Table 1

Emerging themes in lncRNA regulation. Potential groupings of lncRNA based on proposed interactions, functions, and mechanisms. Representative lncRNAs of each group are shown.

FunctionsExamplesActionHypothesized
mechanisms
Cis-tether
cis-targeting
RepA, Xist, Tsix,
Gtl2, Kcnq1ot1,
Airn, Hottip,
ANRIL, Oct4-ps5,
COLDAIR, Evf2,
BDNF-AS
CisCo-transcriptional
targeting of
chromatin factors;
allelic and locus-
specific action;
repressive or
activating
Trans-targetingpRNA, asOct4-ps5TransRNA:DNA triplex
via Hoogsteen base
pairing or
sense:antisense
Watson:Crick base
pairing
EnhancerXite, ncRNA-a7,
eRNAs
CisMediated by RNA,
transcriptional
force, or chromatin
intermediaries
DecoyPTEN-ps
Tsix
Trans
Cis
Competitive
inhibition of target
protein or RNA
ScaffoldMALAT1, TUG1,
NEAT1, HOTAIR,
roX1, roX2
TransRNA subunit of
effector complex
Allosteric
modification
TLSCis (trans also
possible)
Alters conformation
and activity of
protein partners
Coactivator or
co-repressor
SRA, SINE B2,
Jpx, pRNA
Trans (cis also
possible)
Accessory factor for
transcriptional
activation or
repression