while the 3' extremity of human HOTAIR that interact with LSD1 is part of the least conserved DNA sequence within mHotair exon 2 <ref name="ref5" />.
 
The mouse EST (AK035706) homologous to human HOTAIR is comprised of two exons only, with the second half of the first exon showing similarity to exon 4 of HOTAIR, whereas the second exon is homologous to exon 6 of HOTAIR <ref name="ref5" />. This may underlie differences in function since the first three exons of HOTAIR (absent from mHotair) contain binding sites for EZH2, while the 3' extremity of human HOTAIR that interact with LSD1 is part of the least conserved DNA sequence within mHotair exon 2 <ref name="ref5" />.
 
===Misc===
 
Please input misc information here.
 
 
===Transcriptomic Nomeclature===
 
HOTAIR is transcriptionally induced by estradiol (E2). Its promoter contains multiple functional estrogen response elements (EREs). Estrogen receptors (ERs) along with various ER coregulators such as histone methylases MLL1 (mixed lineage leukemia 1) and MLL3 and CREB-binding protein/p300 bind to the promoter of HOTAIR in an E2-dependent manner. Level of histone H3 lysine-4 trimethylation, histone acetylation, and RNA polymerase II recruitment is enriched at the HOTAIR promoter in the presence of E2. Knockdown of ERs and MLLs downregulated the E2-induced HOTAIR expression. Thus, similar to protein-coding gene transcription, E2-induced transcription of antisense transcript HOTAIR is coordinated via ERs and ER coregulators, and this mechanism of HOTAIR overexpression potentially contributes towards breast cancer progression<ref name="ref10" />.
 
  
 
===Regulation===
 
===Regulation===
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HOTAIR is transcriptionally induced by estradiol (E2). Similar to protein-coding gene transcription, E2-induced transcription of antisense transcript HOTAIR is coordinated via ERs and ER coregulators, and this mechanism of HOTAIR overexpression potentially contributes towards breast cancer progression<ref name="ref10" />.
 
The long non-coding RNA HOTAIR has been reported to be a poor prognostic biomarker in a variety of malignant tumors<ref name="ref14" />.
 
The long non-coding RNA HOTAIR has been reported to be a poor prognostic biomarker in a variety of malignant tumors<ref name="ref14" />.
There was a great upregulation of HOTAIR in ESCC compared to their adjacent normal esophageal tissues. Meanwhile, patients with high HOTAIR expression have a significantly poorer prognosis than those with low expression. Moreover, HOTAIR was further validated to promote migration and invasion of ESCC cells in vitro<ref name="ref18" />.
 
Aberrant up-regulation of HOTAIR in gastric adenocarcinoma samples compared with normal adjacent gastric epithelium tissues. Besides, the aberrant expression of HOTAIR was associated with TNM staging and lymph node metastasis of gastric tumors. Here, a potential cooperative expression between HOTAIR and SUZ12 genes in gastric adenocarcinoma tissues is deduced<ref name="ref11" />.HOTAIR upregulation was correlated with NSCLC advanced pathological stage and lymph-node metastasis, HOTAIR is significantly up-regulated in NSCLC tissues, and regulates NSCLC cell invasion and metastasis, partially via the down-regulation of HOXA5. Thus, HOTAIR may represent a new marker of poor prognosis and is a potential therapeutic target for NSCLC intervention<ref name="ref19" />.
 
HOTAIR as an inducer of ubiquitin-mediated proteolysis on post-translational function<ref name="ref20" />. HOTAIR associates with E3 ubiquitin ligases bearing RNA-binding domains, Dzip3 and Mex3b, as well as with their respective ubiquitination substrates, Ataxin-1 and Snurportin-1. In this manner, HOTAIR facilitates the ubiquitination of Ataxin-1 by Dzip3 and Snurportin-1 by Mex3b in cells and in vitro, and accelerates their degradation. HOTAIR levels are highly upregulated in senescent cells, causing rapid decay of targets Ataxin-1 and Snurportin-1, and preventing premature senescence<ref name="ref20" />.HOTAIR, as a platform for protein ubiquitination<ref name="ref20" />.
 
  
===Allelic Information and Variation===
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LncRNA profiling showed that HOTAIR was highly regulated by genistein and its expression was higher in castration-resistant PCa cell lines than in normal prostate cells. miR-34a was also up-regulated by genistein and may directly target HOTAIR in both PC3 and DU145 PCa cells<ref name="ref12" />.
Please input allelic information and variation information here.
 
  
===Evolution===
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There is site-specific cytosine methylation in the lncRNA HOTAIR. Methylation of C1683 may affect the ability of HOTAIR to interact with LSD1<ref name="ref9" />.
Please input evolution information here.
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===Disease===
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B-cell neoplasms,breast cancer,cervical cancer,colon cancer,colorectal cancer,endometrial cancer,gastric cancer,hepatocelluar carcinoma,laryngeal squamous cell carcinoma,liver cancer,lung adenocarcinoma,nasopharyngeal carcinoma,non-small cell lung cancer,oesophageal squamous cell carcinoma,oral squamous cell carcinoma,pancreas cancer,rheumatoid arthritis,small cell lung cancer
  
 
You can also add sub-section(s) at will.
 
You can also add sub-section(s) at will.
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, Maryland 21224, USA<ref name="ref20" />.
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Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, Maryland 21224, USA <ref name="ref20" />.
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Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China <ref name="ref8" />.
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Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, Japan <ref name="ref6" />.
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School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland <ref name="ref5" />.
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The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA <ref name="ref4" />.
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Department of Surgery, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan <ref name="ref3" />.
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Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA <ref name="ref2" /><ref name="ref7" />.
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Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA <ref name="ref1" />.
  
