Difference between revisions of "NONHSAT022111"

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===Characteristics===
 
===Characteristics===
  
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[[File: NEAT1_isoforms.png|right|frame| Processing of two isoforms of NEAT1. NEAT1 has two isoforms. [<ref name="ref19"/>]]]
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[[File: NEAT1_isoforms.png|right|thumb|500px| Processing of two isoforms of NEAT1. NEAT1 has two isoforms. [<ref name="ref19"/>]]]
  
 
Neat1 is broadly expressed and highly abundant lncRNA in mammalian cell nuclei and have two isoforms<ref name="ref19"/>: ~3.7 (NEAT1 v1/ MEN epsilon) and ~23 kb (NEAT1 v2/ MEN beta) transcribed from the MEN1 locus<ref name="ref1"/><ref name="ref2"/><ref name="ref3"/><ref name="ref4"/>.
 
Neat1 is broadly expressed and highly abundant lncRNA in mammalian cell nuclei and have two isoforms<ref name="ref19"/>: ~3.7 (NEAT1 v1/ MEN epsilon) and ~23 kb (NEAT1 v2/ MEN beta) transcribed from the MEN1 locus<ref name="ref1"/><ref name="ref2"/><ref name="ref3"/><ref name="ref4"/>.

Revision as of 09:51, 15 October 2014

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short one


Annotated Information

Name

Neat1: Nuclear enriched abundant transcript 1. This transcript is the short isoform of Neat1, which is named as Neat1 v1 or Neat1_1.

Short isoform - MEN epsilon.

VINC: Virus-inducible ncRNA


Characteristics

Processing of two isoforms of NEAT1. NEAT1 has two isoforms. [[1]]

Neat1 is broadly expressed and highly abundant lncRNA in mammalian cell nuclei and have two isoforms[1]: ~3.7 (NEAT1 v1/ MEN epsilon) and ~23 kb (NEAT1 v2/ MEN beta) transcribed from the MEN1 locus[2][3][4][5].

Long isoform is a continuation of the short isoform [4].

These two isoforms share the same transcriptional start site, but their 3' ends are processed by distinct mechanisms: Canonical polyadenylation or RNase P cleavage[1].

NEAT1_1 is polyadenylated[1].

NEAT1_1 : Components of the CFIm complex, such as CPSF6 and NUDT21 have been recently shown to localize to paraspeckles and to be involved in the 3' end processing of NEAT1 1, confirming the involvement of the canonical polyadenylation in NEAT1 1 maturation[1].

Function

Transcription of Neat1 is essential for the assembly, maintenance and structural integrity of paraspeckles[6][7][5][8]. Newly transcribed Neat1 RNA nucleates the formation of paraspeckles at its transcription site, recruiting paraspeckle proteins. Continued expression is required to maintain paraspeckles, identifying the dynamic nature of this nuclear body [8]. Literature currently provides conflicting evidence about whether Neat1 v1 is sufficient for the formation of paraspeckles, or if this requires full length Neat1 v2 [7] [9].

Neat1 appears to constrain the size and mediate the cylindrical geometry of paraspeckles. Neat1 short and the identical 5' end of Neat1 long plus the 3' of Neat1 long all localise to the periphery of paraspeckles, while the central region of Neat1 long is found in the interior of the nuclear body [10]. Interacts with paraspeckles proteins PSPC1, PSF/SFPQ and NONO/P54NRB either directly or in a complex[6][7][5].

Interaction of short isoform with p54 requires protein interaction regions near the 5' and 3' of the transcript [11]. Neat1 knockout lead to loss of paraspeckles, however mice were viable and fertile with normal morphology and populations of differentiated cells in one Neat1 v1 and v2 expressing tissue tested [12].

Neat1 has also been reported to interact with a number of chromatin binding protein/complexes in mouse embryonic stem cells including PRC1, PRC2, JARID1B, ESET and SUV39H1, with the general pattern being interaction with repressors of gene expression [13].

Components of the CFIm complex, such as CPSF6 and NUDT21 have been recently shown to localize to paraspeckles and to be involved in the 3′ end processing of NEAT1_1, confirming the involvement of the canonical polyadenylation in NEAT1_1 maturation. However, the expression level of NEAT1_1 and NEAT1_2 is likely controlled by HNRNPK, which is a newly identified paraspeckle protein [1].

