Regulatory Functions Reported for Long Non-coding lncRNA molecules




Budding yeast

Galactose metabolism; controls speed of transcriptional induction by galactose

(Wang and Tran 2013)

Fission yeast

Phosphate-induced epigenetic silencing

(Shah, Wittmann et al. 2014)

Budding and fission yeast

Cellular responses to environmental changes

(Yamashita, Shichino et al. 2016)

Fungal pathogen Cryptococcus neoformans

lncRNA RZE1 regulates yeast-to-hypha transition

(Chacko, Zhao et al. 2015)

Plasmodium falciparum

Gametocyte development

(Broadbent, Broadbent et al. 2015)

Plasmodium falciparum

Telomere associated lncRNAs

(Broadbent, Park et al. 2011)


Flower development and timing

(Chekanova 2015)


Stress response lncRNAs

(Di, Yuan et al. 2014)

Arabidopsis thaliana

lncRNA TER regulates telomerase activity

(Nelson and Shippen 2015)


Fruit ripening

(Zhu, Yang et al. 2015)


Sex determination

(Mulvey, Olcese et al. 2014)


X chromosome dosage compensation

(Quinn, Zhang et al. 2016)


Spermatogenesis, synaptic transmission, placenta development

(Necsulea, Soumillon et al. 2014)


mRNA transcription

(Kugel and Goodrich 2013)


Stem cell pluripotency

(Fort, Hashimoto et al. 2014)


Epigenetic chromatin formatting

(Nakagawa and Kageyama 2014)


Placental membrane integrity

(Luo, Shi et al. 2013)


Androgen receptor-regulated transcription

(Yang, Lin et al. 2013)


Synaptic connectivity in brain

(Smalheiser 2014)

Marsupial Monodelphis domestica

Female X chromosome inactivation by repeat-rich lncRNA Rsx

(Grant, Mahadevaiah et al. 2012)

Goat (Capra hircus)

Skin pigmentation

(Ren, Wang et al. 2016)


Enhancer methylation and transcription control

(Berghoff, Clark et al. 2013)


Diurnal metabolic regulation

(Powell, Coulson et al. 2013)


Cell reprogramming to pluripotent stem cells

(Kim, Marinov et al. 2015)


Imprinted Igfr2 silencing

(Santoro, Mayer et al. 2013)


Myogenesis (SINE-containing lncRNA acting on STAU-1 mRNA decay)

(Wang, Gong et al. 2013)


lncRNA Dum regulates myogenic differentiation and muscle regeneration

(Wang, Zhao et al. 2015)


Translation of brain UCHL1 protein involved in preventing neurodegeneration; regulation by SINEB2 recognition

(Carrieri, Cimatti et al. 2012; Zucchelli, Fasolo et al. 2015)


lncRNA Evf2 modulates chromatin formation in forebrain development

(Cajigas, Leib et al. 2015)


lncRNA-HIT mediates TGF beta-induced epithelial to mesenchymal transition in mammary epithelia and is essential for chondrogenic differentiation in the limb mesenchyme (cartilage formation)

(Carlson, Quinn et al. 2015; Richards, Zhang et al. 2015)


lncRNA Fendrr regulates heart and body wall development

(Grote, Wittler et al. 2013)


Male germline development

(Bao, Wu et al. 2013)


Long-term potentiation of synaptic connectivity in adult brain development

(Maag, Panja et al. 2015)


lncRNA ANRIL regulates expression of three cyclin-dependent kinase inhibitors and atherogenesis; Alu exons acquired in primate lineage

(He, Gu et al. 2013; Holdt, Hoffmann et al. 2013)


Primate-specific lncRNA HPAT-5 required for stem cell pluripotency

(Durruthy-Durruthy, Sebastiano et al. 2016)


18,871,097 lncRNA-RNA base-pairings likely involved in processing, stability control and functions of 57,303 transcripts

(Szczesniak and Makalowska 2016)


Centromere function

(Quenet and Dalal 2014)


Steroid receptor activation

(Novikova, Hennelly et al. 2012)


Endocrine regulation

(Knoll, Lodish et al. 2015)


Rb and p53 signaling pathways

(Subramanian, Jones et al. 2013)


lncRNA RoR is a p53 repressor in response to DNA damage; acts as microRNA sponge in transcription factor control

(Zhang, Zhou et al. 2013) (Wang, Xu et al. 2013)


lncRNA LED stimulates p53 activated transcription

(Leveille, Melo et al. 2015)


lncRNA H19 modulates S-adenosylhomocysteine hydrolase and DNA methylation

(Zhou, Yang et al. 2015)


lncRNA HOTAIR regulates chromatin dynamics

(Bhan and Mandal 2015)


lncRNA NBR2 regulates AMP-activated protein kinase under energy stress

(Liu, Xiao et al. 2016)


Xist lncRNA required for X inactivation

(Engreitz, Pandya-Jones et al. 2013; Froberg, Yang et al. 2013)


lncRNA XACT in active X chromosome expression

(Vallot and Rougeulle 2013)


Apoptosis and lysosomal processes (Alu recognition; lncRNA GAS5)

(Mandal, Pandey et al. 2013; Pickard, Mourtada-Maarabouni et al. 2013; Rossi and Antonangeli 2014)


STAU-1 mRNA decay (stimulated by Alu pairing)

(Gong and Maquat 2011)


Cell cycle regulation by lncRNA APTR

(Negishi, Wongpalee et al. 2014)


lncRNA Firre controls mRNA retention in the nucleus, nucleolar anchoring of inactive X

(Yang, Deng et al. 2015; Hacisuleyman, Shukla et al. 2016)


lncRNA ROR regulates stem cell pluripotency; has sequences from >12 mobile elements, including a long HERVH 5’ sequence characteristic of several pluripotent cell lncRNAs; acts as microRNA sponge

(Loewer, Cabili et al. 2010) (Kelley and Rinn 2012; Santoni, Guerra et al. 2012; Wang, Xu et al. 2013)


Stem cell specificities

(Kelley and Rinn 2012; Hu and Shan 2016)


Stem cell pluripotency and cancer cell proliferation; transcription from retroviral promoters

(Ng and Stanton 2013; St Laurent, Shtokalo et al. 2013; Shahryari, Jazi et al. 2015)


Pluripotency and neuronal differentiation regulation of chromatin modifiers and transcription factors

(Ng, Johnson et al. 2012)


lncRNA-mediated regulation of the interferon response

(Valadkhan and Gunawardane 2016)


lncRNA ANRIL regulates inflammatory responses as a novel component of NF-kappaB pathway

(Zhou, Han et al. 2016)


Innate and adaptive immune responses

(Atianand and Fitzgerald 2014; Imamura and Akimitsu 2014; Aune and Spurlock 2016)


lncRNA TINCR regulates epidermal differentiation

(Kretz, Siprashvili et al. 2013)


Neurodevelopment and brain function

(Barry, Briggs et al. 2014; Clark and Blackshaw 2014; Roberts, Morris et al. 2014; Aprea and Calegari 2015; Hecht, Ballesteros-Yanez et al. 2015; D'Haene, Jacobs et al. 2016; Liu, Nowakowski et al. 2016)


Chromatin modification, epigenetic regulation, alternative splicing, and translational control by MALAT1, HOTAIR and TRE lncRNAs represent important examples of lncRNA-mediated control of cell migration and invasion, epithelial-to-mesenchyme transition and metastasis

(Gupta, Shah et al. 2010; Dhamija and Diederichs 2016)





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