 
==References==
 
==References==
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[http://www.lncrnadb.org/hotair/ Annotation originally sourced from lncRNAdb.]
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<references>
 
<references>
<ref name="ref1">Rinn JL1, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY.(2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell. 2007 Jun 29;129(7):1311-23.</ref>
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<ref name="ref1">Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell. 2007 Jun 29;129(7):1311-23.</ref>
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<ref name="ref2">Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.Nature. 2010 Apr 15;464(7291):1071-6.</ref>
  
<ref name="ref2">Gupta RA1, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.Nature. 2010 Apr 15;464(7291):1071-6. doi: 10.1038/nature08975.</ref>
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<ref name="ref3">Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011 Oct 15;71(20):6320-6. doi: 10.1158/0008-5472.CAN-11-1021.</ref>
  
<ref name="ref3">Kogo R1, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. (2013) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011 Oct 15;71(20):6320-6. doi: 10.1158/0008-5472.CAN-11-1021. Epub 2011 Aug 23.</ref>
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<ref name="ref4">Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72. doi: 10.1073/pnas.0904715106.</ref>
  
<ref name="ref4">Khalil AM1, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72. doi: 10.1073/pnas.0904715106. Epub 2009 Jul 1.</ref>
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<ref name="ref5">Schorderet P1, Duboule D.Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011 May;7(5):e1002071. doi: 10.1371/journal.pgen.1002071.</ref>
  
<ref name="ref5">Schorderet P1, Duboule D.(2011)Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011 May;7(5):e1002071. doi: 10.1371/journal.pgen.1002071. Epub 2011 May 26.</ref>
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<ref name="ref6">Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.Genome Res. 2012 May;22(5):947-56. doi: 10.1101/gr.130559.111.</ref>
  
<ref name="ref6">Tani H1, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N.(2012) Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.Genome Res. 2012 May;22(5):947-56. doi: 10.1101/gr.130559.111. Epub 2012 Feb 27.</ref>
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<ref name="ref7">Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes.Science. 2010 Aug 6;329(5992):689-93. doi: 10.1126/science.1192002.</ref>
  
<ref name="ref7">Tsai MC1, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY.(2010) Long noncoding RNA as modular scaffold of histone modification complexes.Science. 2010 Aug 6;329(5992):689-93. doi: 10.1126/science.1192002. Epub 2010 Jul 8.</ref>
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<ref name="ref8">He S, Liu S, Zhu H. The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol. 2011 Apr 16;11:102. doi: 10.1186/1471-2148-11-102.</ref>
  
<ref name="ref8">He S1, Liu S, Zhu H.(2011) The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol. 2011 Apr 16;11:102. doi: 10.1186/1471-2148-11-102.</ref>
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<ref name="ref9">Thomas Amort, Marie F. Soulière, Alexandra Wille, Xi-Yu Jia, Heidi Fiegl, Hildegard Wörle, Ronald Micura, Alexandra Lusser. Long non-coding RNAs as targets for cytosine methylation.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516.</ref>
  
<ref name="ref9">Thomas Amort, Marie F. Soulière, Alexandra Wille, Xi-Yu Jia, Heidi Fiegl, Hildegard Wörle, Ronald Micura, Alexandra Lusser. (2013) Long non-coding RNAs as targets for cytosine methylation.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516. Print 2013.</ref>
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<ref name="ref10">Bhan A, Hussain I, Ansari KI, Kasiri S, Bashyal A, Mandal SS. Antisense transcript long noncoding RNA (lncRNA) HOTAIR is transcriptionally induced by estradiol. J Mol Biol. 2013 Oct 9;425(19):3707-22. doi: 10.1016/j.jmb.2013.01.022.</ref>
  
<ref name="ref10">Bhan A1, Hussain I, Ansari KI, Kasiri S, Bashyal A, Mandal SS. (2013) Antisense transcript long noncoding RNA (lncRNA) HOTAIR is transcriptionally induced by estradiol. J Mol Biol. 2013 Oct 9;425(19):3707-22. doi: 10.1016/j.jmb.2013.01.022. Epub 2013 Jan 31.</ref>
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<ref name="ref11">Hajjari M, Behmanesh M, Sadeghizadeh M, Zeinoddini M. Up-regulation of HOTAIR long non-coding RNA in human gastric adenocarcinoma tissues.Med Oncol. 2013;30(3):670. doi: 10.1007/s12032-013-0670-0.</ref>
  
<ref name="ref11">Hajjari M1, Behmanesh M, Sadeghizadeh M, Zeinoddini M.(2013)Up-regulation of HOTAIR long non-coding RNA in human gastric adenocarcinoma tissues.Med Oncol. 2013;30(3):670. doi: 10.1007/s12032-013-0670-0. Epub 2013 Jul 26.</ref>
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<ref name="ref12">Chiyomaru T, Yamamura S, Fukuhara S, Yoshino H, Kinoshita T, Majid S, Saini S, Chang I, Tanaka Y, Enokida H, Seki N, Nakagawa M, Dahiya R.(2013)Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PLoS One. 2013 Aug 1;8(8):e70372. doi: 10.1371/journal.pone.0070372. </ref>
  
<ref name="ref12">Chiyomaru T1, Yamamura S, Fukuhara S, Yoshino H, Kinoshita T, Majid S, Saini S, Chang I, Tanaka Y, Enokida H, Seki N, Nakagawa M, Dahiya R.(2013)Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PLoS One. 2013 Aug 1;8(8):e70372. doi: 10.1371/journal.pone.0070372. Print 2013.</ref>
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<ref name="ref13">Cui L, Xie XY, Wang H, Chen XL, Liu SL, Hu LN. [Expression of long non-coding RNA HOTAIR mRNA in ovarian cancer].Sichuan Da Xue Xue Bao Yi Xue Ban. 2013 Jan;44(1):57-9.</ref>
  