Expression

A summary of differentially expressed lncRNAs in HIV-1-infected Jurkat and MT4 cells [[14]]

Expressed in a wide range of human and mouse tissues [15][3][4][5]. Although expression of the long isoform (Neat1 v2/ Men beta) is much lower than Neat1 v1/ Men epsilon in many tissues[12].

Up-regulation of Neat1 (and subsequent formation of/increase in paraspeckles) may be a general feature of differentiation. Neat1 is up-regulated upon human ESC differentiation[10], muscle differentiation[5]and in-vitro neuronal differentiation[16].

Up-regulated upon infection of mice with Japanese encephalitis virus or Rabies virus[3]. Expressed in the nucleus accumbens of normal human brains and upregulated in this brain region in heroin abusers [17]. In addition, expression levels are elevated in the caudate nucleus of patients suffering from the neurodegenerative condition, Huntington's disease[18]. Localised to paraspeckles within the nucleus [4] [5].

Mouse Neat1 found to be highly unstable (half-life <2 hr) in N2A (neuroblastoma) and 3T3 cells, although low stability did not prevent paraspeckle formation[19] [20], while human NEAT1 appears to be more stable [19] [7][5].

The two Neat1 isoforms also have differing stability, with the long (v2/Men beta) isoform more stable than than the shorter (v1/Men epsilon) isoform in N2A and 3T3 cells [20]. NEAT1 was exclusively localized in the nuclei of the villous trophoblasts and was expressed in more nuclei and with greater intensity in IUGR placentas than in CTRLs. PSPC1, one of the three main proteins of the paraspeckle, co-localized with NEAT1 in the villous trophoblasts[21].

NEAT1 to be one of several lncRNAs whose expression is changed by HIV-1 infection, and we have characterized its role in HIV-1 replication. NEAT1 play an role in regulating gene expression and modulating protein activities[14].NEAT1 is essential for the integrity of the nuclear paraspeckle substructure[22][21][14].

The expression level of NEAT1_1 and NEAT1_2 is likely controlled by HNRNPK, which is a newly identified paraspeckle protein and interferes with the CFIm complex cleavage to keep NEAT1_2 synthesis low. [1]

Conservation

Placental mammals. Dog Neat1 is found in several genomic locations, version that is found near single dog Malat1 gene is given below[4].

Misc

A conserved tRNA like sequence at the 3' end is cleaved off and processed to generate a short tRNA-like ncRNA from the long (Men beta) transcript, similar to Malat1 [5]. The last ~500bp of the short (Men epsilon) isoform has been shown to be expressed in trophoblast cells with a function potentially independent from the Neat1 transcript. This transcript, TncRNA has its own entry.

Regulation

FUS (Fused in sarcoma (FUS) protein, linked to a number of neurodegenerative disorders, is an essential paraspeckle component, and paraspeckles are nuclear bodies formed by a set of specialized proteins assembled on NEAT1) regulates NEAT1 levels[23][22][21].


