Functional annotation of human long noncoding RNAs via molecular phenotyping.
Jordan A RamilowskiChi Wai YipSaumya AgrawalJen-Chien ChangYari CianiIvan V KulakovskiyMickaël MendezJasmine Li Ching OoiJohn F OuyangNick ParkinsonAndreas PetriLeonie RoosJessica SeverinKayoko YasuzawaImad AbugessaisaAltuna AkalinIvan V AntonovErik ArnerAlessandro BonettiHidemasa BonoBeatrice BorsariFrank BrombacherChristopher JF CameronCarlo Vittorio CannistraciRyan CardenasMelissa CardonHoward ChangJosée DostieLuca DucoliAlexander FavorovAlexandre FortDiego GarridoNoa GilJuliette GimenezReto GulerLusy HandokoJayson HarshbargerAkira HasegawaYuki HasegawaKosuke HashimotoNorihito HayatsuPeter HeutinkTetsuro HiroseEddie L ImadaMasayoshi ItohBogumil KaczkowskiAditi KanhereEmily KawabataHideya KawajiTsugumi KawashimaS Thomas KellyMiki KojimaNaoto KondoHaruhiko KosekiTsukasa KounoAnton KratzMariola Kurowska-StolarskaAndrew Tae Jun KwonJeffrey LeekAndreas LennartssonMarina LizioFernando López-RedondoJoachim LuginbühlShiori MaedaVsevolod J MakeevLuigi MarchionniYulia A MedvedevaAki MinodaFerenc MüllerManuel Muñoz-AguirreMitsuyoshi MurataHiromi NishiyoriKazuhiro R NittaShuhei NoguchiYukihiko NoroRamil NurtdinovYasushi OkazakiValerio OrlandoDenis PaquetteCallum J C ParrOwen J L RackhamPatrizia RizzuDiego Fernando Sánchez MartinezAlbin SandelinPillay SanjanaColin A M SempleYoutaro ShibayamaDivya M SivaramanTakahiro SuzukiSuzannah C SzumowskiMichihira TagamiMartin S TaylorChikashi TeraoMalte ThodbergSupat ThongjueaVidisha TripathiIgor UlitskyRoberto VerardoIlya E VorontsovChinatsu YamamotoRobert S YoungJohn Kenneth BaillieAlistair R R ForrestRoderic GuigóMichael M HoffmanChung Chau HonTakeya KasukawaSakari KauppinenJuha KereBoris LenhardClaudio SchneiderHarukazu SuzukiKen YagiMichiel J L de HoonJay W ShinPiero CarniciPublished in: Genome research (2020)
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
Keyphrases
- gene expression
- endothelial cells
- genome wide identification
- single cell
- induced pluripotent stem cells
- genome wide analysis
- poor prognosis
- network analysis
- pluripotent stem cells
- dna methylation
- single molecule
- rna seq
- long non coding rna
- quality improvement
- genome wide
- machine learning
- extracellular matrix
- data analysis
- bioinformatics analysis