<ref name="ref13">Cui L1, Xie XY, Wang H, Chen XL, Liu SL, Hu LN.(2013)[Expression of long non-coding RNA HOTAIR mRNA in ovarian cancer].Sichuan Da Xue Xue Bao Yi Xue Ban. 2013 Jan;44(1):57-9.</ref>
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<ref name="ref14">Endo H, Shiroki T, Nakagawa T, Yokoyama M, Tamai K, Yamanami H, Fujiya T, Sato I, Yamaguchi K, Tanaka N, Iijima K, Shimosegawa T, Sugamura K, Satoh K.(2013) Enhanced expression of long non-coding RNA HOTAIR is associated with the development of gastric cancer. PLoS One. 2013 Oct 10;8(10):e77070. doi: 10.1371/journal.pone.0077070. </ref>
  
<ref name="ref14">Endo H1, Shiroki T, Nakagawa T, Yokoyama M, Tamai K, Yamanami H, Fujiya T, Sato I, Yamaguchi K, Tanaka N, Iijima K, Shimosegawa T, Sugamura K, Satoh K.(2013) Enhanced expression of long non-coding RNA HOTAIR is associated with the development of gastric cancer. PLoS One. 2013 Oct 10;8(10):e77070. doi: 10.1371/journal.pone.0077070. eCollection 2013.</ref>
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<ref name="ref15">Li D, Feng J, Wu T, Wang Y, Sun Y, Ren J, Liu M. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma.Am J Pathol. 2013 Jan;182(1):64-70. doi: 10.1016/j.ajpath.2012.08.042. </ref>
  
<ref name="ref15">Li D1, Feng J, Wu T, Wang Y, Sun Y, Ren J, Liu M.(2013)Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma.Am J Pathol. 2013 Jan;182(1):64-70. doi: 10.1016/j.ajpath.2012.08.042. Epub 2012 Nov 7.</ref>
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<ref name="ref16">Liu Z, Sun M, Lu K, Liu J, Zhang M, Wu W, De W, Wang Z, Wang R. The long noncoding RNA HOTAIR contributes to cisplatin resistance of human lung adenocarcinoma cells via downregualtion of p21(WAF1/CIP1) expression. PLoS One. 2013 Oct 14;8(10):e77293. doi: 10.1371/journal.pone.0077293. </ref>
  
<ref name="ref16">Liu Z1, Sun M, Lu K, Liu J, Zhang M, Wu W, De W, Wang Z, Wang R.(2013)The long noncoding RNA HOTAIR contributes to cisplatin resistance of human lung adenocarcinoma cells via downregualtion of p21(WAF1/CIP1) expression. PLoS One. 2013 Oct 14;8(10):e77293. doi: 10.1371/journal.pone.0077293. eCollection 2013.</ref>
+
<ref name="ref17">Lv XB, Lian GY, Wang HR, Song E, Yao H, Wang MH. Long noncoding RNA HOTAIR is a prognostic marker for esophageal squamous cell carcinoma progression and survival.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516. </ref>
  
<ref name="ref17">Lv XB1, Lian GY, Wang HR, Song E, Yao H, Wang MH.(2013) Long noncoding RNA HOTAIR is a prognostic marker for esophageal squamous cell carcinoma progression and survival.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516. Print 2013.</ref>
+
<ref name="ref18">Ge XS, Ma HJ, Zheng XH, Ruan HL, Liao XY, Xue WQ, Chen YB, Zhang Y, Jia WH. HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway.Cancer Sci. 2013 Dec;104(12):1675-82. doi: 10.1111/cas.12296. </ref>
  
<ref name="ref18">Ge XS1, Ma HJ, Zheng XH, Ruan HL, Liao XY, Xue WQ, Chen YB, Zhang Y, Jia WH.(2013) HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway.Cancer Sci. 2013 Dec;104(12):1675-82. doi: 10.1111/cas.12296. Epub 2013 Oct 30.</ref>
+
<ref name="ref19">Liu XH, Liu ZL, Sun M, Liu J, Wang ZX, De W. The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer. BMC Cancer. 2013 Oct 8;13:464. doi: 10.1186/1471-2407-13-464.</ref>
  
<ref name="ref19">Liu XH1, Liu ZL, Sun M, Liu J, Wang ZX, De W.(2013) The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer. BMC Cancer. 2013 Oct 8;13:464. doi: 10.1186/1471-2407-13-464.</ref>
+
<ref name="ref20">Yoon JH, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, White EJ, Orjalo AV, Rinn JL, Kreft SG, Wilson GM, Gorospe M. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination.Nat Commun. 2013;4:2939. doi: 10.1038/ncomms3939.</ref>
  
<ref name="ref20">Yoon JH1, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, White EJ, Orjalo AV, Rinn JL, Kreft SG, Wilson GM, Gorospe M.(2013) Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination.Nat Commun. 2013;4:2939. doi: 10.1038/ncomms3939.</ref>
+
<ref name="ref21">Woo CJ and Kingston RE. HOTAIR lifts noncoding RNAs to new levels[J]. Cell, 2007, 129: 1257-1259.</ref>
 