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Labs working on this lncRNA

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References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Zhang, Y., et al. (2014). "Life without A tail: New formats of long noncoding RNAs." Int J Biochem Cell Biol 54C: 338-349.
  2. ↑ Guru, S. C., et al. (1997). "A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus." Genome Res 7(7): 725-735.
  3. ↑ 3.0 3.1 3.2 Saha, S., et al. (2006). "Identification and characterization of a virus-inducible non-coding RNA in mouse brain." J Gen Virol 87(Pt 7): 1991-1995.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 Hutchinson, J. N., et al. (2007). "A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains." BMC Genomics 8: 39.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 Sunwoo H1, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL..(2009).MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009 Mar;19(3):347-59. doi: 10.1101/gr.087775.108. Epub 2008 Dec 22.
  6. ↑ 6.0 6.1 Clemson, C. M., et al. (2009). "An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles." Mol Cell 33(6): 717-726.
  7. ↑ 7.0 7.1 7.2 7.3 Sasaki, Y. T., et al. (2009). "MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles." Proc Natl Acad Sci U S A 106(8): 2525-2530.
  8. ↑ 8.0 8.1 Mao, Y. S., et al. (2011). "Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs." Nat Cell Biol 13(1): 95-101.
  9. ↑ Shevtsov, S. P. and M. Dundr (2011). "Nucleation of nuclear bodies by RNA." Nat Cell Biol 13(2): 167-173.
  10. ↑ 10.0 10.1 Chen, L. L. and G. G. Carmichael (2009). "Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA." Mol Cell 35(4): 467-478.
  11. ↑ Murthy, U. M. and P. N. Rangarajan (2010). "Identification of protein interaction regions of VINC/NEAT1/Men epsilon RNA." FEBS Lett 584(8): 1531-1535.
  12. ↑ 12.0 12.1 Nakagawa, S., et al. (2011). "Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice." J Cell Biol 193(1): 31-39.
  13. ↑ Guttman, M., et al. (2011). "lincRNAs act in the circuitry controlling pluripotency and differentiation." Nature 477(7364): 295-300.
  14. ↑ 14.0 14.1 14.2 Zhang, Q., et al. (2013). "NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression." MBio 4(1): e00596-00512.
  15. ↑ Peyman, J. A. (1999). "Repression of major histocompatibility complex genes by a human trophoblast ribonucleic acid." Biol Reprod 60(1): 23-31.
  16. ↑ Mercer, T. R., et al. (2010). "Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation." BMC Neurosci 11: 14.
  17. ↑ Michelhaugh, S. K., et al. (2011). "Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers." J Neurochem 116(3): 459-466.
  18. ↑ Johnson, R. (2012). "Long non-coding RNAs in Huntington's disease neurodegeneration." Neurobiol Dis 46(2): 245-254.
  19. ↑ 19.0 19.1 Friedel, C. C., et al. (2009). "Conserved principles of mammalian transcriptional regulation revealed by RNA half-life." Nucleic Acids Res 37(17): e115.
  20. ↑ 20.0 20.1 Clark, M. B., et al. (2012). "Genome-wide analysis of long noncoding RNA stability." Genome Res 22(5): 885-898.
  21. ↑ 21.0 21.1 21.2 Gremlich, S., et al. (2014). "The long non-coding RNA NEAT1 is increased in IUGR placentas, leading to potential new hypotheses of IUGR origin/development." Placenta 35(1): 44-49.
  22. ↑ 22.0 22.1 Hirose, T., et al. (2014). "NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies." Mol Biol Cell 25(1): 169-183.
  23. ↑ Shelkovnikova, T. A., et al. (2014). "Compromised paraspeckle formation as a pathogenic factor in FUSopathies." Hum Mol Genet 23(9): 2298-2312.


