ENST00000553584.1

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Annotated Information

Name

Rian: RNA Imprinted and Accumulated in Nucleus . Irm: Imprinted RNA near Meg3/Gtl2. MEG8: Maternally expressed gene 8

Disease

Prader-Willi/Angelman syndrome

Characteristics

These overlapping but non-identical transcripts are found in the Dlk1-Dio3 imprinted region (Hatada (2001), Royo (2007), Hagan (2009)) and should probably be viewed as different isoforms of the Rian gene. The human and mouse loci are quite similar, whereas the rat loci (Bsr gene) has undergone significant divergence and so has its own entry in the database. Spliced lncRNAs that contain a number of intronic snoRNAs and sometimes miRNAs (Cavaillé (2002), Royo (2007), Hagan (2009)). In human and mouse, transcription of the Meg8 isoform can extend through the snoRNA clusters. Mouse Meg8 is ~4.4kb with over 20 exons. In mouse the ~2.5 kb Irm transcript contains the last 10 exons of Meg8 but has its own transcriptional start site. Mouse Meg8 contains intronic miRNAs not found in Irm (Hagan (2009)). RNA sequencing confirms a large number of isoforms with alternative splicing and also retained introns exist at this locus though no evidence was found for Rian overlapping the Meg9/Mirg transcript (Guttman (2010)). It is unclear if the Irm isoform exists in humans.

Function

LncRNAs contain a number of miRNAs and snoRNAs, little is known about the molecular function of the lncRNAs. Rian transcript(s) bind to the PRC2 chromatin modifying complex in mouse embryonic stem cells (Zhao (2010), Guttman (2011)). Rian was also found to interact with a number of other chromatin binding protein(s)/complexes in mouse embryonic stem cells including PRC1, JARID1B, JARID1C and CBX3, with the general pattern being interaction with repressors of gene expression (Guttman (2011)). Aberrant repression of Rian and other maternally expressed lncRNAs from the DLK1-Dio3 imprinting cluster is present in most induced pluripotent stem cell (iPSC) lines and is responsible for the failure of iPSCs to form viable mice, with embryos dying mid-gestation (Stadtfeld (2010)).

Expression

Imprinted: Maternally expressed (Hatada (2001), Charlier (2001), Cavaillé (2002)). Expressed predominately in brain (Hatada (2001)), embryo and muscle (Charlier (2001)) with generally weak expression in other tissues (Hagan (2009)). Expressed in mouse embryonic stem cells (Guttman (2011)). In mouse the longer 'Meg8' transcript is also expressed in skin whereas the shorter 3' 'Irm' is not (Hagan (2009)). Up-regulated during differentiation of neuronal progenitors to GABAergic neurons in vitro (Mercer (2010)). Localised to the nucleus (Hatada (2001)). Intronic snoRNAs also show brain and embryo imprinted expression ((Cavaillé (2002)).

Conservation

Bsr and Rian/MEG8/Irm are not highly conserved between species ((Cavaillé (2002)). However, some Rian exons show good homology to Bsr and while many snoRNAs are specific to one species others are homologous (Hatada (2001), Cavaillé (2002)). Rian gene is present in mammals.

Misc

Human UCSC browser link below is for Refseq Meg8, however it is clear from known human mRNAs that transcripts from the Meg8 locus can extend much further than the current Refseq annotation.

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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References

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID	ENST00000553584.1
Source	Gencode19
Same with	lnc-DLK1-6:3,NONHSAT039802
Classification	intergenic
Length	498 nt
Genomic location	chr14+:101361107..101373305
Exon number	4
Exons	101361107..101361376,101365294..101365422,101372435..101372500,101373273..101373305
Genome context
Sequence	000001 GGTCTGAAAA ATGATATTCA TTGTCCTAAT GTGTAAATTT CGACAATTTG CAAATTTGTA GATTCTTTAG AATAGAACTA 000080 000081 ACTCAAGCCC TTCATTCTGC AGCTGAGGCT CACTGCCCCC AGTGGGCAGT GGGTCCAGGG GGTTTCTGAG GACAGGGCAT 000160 000161 GACCCAGCCC TGCTGCCCCC AAGATGGCAC CTGGCTTGGA GGGGTGAGGG GCCCTGTTAG TCTGACTTTG AAGAAGACCA 000240 000241 GCCTTCCAGA CTCGCTTGGT GCCCTGACAG GAGCCCTGGG CTCCCCCAGT GTTGCCTGGG TCTGACTTTG CCTCAGTGAA 000320 000321 AACTGCCTCG AATTCTTTCT TGCACCGATG GGCAGATGGG CAGTGTCGGA GGATCGTGTC ATCTGTCCCG TGGCGCTGGT 000400 000401 TGGCTTGGTC AAGTCAGTGT TCAAACTATC TCCTGCTCTT TCAAGGGGAT CTGGGGCTCT AGAAGATTAG AGGACTTGGA 000480 000481 GAGGTTAGTG ACTTGCTC

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