</references>
 
</references>
  
Line 122: Line 147:
 
sequence = <dnaseq>ACATTCTGCCCTGATTTCCGGAACCTGGAAGCCTAGGCAGGCAGTGGGGAACTCTGACTCGCCTGTGCTCTGGAGCTTGATCCGAAAGCTTCCACAGTGAGGACTGCTCCGTGGGGGTAAGAGAGCACCAGGCACTGAGGCCTGGGAGTTCCACAGACCAACACCCCTGCTCCTGGCGGCTCCCACCCGGGACTTAGACCCTCAGGTCCCTAATATCCCGGAGGTGCTCTCAATCAGAAAGGTCCTGCTCCGCTTCGCAGTGGAATGGAACGGATTTAGAAGCCTGCAGTAGGGGAGTGGGGAGTGGAGAGAGGGAGCCCAGAGTTACAGACGGCGGCGAGAGGAAGGAGGGGCGTCTTTATTTTTTTAAGGCCCCAAAGAGTCTGATGTTTACAAGACCAGAAATGCCACGGCCGCGTCCTGGCAGAGAAAAGGCTGAAATGGAGGACCGGCGCCTTCCTTATAAGTATGCACATTGGCGAGAGAAGTGCTGCAACCTAAACCAGCAATTACACCCAAGCTCGTTGGGGCCTAAGCCAGTACCGACCTGGTAGAAAAAGCAACCACGAAGCTAGAGAGAGAGCCAGAGGAGGGAAGAGAGCGCCAGACGAAGGTGAAAGCGAACCACGCAGAGAAATGCAGGCAAGGGAGCAAGGCGGCAGTTCCCGGAACAAACGTGGCAGAGGGCAAGACGGGCACTCACAGACAGAGGTTTATGTATTTTTATTTTTTAAAATCTGATTTGGTGTTCCATGAGGAAAAGGGAAAATCTAGGGAACGGGAGTACAGAGAGAATAATCCGGGTCCTAGCTCGCCACATGAACGCCCAGAGAACGCTGGAAAAACCTGAGCGGGTGCCGGGGCAGCACCCGGCTCGGGTCAGCCACTGCCCCACACCGGGCCCACCAAGCCCCGCCCCTCGCGGCCACCGGGGCTTCCTTGCTCTTCTTATCATCTCCATCTTTATGATGAGGCTTGTTAACAAGACCAGAGAGCTGGCCAAGCACCTCTATCTCAGCCGCGCCCGCTCAGCCGAGCAGCGGTCGGTGGGGGGACTGGGAGGCGCTAATTAATTGATTCCTTTGGACTGTAAAATATGGCGGCGTCTACACGGAACCCATGGACTCATAAACAATATATCTGTTGGGCGTGAGTGCACTGTCTCTCAAATAATTTTTCCATAGGCAAATGTCAGAGGGTTCTGGATTTTTAGTTGCTAAGGAAAGATCCAAATGGGACCAATTTTAGGAGGCCCAAACAGAGTCCGTTCAGTGTCAGAAAATGCTTCCCCAAAGGGGTTGGGAGTGTGTTTTGTTGGAAAAAAGCTTGGGTTATAGGAAAGCCTTTCCCTGCTACTTGTGTAGACCCAGCCCAATTTAAGAATTACAAGGAAGCGAAGGGGTTGTGTAGGCCGGAAGCCTCTCTGTCCCGGCTGGATGCAGGGGACTTGAGCTGCTCCGGAATTTGAGAGGAACATAGAAGCAAAGGTCCAGCCTTTGCTTCGTGCTGATTCCTAGACTTAAGATTCAAAAACAAATTTTTAAAAGTGAAACCAGCCCTAGCCTTTGGAAGCTCTTGAAGGTTCAGCACCCACCCAGGAATCCACCTGCCTGTTACACGCCTCTCCAAGACACAGTGGCACCGCTTTTCTAACTGGCAGCACAGAGCAACTCTATAATATGCTTATATTAGGTCTAGAAGAATGCATCTTGAGACACATGGGTAACCTAATTATATAATGCTTGTTCCATACAGGAGTGATTATGCAGTGGGACCCTGCTGCAAACGGGACTTTGCACTCTAAATATAGACCCCAGCTTGGGACAAAAGTTGCAGTAGAAAAATAGACATAGGAGAACACTTAAATAAGTGATGCATGTAGACACAGAAGGGGTATTTAAAAGACAGAAATAATAGAAGTACAGAAGAACAGAAAAAAAATCAGCAGATGGAGATTACCATTCCCAATGCCTGAACTTCCTCCTGCTATTAAGATTGCTAGAGAATTGTGTCTTAAACAGTTCATGAACCCAGAAGAATGCAATTTCAATGTATTTAGTACACACACAGTATGTATATAAACACAACTCACAGAATATATTTTCCATACATTGGGTAGGTATGCACTTTGTGTATATATAATAATGTATTTTCCATGCAGTTTTAAAATGTAGATATATTAATATCTGGATGCATTTTCTGTGCACTGGTTTTATATGCCTTATGGAGTATATACTCACATGTAGCTAAATAGACTCAGGACTGCACATTCCTTGTGTAGGTTGTGTGTGTGTGGTGGTTTTATGCATAAATAAAGTTTTACATGTGGTGAAAAAA</dnaseq>|
 