Basic Information

Transcript ID

NONHSAT022111

Source

NONCODE4.0

Same with

,

Classification

intergenic

Length

3756 nt

Genomic location

chr11+:65190269..65194003

Exon number

1

Exons

65190269..65194003

Genome context

Sequence
000001 GGAGTTAGCG ACAGGGAGGG ATGCGCGCCT GGGTGTAGTT GTGGGGGAGG AAGTGGCTAG CTCAGGGCTT CAGGGGACAG 000080
000081 ACAGGGAGAG ATGACTGAGT TAGATGAGAC GAGGGGGCGG GCTGGGGGTG CGAGAAGGAA GCTTGGCAAG GAGACTAGGT 000160
000161 CTAGGGGGAC CACAGTGGGG CAGGCTGCAT GGAAAATATC CGCAGGGTCC CCCAGGCAGA ACAGCCACGC TCCAGGCCAG 000240
000241 GCTGTCCCTA CTGCCTGGTG GAGGGGGAAC TTGACCTCTG GGAGGGCGCC GCTCTTGCAT AGCTGAGCGA GCCCGGGTGC 000320
000321 GCTGGTCTGT GTGGAAGGAG GAAGGCAGGG AGAGGTAGAA GGGGTGGAGG AGTCAGGAGG AATAGGCCGC AGCAGCCCTG 000400
000401 GAAATGATCA GGAAGGCAGG CAGTGGGTGC AGGGCTGCAG GAGGGCCGGG AGGGCTAATC TTCAACTTGT CCATGCCAGC 000480
000481 AGCCCCTTTT TTTCCAGACC AAGGGCTGTG AACCCGCCTG GGGATGAGGC CTGGTCTTGT GGAACTGAAC TTAGCTCGAC 000560
000561 GGGGCTGACC GCTCTGGCCC AGGGTGGTAT GTAATTTTCG CTCGGCCTGG GACGGGGCCC AGGCCGGGCC CAGCCTGGTG 000640
000641 GAGCGTCCAG GTCTGGGTGC GAAGCCAGGC CCCTGGGCGG AGGTGAGGGG TGGTCTGAGG AGTGATGTGG AGTTAAGGCG 000720
000721 CCATCCTCAC CGGTGACTGG TGCGGCACCT AGCATGTTTG ACAGGCGGGG ACTGCGAGGC ACGCTGCTCG GGTGTTGGGG 000800
000801 ACAACATTGA CCAACGCTTT ATTTTCCAGG TGGCAGTGCT CCTTTTGGAC TTTTCTCTAG GTTTGGCGCT AAACTCTTCT 000880
000881 TGTGAGCTCA CTCCACCCCT TCTTCCTCCC TTTAACTTAT CCATTCACTT AAAACATTAC CTGGTCATCT GGTAAGCCCG 000960
000961 GGACAGTAAG CCGAGTGGCT GTTGGAGTCG GTATTGTTGG TAATGGTGGA GGAAGAGAGG CCTTCCCGCT GAGGCTGGGG 001040
001041 TGGGGCGGAT CGGTGTTGCT TGCCTGCAGA GAGGGTGGGG AGTGAATGTG CACCCTTGGG TGGGCCTGCA GCCATCCAGC 001120
001121 TGAAAGTTAC AAAAATGCTT CATGGACCGT GGTTTGTTAC TATAGTGTTC CTCATGGCGA GCAGATGGAA CCGGGAGACA 001200
001201 TGGAGTCCCT GGCCAGTGTG AGTCCTAGCA TTGCAGGAGG GGAGACCCTG GAGGAGAGAG CCCGCCTCAA TTGATGCCTG 001280
001281 CAGATTGAAT TTCCAGAGGC TTAGGAGGAG GAAGTTCTCC AATGTTCTGT TTCCAGGCCT TGCTCAGGAA GCCCTGTATT 001360
001361 CAGGAGGCTA CCATTTAAAG TTTGCAGATG AGCTTATGGG GGGCAATCTT AAAAAGTCCA CAGCAGATGC ATCCGGCTCG 001440
001441 AGGGGCCATC AGCTTTGAAT AAATGCTTGT TCCAGAGCCC ATGAATGCCA GCAGGCACCC CTCCTTTCCT GGGGTAAAGG 001520
001521 TTTTCAGATG CTGCATCTTC TAAATTGAGC CTCCGGTCAT ACTAGTTTTG TGCTTGGAAC CTTGCTTCAA GAAGATCCCT 001600
001601 AAGCTGTAGA ACATTTTAAC GTTGATGCCA CAACGCAGAT TGATGCCTTG TAGATGGAGC TTGCAGATGG AGCCCCGTGA 001680
001681 CCTCTCACCT ACCCACCTGT TTGCCTGCCT TCTTGTGCGT TTCTCGGAGA AGTTCTTAGC CTGATGAAAT AACTTGGGGC 001760
001761 GTTGAAGAGC TGTTTAATTT TAAATGCCTT AGACTGGGGA TATATTAGAG GAAGCAGATT GTCAAATTAA GGGTGTCATT 001840
