NONHSAT028508

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Annotated Information

Name

HOTAIR: Hox antisense intergenic RNA

Characteristics

2.2 kb; spliced, polyadenylated and comprised of 6 exons in humans (Rinn (2007)). Transcribed from the HOXC locus from a position intergenic and antisense to the flanking HOXC11 and HOXC12 genes (Rinn (2007)). Expression Expressed in posterior and distal fibroblasts (Rinn (2007)). Expression level in cancer is an efficient predictor of metastasis and survival with high expression levels predictive of poor outcomes (Gupta (2010)). 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 (Kogo (2011)) . Some HOTAIR transcripts localise to the nucleus (Khalil (2009)). 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 (Schorderet (2011)). Transcript found to be quite unstable with a half-life >4 hr in human Hela cells (Tani (2012)).

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 (Rinn (2007), Tsai (2010)). HOTAIR acts as a scaffold for protein complexes. A 5' domain binds PRC2 while a 3' domain binds LSD1 [v (Tsai (2010))]. Oncogene - regulates metastatic progression (Gupta (2010))(Schorderet (2011)). 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 (Gupta (2010)). 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 (Schorderet (2011)).

Expression

Expressed in posterior and distal fibroblasts (Rinn (2007)). Expression level in cancer is an efficient predictor of metastasis and survival with high expression levels predictive of poor outcomes (Gupta (2010)). 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 (Kogo (2011)) . Some HOTAIR transcripts localise to the nucleus (Khalil (2009)). 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 (Schorderet (2011)). Transcript found to be quite unstable with a half-life >4 hr in human Hela cells (Tani (2012)).

Conservation

HOTAIR exists in mammals but with poor sequence conservation (Rinn (2007))(He (2011)). A 239 bp domain in HOTAIR exon 6 is especially conserved in mammals (He (2011)). 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 (Schorderet (2011)). 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 (Schorderet (2011)).

Misc

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Transcriptomic Nomeclature

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Regulation

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Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

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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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