sequence = <dnaseq>ACATTCTGCCCTGATTTCCGGAACCTGGAAGCCTAGGCAGGCAGTGGGGAACTCTGACTCGCCTGTGCTCTGGAGCTTGATCCGAAAGCTTCCACAGTGAGGACTGCTCCGTGGGGGTAAGAGAGCACCAGGCACTGAGGCCTGGGAGTTCCACAGACCAACACCCCTGCTCCTGGCGGCTCCCACCCGGGACTTAGACCCTCAGGTCCCTAATATCCCGGAGGTGCTCTCAATCAGAAAGGTCCTGCTCCGCTTCGCAGTGGAATGGAACGGATTTAGAAGCCTGCAGTAGGGGAGTGGGGAGTGGAGAGAGGGAGCCCAGAGTTACAGACGGCGGCGAGAGGAAGGAGGGGCGTCTTTATTTTTTTAAGGCCCCAAAGAGTCTGATGTTTACAAGACCAGAAATGCCACGGCCGCGTCCTGGCAGAGAAAAGGCTGAAATGGAGGACCGGCGCCTTCCTTATAAGTATGCACATTGGCGAGAGAAGTGCTGCAACCTAAACCAGCAATTACACCCAAGCTCGTTGGGGCCTAAGCCAGTACCGACCTGGTAGAAAAAGCAACCACGAAGCTAGAGAGAGAGCCAGAGGAGGGAAGAGAGCGCCAGACGAAGGTGAAAGCGAACCACGCAGAGAAATGCAGGCAAGGGAGCAAGGCGGCAGTTCCCGGAACAAACGTGGCAGAGGGCAAGACGGGCACTCACAGACAGAGGTTTATGTATTTTTATTTTTTAAAATCTGATTTGGTGTTCCATGAGGAAAAGGGAAAATCTAGGGAACGGGAGTACAGAGAGAATAATCCGGGTCCTAGCTCGCCACATGAACGCCCAGAGAACGCTGGAAAAACCTGAGCGGGTGCCGGGGCAGCACCCGGCTCGGGTCAGCCACTGCCCCACACCGGGCCCACCAAGCCCCGCCCCTCGCGGCCACCGGGGCTTCCTTGCTCTTCTTATCATCTCCATCTTTATGATGAGGCTTGTTAACAAGACCAGAGAGCTGGCCAAGCACCTCTATCTCAGCCGCGCCCGCTCAGCCGAGCAGCGGTCGGTGGGGGGACTGGGAGGCGCTAATTAATTGATTCCTTTGGACTGTAAAATATGGCGGCGTCTACACGGAACCCATGGACTCATAAACAATATATCTGTTGGGCGTGAGTGCACTGTCTCTCAAATAATTTTTCCATAGGCAAATGTCAGAGGGTTCTGGATTTTTAGTTGCTAAGGAAAGATCCAAATGGGACCAATTTTAGGAGGCCCAAACAGAGTCCGTTCAGTGTCAGAAAATGCTTCCCCAAAGGGGTTGGGAGTGTGTTTTGTTGGAAAAAAGCTTGGGTTATAGGAAAGCCTTTCCCTGCTACTTGTGTAGACCCAGCCCAATTTAAGAATTACAAGGAAGCGAAGGGGTTGTGTAGGCCGGAAGCCTCTCTGTCCCGGCTGGATGCAGGGGACTTGAGCTGCTCCGGAATTTGAGAGGAACATAGAAGCAAAGGTCCAGCCTTTGCTTCGTGCTGATTCCTAGACTTAAGATTCAAAAACAAATTTTTAAAAGTGAAACCAGCCCTAGCCTTTGGAAGCTCTTGAAGGTTCAGCACCCACCCAGGAATCCACCTGCCTGTTACACGCCTCTCCAAGACACAGTGGCACCGCTTTTCTAACTGGCAGCACAGAGCAACTCTATAATATGCTTATATTAGGTCTAGAAGAATGCATCTTGAGACACATGGGTAACCTAATTATATAATGCTTGTTCCATACAGGAGTGATTATGCAGTGGGACCCTGCTGCAAACGGGACTTTGCACTCTAAATATAGACCCCAGCTTGGGACAAAAGTTGCAGTAGAAAAATAGACATAGGAGAACACTTAAATAAGTGATGCATGTAGACACAGAAGGGGTATTTAAAAGACAGAAATAATAGAAGTACAGAAGAACAGAAAAAAAATCAGCAGATGGAGATTACCATTCCCAATGCCTGAACTTCCTCCTGCTATTAAGATTGCTAGAGAATTGTGTCTTAAACAGTTCATGAACCCAGAAGAATGCAATTTCAATGTATTTAGTACACACACAGTATGTATATAAACACAACTCACAGAATATATTTTCCATACATTGGGTAGGTATGCACTTTGTGTATATATAATAATGTATTTTCCATGCAGTTTTAAAATGTAGATATATTAATATCTGGATGCATTTTCTGTGCACTGGTTTTATATGCCTTATGGAGTATATACTCACATGTAGCTAAATAGACTCAGGACTGCACATTCCTTGTGTAGGTTGTGTGTGTGTGGTGGTTTTATGCATAAATAAAGTTTTACATGTGGTGAAAAAA</dnaseq>|
 
}}
 
}}
[[Category:Intergenic]][[Category:NONHSAG011264]]
+
[[Category:Intergenic]][[Category:NONHSAG011264]][[Category:Transcripts]][[Category:Transcripts]]

Latest revision as of 10:32, 12 June 2021

HOTAIR epigenetically silence gene expression at many sites across the genome by recruitment of chromatin modifying complexes and the abnormal expression of HOTAIR is highly correlated with the development of many kinds of human cancers.

Annotated Information

Name

Approved symbol: HOTAIR

Approved name: HOX transcript antisense RNA

HGNC ID: HGNC:33510

Previous names: HOX transcript antisense RNA (non-protein coding)

Alias symbols: HOXC-AS4; HOXC11-AS1; NCRNA00072

Alias names: HOXC cluster antisense RNA 4 (non-protein coding); non-protein coding RNA 72

RefSeq ID: NR_003716

LncBook ID: HSALNT0289004

Characteristics

2.2 kb; spliced, polyadenylated and comprised of 6 exons in humans [1].

Transcribed from the HOXC locus from a position intergenic and antisense to the flanking HOXC11 and HOXC12 genes [1].

Some HOTAIR transcripts localise to the nucleus [2].

Transcript found to be quite unstable with a half-life >4 hr in human Hela cells[3].

