Table 1

Identification of islet lncRNAs

Tissue/cell typelncRNAs identifiedlncRNA annotation parametersReference
Human and mouse islets; human purified β-cells1,128 lncRNAs>200-nt long; overlap with a H3K4me3 peak; >0.5 RPKM; lack of evidence for splicing to any annotated coding geneMorán et al., 2012 (28)
Mouse β- and non–β-cell islet endocrine cells2,790 transcripts, 2,425 loci, 1,342 novel genesNo overlap with annotated gene or 5′ or 3′ UTR of a Ref-seq protein-coding gene; >200-nt long; PhyloCSF score <0Ku et al., 2012 (44)
FACS purified human β- and α-cells12 β-cell–specific and 5 α-cell–specific noncoding transcript>200-nt long; >1 RPKM; no overlap with the UCSC Repeat Masker track or other ncRNAs; within 5 kb of a H3K4me3 peakBramswig et al., 2013 (41)
Human islets; β-cells; non–β-cell islet endocrine cells280 lncRNAs enriched in β-cells compared with whole islets or non–β-endocrine cellsLimited analyses to annotated lncRNAs in Morán et al. (28) Nica et al., 2013 (43)
Human islets exposed to inflammatory cytokines262 lncRNAs, 177 novel, none differentially expressed>200-nt long; >1 exon; negative CPAT score; novel lncRNAs did not match with known human lncRNA sequences in the NONCODE databaseLi et al., 2014 (42)
89 human islet samples493 Ref-seq lncRNAs expressed in human islets, 54 lncRNAs with HbA1c eQTLsNo overlap with any annotated genes; >1 exon; expressed (nonnull read coverage) in at least 5% of the samples; negative CPAT scoreFadista et al., 2014 (40)
FACS purified mouse β- and α-cells145 novel lncRNAsNo overlap with any known Ref-seq or UCSC gene; transcript length >3 kb; >1 RPKM; no overlap with known rRNA loci; PhastCons score >0.4Benner et al., 2014 (45)
41 human islet samples2,226 de novo lncRNAsH3K4me3 enrichment +1 kb to −0.5 kb from the transcript 5′ end; CPAT score <0.364; no sense overlap with a coding exon; >0.05 FPKM in β-cells; acinar to β-cell expression ratio <3Akerman et al., 2017 (39)
Islets from mice fed a regular or high-fat diet1,761 annotated lncRNAs, 1,558 novel lncRNAs>200-nt long; at least 2 exons; FPKM >5; GeneID v1.4.4 coding potential score <4Motterle et al., 2017 (46)
  • CPAT, coding potential assessment tool (68); FACS, fluorescent automated cell sorting; FPKM, fragments per kilobase million; PhastCons, phylogenetic analysis with space/time models (Phast) conservation (Cons) (69); PhyloCSF, phylo codon substitution frequencies (70); RPKM, reads per kilobase million; UCSC, University of California Santa Cruz; UTR, untranslated region.