Table 1.

Long non-coding RNAs whose loss results in increased expression of a neighbouring transcription-factor gene

lncRNA	TF gene	Effect in cis or in trans	lncRNA transcription required	Modulation of enhancer– promoter contacts	TF–lncRNA feedback	Response signalling	Mouse phenotype of lncRNA loss	Dosage-sensitive phenotype of the human TF gene	Refs.a
Halr1	Hoxa1 Hoxa2	Cis	Yes	Yes	Negative feedback	Retinoic acid	-	Haploinsufficiency: ear defects	62–64
HASTER	HNF1A	Cis	No	Yes	Negative feedback	Unknown	Diabetes	Haploinsufficiency: diabetes	70
CHASERR	CHD2	Cis	Yes	Yes	Negative feedback	Unknown	Lethal	Haploinsufficiency: neurodevelopmental	71
Hand2os1	Hand2	Unknown	Unknown	Unknown	Unknown	Unknown	Cardiac abnormalities	Haploinsufficiency: cardiac	65,66
Hdnr	Hand2	Unknown	Yes	Unknown	Possibleb	Unknown	Cardiac abnormalities	Haploinsufficiency: cardiac	67
Flicr	Foxp3	Cis	Yes	Unknown	Unknown	IL-2	Reduced type 1 diabetes	No (X-linked autoimmune disease)	69
PVT1	MYC	Cis	Yes	Yes	Possibleb	Stress, p53	Loss of function: tumour suppression	Gain of function: oncogenic	14,74
METEOR	EOMES	Unknown	No	Yes	Unknown	Unknown	-	-	16
Evf2	Dlx6	Cis	No	Unknown	Unknown	Unknown	Neurodevelopmental	Haploinsufficiency: split-hand and foot malformation	72
Playrr	Pitx2	Unknown	Yes	Unknown	Negative cross-regulation	Unknown	Cardiac arrhythmias	Haploinsufficiency: Rieger syndrome	75
NXTAR	AR	Unknown	Yes	Unknown	Negative cross-regulation	Androgen	-	Gain of function : oncogenic	78
FENDRR	FOXF1	Possibly trans	Yes	Unknown	Negative feedback	Unknown	Vascular malformations (AVCD-MPV)	Haploinsufficiency: vascular malformations (AVCD-MPV)	68

AVCD-MPV, alveolar capillary dysplasia and misalignment of pulmonary veins.;

^aReferences of long non-coding RNA (lncRNA) mutation studies showing increased expression of a proximal transcription regulator gene.

^bEvidence for regulation of a lncRNA gene by the transcription factor (TF), but no direct evidence for a feedback mechanism.