Function

Changes in mRNA and occupancy of H3K4me2, H3K27me3, LSD1, and SUZ12 across HOXD locus after RNAi of HOTAIR in foreskin fibroblasts. Yellow boxes indicate regions of notable correlation between gain of H3K4me2 and concordant loss of LSD1, H3K27me3, and SUZ12. [4]

Originally identified as silencing the HoxD locus[5] but has since been found to epigenetic silence gene expression at many sites across the genome by recruitment of PRC2 and LSD1/CoREST/REST repressive chromatin modifying complexes [1][4].

HOTAIR has been suggested to function at the chromatin level by interacting with chromatin modifying protein complexes [6]. It has been reported that HOTAIR expression is correlated with SUZ12 expression level and therefore may affect the epigenetic state of cancer tissues[7]. HOTAIR acts as a scaffold for protein complexes. A 5' domain binds PRC2 while a 3' domain binds LSD1[4]. Oncogenic effects of HOTAIR upregulation were dependent on PRC2 [8].

Oncogene - regulates metastatic progression in many kinds of cancers [8][9][10][11][12][7]. It is crucial for cell growth and viability and its knockdown induced apoptosis in breast cancer cells[13]. There was a great upregulation of HOTAIR in Esophageal squamous cell carcinoma (ESCC) compared to their adjacent normal esophageal tissues. Meanwhile, patients with high HOTAIR expression have a significantly poorer prognosis than those with low expression. Moreover, HOTAIR was further validated to promote migration and invasion of ESCC cells in vitro[10]. Knockdown of HOTAIR decreased prostate cancer (PCa) cell proliferation, migration and invasion and induced apoptosis and cell cycle arrest [11]. High HOTAIR expression tightly correlated with the presence of liver metastasis and associated with poor prognosis [12]. The aberrant expression of HOTAIR was associated with TNM staging and lymph node metastasis of gastric tumors[7]. Reduced expression of HOTAIR in KATO III suppressed peritoneal dissemination suggest that HOTAIR plays a pivotal role in the development of gastric cancer[14].

It is also highly correlated with malignant degree of cancer and the therapeutic effect [15][8][16][17][18].

Deletion of the HoxC cluster containing the cognate Hotair transcript in mouse showed little phenotypic effect, with little change in the expression on levels of H3K27me3 coverage in corresponding human HOTAIR Hoxd target genes [9].

HOTAIR acts as an inducer of ubiquitin-mediated proteolysis on post-translational function[19]. HOTAIR associates with E3 ubiquitin ligases bearing RNA-binding domains, Dzip3 and Mex3b, as well as with their respective ubiquitination substrates, Ataxin-1 and Snurportin-1. HOTAIR levels are highly upregulated in senescent cells, causing rapid decay of targets Ataxin-1 and Snurportin-1, and preventing premature senescence[19].

Expression

Expressed in posterior and distal fibroblasts [1].

In situ hybridization analysis of the mouse cognate RNA (mHotair) showed expression similar to Hoxc11, with distinct levels in parts of the proximal hindlimbs, genital bud and tail in embryos at E11.5, as well as in in posterior part of the hindlimb and genital bud at E12.5 [9].

It is up-regulated in breast cancer [8][13], colorectal cancer (CRC) [12], Esophageal squamous cell carcinoma (ESCC) [10], ovarian cancer [15], gastric adenocarcinoma samples [7],Non-small-cell lung carcinoma (NSCLC) [16], laryngeal squamous cell cancer (LSCC) [17],cisplatin-resistant A549/DDP cells [20].

Conservation

HOTAIR exists in mammals but with poor sequence conservation [1][21]. A 239 bp domain in HOTAIR exon 6 is especially conserved in mammals [21].

The mouse EST (AK035706) homologous to human HOTAIR is comprised of two exons only, with the second half of the first exon showing similarity to exon 4 of HOTAIR, whereas the second exon is homologous to exon 6 of HOTAIR [9]. This may underlie differences in function since the first three exons of HOTAIR (absent from mHotair) contain binding sites for EZH2, while the 3' extremity of human HOTAIR that interact with LSD1 is part of the least conserved DNA sequence within mHotair exon 2 [9].

Regulation

HOTAIR is transcriptionally induced by estradiol (E2). Similar to protein-coding gene transcription, E2-induced transcription of antisense transcript HOTAIR is coordinated via ERs and ER coregulators, and this mechanism of HOTAIR overexpression potentially contributes towards breast cancer progression[13]. The long non-coding RNA HOTAIR has been reported to be a poor prognostic biomarker in a variety of malignant tumors[14].

LncRNA profiling showed that HOTAIR was highly regulated by genistein and its expression was higher in castration-resistant PCa cell lines than in normal prostate cells. miR-34a was also up-regulated by genistein and may directly target HOTAIR in both PC3 and DU145 PCa cells[11].

There is site-specific cytosine methylation in the lncRNA HOTAIR. Methylation of C1683 may affect the ability of HOTAIR to interact with LSD1[6].

Disease

B-cell neoplasms,breast cancer,cervical cancer,colon cancer,colorectal cancer,endometrial cancer,gastric cancer,hepatocelluar carcinoma,laryngeal squamous cell carcinoma,liver cancer,lung adenocarcinoma,nasopharyngeal carcinoma,non-small cell lung cancer,oesophageal squamous cell carcinoma,oral squamous cell carcinoma,pancreas cancer,rheumatoid arthritis,small cell lung cancer

You can also add sub-section(s) at will.

Labs working on this lncRNA

Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, Maryland 21224, USA [19].

Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China [21].

Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, Japan [3].

School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland [9].

The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA [2].

Department of Surgery, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [12].

Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA [8][4].

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA [1].

References

Annotation originally sourced from lncRNAdb.

