NEAT1
Species: Homo sapiens
Position: chr11: 65422773-65445540
Known as: NEAT1 , ENSG00000245532
Transcript: NR_131012 , NR_028272 , ENST00000501122 , ENST00000601801 , ENST00000499732
Sequence: Download
Description:
NEAT1 (nuclear paraspeckle assembly transcript 1) is a mammalian-specific long noncoding RNA that is important for the reproductive physiology of mice, cancer development, and the formation of subnuclear bodies termed paraspeckles. The two major isoforms of NEAT1 (3.7 kb NEAT1_1 and 23 kb NEAT1_2 in human) are generated from a common promoter and are produced through the use of alternative transcription termination sites. The shorter isoform NEAT1_1 is not a major component of paraspeckles. In addition, NEAT1_1 localizes in numerous nonparaspeckle termed as "microspeckles", which may carry paraspeckle-independent functions. The study of Li et al. h highlights the complexity of lncRNA and show cases how genome editing tools are useful in dissecting the structural and functional roles of overlapping transcripts.
sgRNAs
| sgRNA_ID | Sequence | Position (Chr) | Position (Lnc) | Length | PAM | Type | Validity | Cell line | Note | Ref. |
|---|---|---|---|---|---|---|---|---|---|---|
| sgRNA1 | TTTGGGAGGCGAATGCCATG | 65422544-65422563(-) | up stream | 20 | AGG | CRISPRa | High activity | HAP1;U2OS | activated NEAT1 expression more than 2-fold | [1] |
| sgRNA2 | AGCACTGTTAAAGAGAAGCG | 65422596-65422615(+) | up stream | 20 | GGG | CRISPRa | High activity | HAP1;U2OS | activated NEAT1 expression more than 2-fold | [1] |
| sgRNA3 | AGTCTCTCCGGGCAGGGTCG | 65422672-65422691(+) | up stream | 20 | GGG | CRISPRa | High activity | HAP1;U2OS | activated NEAT1 expression more than 2-fold | [1] |
| sgRNA4 | CTGGGAGACCATGCACCGCC | 65422648-65422667(+) | up stream | 20 | CGG | CRISPRa | High activity | HAP1;U2OS | strongly activated NEAT1 expression (~4-fold) | [1] |
| sgRNA5 | AGAGACTCCCGGGCGGTGCA | 65422659-65422678(-) | up stream | 20 | TGG | CRISPRa | High activity | HAP1;U2OS | activated NEAT1 expression more than 2-fold | [1] |
| sgRNA6 | GCACCGCCCGGGAGTCTCTC | 65422660-65422679(+) | up stream | 20 | CGG | CRISPRa | High activity | HAP1;U2OS | activated NEAT1 expression more than 2-fold | [1] |
| sgRNA7 | GGCTATAAAAGCAAAAGTTG | 65422764-65422783(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | U2OS | NA | [2] |
| sgRNA8 | GTCCAGCCGGAGTTAGCGAC | 65422790-65422809(+) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | U2OS | NA | [2] |
| sgRNA9 | ATTGCCTTCATAACGACTT | 65426572-65426590(+) | gene body (near 5') | 19 | TGG | CRISPRko | Experimental validated | U2OS | NA | [2] |
| sgRNA10 | GCGACAGGGAGGGATGCGCGCC | 65422805-65422826(+) | gene body (near 5') | 22 | TGG | CRISPRi | Experimental validated | K562 | NA | [3] |
| sgRNA11 | GCGCGCCTGGGTGTAGTTGT | 65422820-65422839(+) | gene body (near 5') | 20 | GGG | CRISPRi | Experimental validated | K562 | NA | [3] |
| sgRNA12 | GAAGTGGCTAGCTCAGGGCTTC | 65422847-65422868(+) | gene body (near 5') | 22 | AGG | CRISPRi | Experimental validated | K562 | NA | [3] |
| sgRNA13 | GGAGCCGCCGGGGTCGCTTG | 65422412-65422431(-) | up stream | 20 | AGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA14 | ATACACTGGGGTCCTTGCGT | 65422619-65422638(+) | up stream | 20 | GGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA15 | CTGAGCGAGCCCGGGTGCGC | 65423100-65423119(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA16 | TATGTAATTTTCGCTCGGCC | 65423385-65423404(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA17 | ACGGACCCGCCGTGGGCCCA | 65444590-65444609(+) | gene body (near 3') | 20 | GGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA18 | GCTTGTGCCTCTGCTCGTGA | 65445162-65445181(+) | gene body (near 3') | 20 | AGG | CRISPRko | Experimental validated | J3C9;J3E5 | NA | [4] |
| sgRNA19 | AGAGGCCTTCCCGCTGAGGC | 65423813-65423832(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA20 | TCCGACTTCATTTCGAGTGA | 65444793-65444812(+) | gene body (near 3') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA21 | TACCGCATATCTGTGTACAT | 65436801-65436820(+) | gene body (near 3') | 20 | GGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA22 | TGACTTGATTTGGCTGTGCA | 65439390-65439409(+) | gene body (near 3') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA23 | ATTGTGTTGTGCTAAACGCT | 65424635-65424654(+) | gene body (near 5') | 20 | GGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA24 | CTTGATTTGGCTGTGCAAGG | 65439393-65439412(+) | gene body (near 3') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA25 | GAAGTTAATATTGACTGACC | 65432625-65432644(-) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA26 | GTGGGCTTTTAACGTATTTA | 65425587-65425606(+) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA27 | GATTCACGGGGTATAAATGT | 65427896-65427915(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA28 | TTGGACTTAAGGGCATCATC | 65440901-65440920(+) | gene body (near 3') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA29 | TATTACCTTGGCCTAGGGGG | 65433884-65433903(-) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA30 | TCCCTCCCTGTCGCTAACTC | 65422799-65422818(-) | gene body (near 5') | 20 | CGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA31 | GTACCTTATAACGTTGGATT | 65431993-65432012(-) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA32 | AAATATCCGCAGGGTCCCCC | 65422991-65423010(+) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA33 | CACCGTGTTATACTCGATTC | 65435781-65435800(-) | gene body (near 3') | 20 | CGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA34 | AATGGCTTTTGGGGTACAAA | 65432706-65432725(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA35 | GGCACTGGACATAAGCCCCC | 65438180-65438199(+) | gene body (near 3') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA36 | CCACCTGGAAAATAAAGCGT | 65423611-65423630(-) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA37 | CATTTAAACCTTCTTCCCCG | 65429804-65429823(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA38 | GTACACTACTGACAAACGGG | 65427521-65427540(+) | gene body (near 5') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA39 | ACTTTATTTGTGCTGTAAAG | 65426491-65426510(-) | gene body (near 5') | 20 | GGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA40 | TACGCGGGGAAACGTGCCAC | 65443855-65443874(-) | gene body (near 3') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA41 | GGCGGGTCGTCCTAACTAGC | 65428740-65428759(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA42 | GCAAAACCTTACACCCCAAG | 65427206-65427225(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA43 | TACCACTTAGAACTCTAACC | 65426847-65426866(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA44 | GAGGGTGGCTGCACAGTCGA | 65441886-65441905(+) | gene body (near 3') | 20 | GGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA45 | GCAAAACCTGAGTGCGGCCA | 65445476-65445495(-) | gene body (near 3') | 20 | TGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA46 | GGATATCATATACTCACAAC | 65430800-65430819(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA47 | CACATGGTTAGTGGTCAAAG | 65432254-65432273(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA48 | GGGAGGCGCGGAGCCGCCGC | 65445428-65445447(+) | gene body (near 3') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA49 | CCTGATGTTAGTGGCTATGT | 65430828-65430847(-) | gene body (near 5') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA50 | TCATATATGGAGCGTCGTAG | 65434805-65434824(-) | gene body (near 3') | 20 | AGG | CRISPRko | Experimental validated | HAP1 | NA | [5] |
| sgRNA51 | GAACTGAACTTAGCTCGACG | 65423339-65423358(+) | gene body (near 5') | 20 | GGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA52 | AAGGAATCCACAGCTGACGG | 65444827-65444846(+) | gene body (near 3') | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA53 | GTGTTGTGCTAAACGCTGGG | 65424638-65424657(+) | gene body (near 5') | 20 | AGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA54 | CTTTGCAAACCTAGGGGTGG | 65417537-65417556(+) | up stream | 20 | AGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA55 | GGTCCTCTCCTCATGTGCCG | 65435712-65435731(+) | gene body (near 3') | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA56 | GGTGGGGGATCATGACCTGA | 65427404-65427423(+) | gene body (near 5') | 20 | AGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA57 | AATTGGTAAAGTAATACCAA | 65426119-65426138(+) | gene body (near 5') | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA58 | CTAGGGGCCGCTGGAGGTGC | 65417729-65417748(+) | up stream | 20 | AGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA59 | CGTCCAGCACGGCTGGGCCG | 65445557-65445576(+) | down stream | 20 | GGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA60 | TTACTAGGAGAAGGGAATGG | 65424736-65424755(+) | gene body (near 5') | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA61 | GGCCCAGCCACGCATTCCAC | 65417777-65417796(+) | up stream | 20 | AGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA62 | GCGCCAGGATTCCCAGTGGG | 65417602-65417621(+) | up stream | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA63 | CCTAGCATGTTTGACAGGCG | 65423545-65423564(+) | gene body (near 5') | 20 | GGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA64 | GTGTGGCTAGCTCTTCCCAC | 65438012-65438031(+) | gene body (near 3') | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
| sgRNA65 | GGTTAGCACAGGCGAAAGTG | 65417646-65417665(+) | up stream | 20 | TGG | CRISPRko | Partial validated | Huh7.5 | NA | [6] |
GBrowser
Links
Reference
1. Yamazaki T, Fujikawa C, Kubota A, Takahashi A, Hirose T (2018). CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles. Biochem Biophys Res Commun.
2. Li R, Harvey AR, Hodgetts SI, Fox AH (2017). Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles. RNA 23(6): 872-881.
3. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, et al. (2014). Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell 159(3): 647-61.
4. Liu H, Hu PW, Couturier J, Lewis DE, Rice AP (2018). HIV-1 replication in CD4+ T cells exploits the down-regulation of antiviral NEAT1 long non-coding RNAs following T cell activation. Virology 522: 193-198.
5. Yamazaki T, Souquere S, Chujo T, Kobelke S, Chong YS, et al. (2018). Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation. Mol Cell 70(6): 1038-1053.e7.
6. Zhu S, Li W, Liu J, Chen CH, Liao Q, et al. (2016). Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 34(12): 1279-1286.