001841 GTGTTGTGCT AAACGCTGGG AGGGTACAAG TTGGTCATTC CTAAATCTGT GTGTGAGAAA TGGCAGGTCT AGTTTGGGCA 001920
001921 TTGTGATTGC ATTGCAGATT ACTAGGAGAA GGGAATGGTG GGTACACCGG TAGTGCTCTT TTGTTCTTGC TTCGTTTTTT 002000
002001 TAAACTTGAA CTTTACTTCG TTAGATTTCA TAATACTTTC TTGGCATTCT AGTAAGAGGA CCCTGAGGTG GGAGTTGTGG 002080
002081 GGGACGGGGA GAAGGGGACA GCTTGGCACC GGTCCCGTGG GCGTTGCAGT GTGGGGGATG GGGGTATGCA GCTTGGCACT 002160
002161 GGTACTGGGA GGGATGAGGG TGAAGAAGGG GAGAGGGTTG GTTAGAGATA CAGTGTGGGT GGTGGGGGTG GTAGGAAATG 002240
002241 CAGGTTGAAG GGAATTCTCT GGGGCTTTGG GGAATTTAGT GCGTGGGTGA GCCAAGAAAA TACTAATTAA TAATAGTAAG 002320
002321 TTGTTAGTGT TGGTTAAGTT GTTGCTTGGA AGTGAGAAGT TGCTTAGAAA CTTTCCAAAG TGCTTAGAAC TTTAAGTGCA 002400
002401 AACAGACAAA CTAACAAACA AAAATTGTTT TGCTTTGCTA CAAGGTGGGG AAGACTGAAG AAGTGTTAAC TGAAAACAGG 002480
002481 TGACACAGAG TCACCAGTTT TCCGAGAACC AAAGGGAGGG GTGTGTGATG CCATCTCACA GGCAGGGGAA ATGTCTTTAC 002560
002561 CAGCTTCCTC CTGGTGGCCA AGACAGCCTG TTTCAGAGGG TTGTTTTGTT TGGGGTGTGG GTGTTATCAA GTGAATTAGT 002640
002641 CACTTGAAAG ATGGGCGTCA GACTTGCATA CGCAGCAGAT CAGCATCCTT CGCTGCCCCT TAGCAACTTA GGTGGTTGAT 002720
002721 TTGAAACTGT GAAGGTGTGA TTTTTTCAGG AGCTGGAAGT CTTAGAAAAG CCTTGTAAAT GCCTATATTG TGGGCTTTTA 002800
002801 ACGTATTTAA GGGACCACTT AAGACGAGAT TAGATGGGCT CTTCTGGATT TGTTCCTCAT TTGTCACAGG TGTCTTGTGA 002880
002881 TTGAAAATCA TGAGCGAAGT GAAATTGCAT TGAATTTCAA GGGAATTTAG TATGTAAATC GTGCCTTAGA AACACATCTG 002960
002961 TTGTCTTTTC TGTGTTTGGT CGATATTAAT AATGGCAAAA TTTTTGCCTA TCTAGTATCT TCAAATTGTA GTCTTTGTAA 003040
003041 CAACCAAATA ACCTTTTGTG GTCACTGTAA AATTAATATT TGGTAGACAG AATCCATGTA CCTTTGCTAA GGTTAGAATG 003120
003121 AATAATTTAT TGTATTTTTA ATTTGAATGT TTGTGCTTTT TAAATGAGCC AAGACTAGAG GGGAAACTAT CACCTAAAAT 003200
003201 CAGTTTGGAA AACAAGACCT AAAAAGGGAA GGGGATGGGG ATTGTGGGGA GAGAGTGGGC GAGGTGCCTT TACTACATGT 003280
003281 GTGATCTGAA AACCCTGCTT GGTTCTGAGC TGCGTCTATT GAATTGGTAA AGTAATACCA ATGGCTTTTT ATCATTTCCT 003360
003361 TCTTCCCTTT AAGTTTCACT TGAAATTTTA AAAATCATGG TTATTTTTAT CGTTGGGATC TTTCTGTCTT CTGGGTTCCA 003440
003441 TTTTTTAAAT GTTTAAAAAT ATGTTGACAT GGTAGTTCAG TTCTTAACCA ATGACTTGGG GATGATGCAA ACAATTACTG 003520
003521 TCGTTGGGAT TTAGAGTGTA TTAGTCACGC ATGTATGGGG AAGTAGTCTC GGGTATGCTG TTGTGAAATT GAAACTGTAA 003600
003601 AAGTAGATGG TTGAAAGTAC TGGTATGTTG CTCTGTATGG TAAGAACTAA TTCTGTTACG TCATGTACAT AATTACTAAT 003680
003681 CACTTTTCTT CCCCTTTACA GCACAAATAA AGTTTGAGTT CTAAACTCAT TAGAAAAAAA AAAAAAAAAA AAAAAA
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