  1. 1.0 1.1 1.2 1.3 1.4 1.5 Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell. 2007 Jun 29;129(7):1311-23.
  2. 2.0 2.1 Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72. doi: 10.1073/pnas.0904715106.
  3. 3.0 3.1 Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.Genome Res. 2012 May;22(5):947-56. doi: 10.1101/gr.130559.111.
  4. 4.0 4.1 4.2 4.3 Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes.Science. 2010 Aug 6;329(5992):689-93. doi: 10.1126/science.1192002.
  5. Woo CJ and Kingston RE. HOTAIR lifts noncoding RNAs to new levels[J]. Cell, 2007, 129: 1257-1259.
  6. 6.0 6.1 Thomas Amort, Marie F. Soulière, Alexandra Wille, Xi-Yu Jia, Heidi Fiegl, Hildegard Wörle, Ronald Micura, Alexandra Lusser. Long non-coding RNAs as targets for cytosine methylation.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516.
  7. 7.0 7.1 7.2 7.3 Hajjari M, Behmanesh M, Sadeghizadeh M, Zeinoddini M. Up-regulation of HOTAIR long non-coding RNA in human gastric adenocarcinoma tissues.Med Oncol. 2013;30(3):670. doi: 10.1007/s12032-013-0670-0.
  8. 8.0 8.1 8.2 8.3 8.4 Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.Nature. 2010 Apr 15;464(7291):1071-6.
  9. 9.0 9.1 9.2 9.3 9.4 9.5 Schorderet P1, Duboule D.Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011 May;7(5):e1002071. doi: 10.1371/journal.pgen.1002071.
  10. 10.0 10.1 10.2 Ge XS, Ma HJ, Zheng XH, Ruan HL, Liao XY, Xue WQ, Chen YB, Zhang Y, Jia WH. HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway.Cancer Sci. 2013 Dec;104(12):1675-82. doi: 10.1111/cas.12296.
  11. 11.0 11.1 11.2 Chiyomaru T, Yamamura S, Fukuhara S, Yoshino H, Kinoshita T, Majid S, Saini S, Chang I, Tanaka Y, Enokida H, Seki N, Nakagawa M, Dahiya R.(2013)Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PLoS One. 2013 Aug 1;8(8):e70372. doi: 10.1371/journal.pone.0070372.
  12. 12.0 12.1 12.2 12.3 Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011 Oct 15;71(20):6320-6. doi: 10.1158/0008-5472.CAN-11-1021.
  13. 13.0 13.1 13.2 Bhan A, Hussain I, Ansari KI, Kasiri S, Bashyal A, Mandal SS. Antisense transcript long noncoding RNA (lncRNA) HOTAIR is transcriptionally induced by estradiol. J Mol Biol. 2013 Oct 9;425(19):3707-22. doi: 10.1016/j.jmb.2013.01.022.
  14. 14.0 14.1 Endo H, Shiroki T, Nakagawa T, Yokoyama M, Tamai K, Yamanami H, Fujiya T, Sato I, Yamaguchi K, Tanaka N, Iijima K, Shimosegawa T, Sugamura K, Satoh K.(2013) Enhanced expression of long non-coding RNA HOTAIR is associated with the development of gastric cancer. PLoS One. 2013 Oct 10;8(10):e77070. doi: 10.1371/journal.pone.0077070.
  15. 15.0 15.1 Cui L, Xie XY, Wang H, Chen XL, Liu SL, Hu LN. [Expression of long non-coding RNA HOTAIR mRNA in ovarian cancer].Sichuan Da Xue Xue Bao Yi Xue Ban. 2013 Jan;44(1):57-9.
  16. 16.0 16.1 Liu XH, Liu ZL, Sun M, Liu J, Wang ZX, De W. The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer. BMC Cancer. 2013 Oct 8;13:464. doi: 10.1186/1471-2407-13-464.
  17. 17.0 17.1 Li D, Feng J, Wu T, Wang Y, Sun Y, Ren J, Liu M. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma.Am J Pathol. 2013 Jan;182(1):64-70. doi: 10.1016/j.ajpath.2012.08.042.
  18. Lv XB, Lian GY, Wang HR, Song E, Yao H, Wang MH. Long noncoding RNA HOTAIR is a prognostic marker for esophageal squamous cell carcinoma progression and survival.PLoS One. 2013 May 23;8(5):e63516. doi: 10.1371/journal.pone.0063516.
  19. 19.0 19.1 19.2 Yoon JH, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, White EJ, Orjalo AV, Rinn JL, Kreft SG, Wilson GM, Gorospe M. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination.Nat Commun. 2013;4:2939. doi: 10.1038/ncomms3939.
  20. Liu Z, Sun M, Lu K, Liu J, Zhang M, Wu W, De W, Wang Z, Wang R. The long noncoding RNA HOTAIR contributes to cisplatin resistance of human lung adenocarcinoma cells via downregualtion of p21(WAF1/CIP1) expression. PLoS One. 2013 Oct 14;8(10):e77293. doi: 10.1371/journal.pone.0077293.
  21. 21.0 21.1 21.2 He S, Liu S, Zhu H. The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol. 2011 Apr 16;11:102. doi: 10.1186/1471-2148-11-102.


