Lnc-PDIA4-1:1

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Annotated Information

Transcriptomic Nomeclature

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Function

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Regulation

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Expression

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Allelic Information and Variation

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Evolution

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Basic Information

Transcript ID	lnc-PDIA4-1:1
Source	LNCipedia2.1
Same with	,
Classification	intergenic
Length	113 nt
Genomic location	chr7-:148684227..148684340
Exon number	1
Exons	148684227..148684340
Genome context
Sequence	000001 GGCTGGTCCG AAGGTAGTGA GTTATCTCAA TTGATTGTTC ACAGTCAGTT ACAGATCGAA CTCCTTGTTC TACTCTTTCC 000080 000081 CCCCTTCTCA CTACTGCACT TGACTAGTCT TTT

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Annotation (From lncRNAdb)

[lnc-PDIA4-1:1]

Section	Description
ID	Y RNAs
Characteristics	83-112 nt. Four human Y RNAs (hY1, 112nt; hY3, 101nt; hY4, 93nt; and hY5, 83nt) encoded in single copy genes, which are present in a cluster in human chromosome 7 (Maraia (1994)). Pyrimidine-rich, transcribed by RNA polymerase III, and contain a 5-triphosphate and a retained 3' poly(U) tail (Hendrick (1981)). Y RNAs form characteristic stem-loop structures, with a highly conserved double-stranded stem formed by partially complementary 5' and 3' terminal domains, linked by a loop domain containing secondary stem-loops (Teunissen (2000), O'Brien (1993), van Gelder (1994)). Parts of the RNA structure appear to be flexible, able to adopt different conformations. Y RNAs contain an essential characteristic bulged C in the middle portion of the stem (in position 8 or 9), as well as the characteristic pyrimidine-rich region that is single-stranded in the secondary structures (Teunissen (2000), Green (1998)).
Expression	All four Y RNAs are primarily cytoplasmic, they are also detected in perinucleolar compartments, discrete structures near the nucleolar rim (Matera (1995)). Y RNAs are expressed in similar levels in all human tissues and cell lines investigated, with all Y RNAs showing a positively correlated expression across different tissue types (Christov (2008))(Pruijn (1993)). Y RNAs are up-regulated in a number of human solid tumours compared to corresponding nonmalignant tissues. In particular, hY1 and hY3 RNAs are over-expressed in carcinomas and adenocarcinomas of the bladder, cervix, colon, kidney, lung and prostate (Christov (2008)).
Function	The different Y RNAs may have multiple roles. Y RNAs were identified as the RNA component of the 'small cytoplasmic' (sc) Ro autoantigen (soluble ribonucleoproteins (RNP) detected in sera of systemic lupus erythematosis patients), binding the autoantigen La and Ro proteins (Lerner (1981)). Y RNAs have been shown to be required for semiconservative chromosomal DNA replication in vitro, in a mammalian cell-free experimental system. hY1, hY3, hY4 and hY5 RNAs are functionally redundant (Christov (2006)), and have been shown to act at the initiation step of DNA replication* (Krude (2009)). (*See Krude (2010) for review). Regulate cell DNA replication and cell proliferation, with knock-down of hY1 and hY3 RNA in human cells causing a cytostatic arrest of cell proliferation (Christov (2008), Krude (2009), Christov (2006)). Bind to Ro proteins through their terminal stem, which contains conserved binding sites for Ro60 and La proteins (Green (1998)). The central portion of the double-stranded stem is essential for reconstituting chromosomal DNA replication, while the central loop and the terminal stem are not (Gardiner (2009)). Different proteins may also bind Y RNAs or be present in human Ro RNPs, such as hnRNP K, PTB, RoBP1 and nucleolin (Bouffard (2000), Fabini (2000), Fouraux (2002)), indicating that Y RNAs may be involved in their regulation, such as in the control of alternative splicing. hY5 RNA uniquely binds to ribosomal protein L5 and its binding partner 5S RNA, with Ro-Y5 suggested to have a specialized role in 5S ribosomal RNA quality control (Hogg (2007)). Ro60 protein had been previously shown to bind misfolded small RNAs and suggested to be involved in quality control of the RNAs (Shi (1996), Stein (2005), Fuchs (2006)). A role is also proposed in the regulation of the translation of ribosomal mRNA (Pellizzoni (1998)).
Conservation	A single cluster of functional Y RNA genes is preserved throughout tetrapod evolution, which however exhibits clade-specific tandem duplications, gene-losses, and rearrangements (Mosig (2007)). Homologues of functional Y RNAs are present throughout vertebrates, with conserved synteny, but numbers vary between species, with individual gene-loss events having occurred during evolution in most classes (the mouse expresses only Y1 and Y3 RNAs, zebrafish only Y1, and chicken Y3 and Y4). No Y RNA gene has been identified in some species such as Drosophila melanogaster and Schistosoma species. (Copeland (2009), Pruijn (1993), Mosig (2007), Gardiner (2009), O'Brien (1993), Perreault (2007), Farris (1995)). Y3 is the most conserved Ro RNA, not only by its more consistent presence in other species, but also at the levels of sequence divergence and secondary structure similarity (Farris (1995)). Recently, the 'sbRNAs' or stem-bulge RNAs from Caenorhabditis elegans have been identified as homologs of vertebrate Y RNAs present in nematode worms, showing the characteristic Ro protein binding motif (Boria (2010)). An Y-like RNA (as well as other small RNAs) has been also identified in the bacterium Deinococcus radiodurans binding to an ortholog of Ro60 (Rsr), which accumulate following UV irradiation, and contribute to the resistance to irradiation (Chen (2000)).
Misc	Thousands of Y RNA 'retropseudogenes' are present among various species (Perreault (2007)). It has been suggested that hY RNAs represent a novel class of nonautonomous, L1-dependent, retrotransposable elements (Perreault (2005)).

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