Basic Information

Transcript ID

NONHSAT028508

Source

NONCODE4.0

Same with

,

Classification

intergenic

Length

2337 nt

Genomic location

chr12-:54356092..54362540

Exon number

6

Exons

54356092..54357908,54358015..54358067,54359748..54359871,54360060..54360161,54361053..54361178,54362401..54362540

Genome context

Sequence
000001 ACATTCTGCC CTGATTTCCG GAACCTGGAA GCCTAGGCAG GCAGTGGGGA ACTCTGACTC GCCTGTGCTC TGGAGCTTGA 000080
000081 TCCGAAAGCT TCCACAGTGA GGACTGCTCC GTGGGGGTAA GAGAGCACCA GGCACTGAGG CCTGGGAGTT CCACAGACCA 000160
000161 ACACCCCTGC TCCTGGCGGC TCCCACCCGG GACTTAGACC CTCAGGTCCC TAATATCCCG GAGGTGCTCT CAATCAGAAA 000240
000241 GGTCCTGCTC CGCTTCGCAG TGGAATGGAA CGGATTTAGA AGCCTGCAGT AGGGGAGTGG GGAGTGGAGA GAGGGAGCCC 000320
000321 AGAGTTACAG ACGGCGGCGA GAGGAAGGAG GGGCGTCTTT ATTTTTTTAA GGCCCCAAAG AGTCTGATGT TTACAAGACC 000400
000401 AGAAATGCCA CGGCCGCGTC CTGGCAGAGA AAAGGCTGAA ATGGAGGACC GGCGCCTTCC TTATAAGTAT GCACATTGGC 000480
000481 GAGAGAAGTG CTGCAACCTA AACCAGCAAT TACACCCAAG CTCGTTGGGG CCTAAGCCAG TACCGACCTG GTAGAAAAAG 000560
000561 CAACCACGAA GCTAGAGAGA GAGCCAGAGG AGGGAAGAGA GCGCCAGACG AAGGTGAAAG CGAACCACGC AGAGAAATGC 000640
000641 AGGCAAGGGA GCAAGGCGGC AGTTCCCGGA ACAAACGTGG CAGAGGGCAA GACGGGCACT CACAGACAGA GGTTTATGTA 000720
000721 TTTTTATTTT TTAAAATCTG ATTTGGTGTT CCATGAGGAA AAGGGAAAAT CTAGGGAACG GGAGTACAGA GAGAATAATC 000800
000801 CGGGTCCTAG CTCGCCACAT GAACGCCCAG AGAACGCTGG AAAAACCTGA GCGGGTGCCG GGGCAGCACC CGGCTCGGGT 000880
000881 CAGCCACTGC CCCACACCGG GCCCACCAAG CCCCGCCCCT CGCGGCCACC GGGGCTTCCT TGCTCTTCTT ATCATCTCCA 000960
000961 TCTTTATGAT GAGGCTTGTT AACAAGACCA GAGAGCTGGC CAAGCACCTC TATCTCAGCC GCGCCCGCTC AGCCGAGCAG 001040
001041 CGGTCGGTGG GGGGACTGGG AGGCGCTAAT TAATTGATTC CTTTGGACTG TAAAATATGG CGGCGTCTAC ACGGAACCCA 001120
001121 TGGACTCATA AACAATATAT CTGTTGGGCG TGAGTGCACT GTCTCTCAAA TAATTTTTCC ATAGGCAAAT GTCAGAGGGT 001200
001201 TCTGGATTTT TAGTTGCTAA GGAAAGATCC AAATGGGACC AATTTTAGGA GGCCCAAACA GAGTCCGTTC AGTGTCAGAA 001280
001281 AATGCTTCCC CAAAGGGGTT GGGAGTGTGT TTTGTTGGAA AAAAGCTTGG GTTATAGGAA AGCCTTTCCC TGCTACTTGT 001360
001361 GTAGACCCAG CCCAATTTAA GAATTACAAG GAAGCGAAGG GGTTGTGTAG GCCGGAAGCC TCTCTGTCCC GGCTGGATGC 001440
001441 AGGGGACTTG AGCTGCTCCG GAATTTGAGA GGAACATAGA AGCAAAGGTC CAGCCTTTGC TTCGTGCTGA TTCCTAGACT 001520
001521 TAAGATTCAA AAACAAATTT TTAAAAGTGA AACCAGCCCT AGCCTTTGGA AGCTCTTGAA GGTTCAGCAC CCACCCAGGA 001600
001601 ATCCACCTGC CTGTTACACG CCTCTCCAAG ACACAGTGGC ACCGCTTTTC TAACTGGCAG CACAGAGCAA CTCTATAATA 001680
001681 TGCTTATATT AGGTCTAGAA GAATGCATCT TGAGACACAT GGGTAACCTA ATTATATAAT GCTTGTTCCA TACAGGAGTG 001760
001761 ATTATGCAGT GGGACCCTGC TGCAAACGGG ACTTTGCACT CTAAATATAG ACCCCAGCTT GGGACAAAAG TTGCAGTAGA 001840
001841 AAAATAGACA TAGGAGAACA CTTAAATAAG TGATGCATGT AGACACAGAA GGGGTATTTA AAAGACAGAA ATAATAGAAG 001920
001921 TACAGAAGAA CAGAAAAAAA ATCAGCAGAT GGAGATTACC ATTCCCAATG CCTGAACTTC CTCCTGCTAT TAAGATTGCT 002000
002001 AGAGAATTGT GTCTTAAACA GTTCATGAAC CCAGAAGAAT GCAATTTCAA TGTATTTAGT ACACACACAG TATGTATATA 002080
002081 AACACAACTC ACAGAATATA TTTTCCATAC ATTGGGTAGG TATGCACTTT GTGTATATAT AATAATGTAT TTTCCATGCA 002160
002161 GTTTTAAAAT GTAGATATAT TAATATCTGG ATGCATTTTC TGTGCACTGG TTTTATATGC CTTATGGAGT ATATACTCAC 002240
002241 ATGTAGCTAA ATAGACTCAG GACTGCACAT TCCTTGTGTA GGTTGTGTGT GTGTGGTGGT TTTATGCATA AATAAAGTTT 002320
002321 TACATGTGGT GAAAAAA
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