Table 3.

Mechanism of chromatin targeting of lncRNAs: Examples of diverse chromatin enriched lncRNAs that target chromatin via proteins with dual DNA-RNA binding properties, by triplex structure or R-loop formation. Techniques used to validate their chromatin interaction property and also their mode (triplex and R-loops) of targeting to chromatin.

Long Noncod RNA	Function	Site of Action	Technique/Approach	Interacting Protein	Ref.
lncRNAs in interaction with RBPs with dual DNA and RNA-binding specificities
linc-YY1	YY1-mediated regulation of myogenesis	In-trans affects the eviction of YY1/PRC2 from the YY1 target genes	Detection: Poly A+ RNA seq from proliferating and differentiating C2C12 cells Interaction: Native IP using biotinylated in vitro-synthesized RNA. RIP suggested interaction with EZH2, SUZ12 and YY1	386–851 bp region of the linc-YY1 interacts most efficiently with YY1.	[120]
RMST	REST dependent regulation of pluripotency and neuronal differentiation via SOX2 pathway	In-trans	Detection: Custom designed micro-array. Total RNA obtained from hESCs differentiated into neural progenitors and neurons Interaction: Biotinylated antisense oligo-based RNA pull down, f-RIP	hnRNPA2/B1 and SOX2 REST dependent Neuronal differentiation. Dictates the binding of SOX2 at the target gene promoters, implicated in neurogenesis.	[121,122]
LUNAR1	Notch regulated enhancing of IGF1 signaling	In-cis (looping as eRNA locus)	Detection: RNA-seq generated from multiple human T-ALL cell lines and primary leukemia samples Interaction: Hi-C, ChIRP, ChIP	Interacts with IGF1R intronic enhancer to recruit Mediator and RNAP2	[123]
linc-p21	Transcriptional repressor in p53-dependent response	In-trans	Detection: RNA-seq from genetically modified cell lines for knockdown and restorable p53 levels Interaction: Biotinylated antisense oligo-based RNA pull down, f-RIP, RIP	hnRNP-K: 780 nt region at the 5′ end of lincRNA-p21interacts with hnRNPK1	[124]
SAMMSON	Regulation of mitochondrial homeostasis and metabolism	In-trans	Detection: GWAS of chromosome 3p melanoma specific focal amplification (Copy Number gain) from clinical SNP array data (TCGA) Interaction: RAP–MS, ChIRP, RAP-western blotting	p32	[125]
lncRNAs in higher-order structures
Xist	X chromosome inactivation	In-cis	Detection: Allelic RT-PCR, RNA-FISH Interaction: RIP, RIP-seq, RAP, RAP–MS, ChIRP-MS	EZH2 (PRC2) SHARP, SAF-A and LBR. hnRNPK binds to a 600 nt region of Xist RNA and recruits Polycomb-initiating complex PCGF3/5-PRC1 Xist lncRNA binds 81 proteins. Protein Spen interacts via RepA region	[31,67] [58] [126] [127]
Firre	Role in adipogenesis; by mediating inter-chromosomal interactions	In-cis but colocalize with spatially proximal trans genomic locations	Detection: PolyA+ RNA-seq of primary brown and white adipocytes, preadipocytes, and cultured adipocytes Interaction: RAP, ChIRP, CHART, ChOP	Interacts with hnRNPU through a 156-bp repeat RNA domain	[89,90]
NEAT1	Nucleation and maintenance of paraspeckles	In-trans	Detection: qRT-PCR of HeLa cell nuclei fractionated by sucrose step-gradient centrifugation, Co-localization with paraspeckle protein PSF(SFPQ), PSP1, and p54. Custom microarray from (C2C12 cells) myoblast differentiation stages Interaction: UV-RIP, qRT-PCR of co-IP	Paraspeckle proteins	[128,129,130]
MALAT1	Splicing, CeRNA	In-trans	Detection: Subtractive hybridization in cancer cell lines Interaction: Co-RNA-FISH, qRT-PCR of co-IP	SRSF1 to regulate splicing of mRNAs	[131,132,133,134]
LncRNAs forming R-loops and triple helixes
MEG3	Tumor suppressor lncRNA, Transcriptional repression of TGF-β pathway genes via triplex formation	In-trans	Detection: ChRIP-seq using antibodies against H3K27me3 and EZH2 from BT549 cell line Interaction: ChRIP, RIP, ChOP-seq, EMSA	EZH2(PRC2)	[33,57,94,101]
Khps1	Transcriptional activation of SPHK1 via triplex mediated chromatin changes	In-cis	Detection: RNA-seq (not clear of exactly what) Interaction: RIP, Triplex forming EMSA	p300/CBP	[135,136]
COOLAIR	Regulates seed dormancy and flowering time through the regulation of FLC expression and flowering	In-cis	Detection: qRT-PCR, RNA-seq Interaction: R-loop foot printing, ChIRP	AtNDX binds to COOLAIR promoter to stabilize R-loops	[137,138]; [139]
VIM-AS1	Promote transcriptional activation of the VIM1 gene	In-cis	Detection: Colon cancer hyper methylation associated positive correlation with divergent VIM1 gene Interaction: R-loop foot printing, EMSA, RNase H1 assay, DRIP with S9.6	Interacts with single stranded DNA(R-loop) to enhance NF-κB binding at the VIM1 promoter	[140]
TERRA	Maintenance of short telomeric structure by regulating the rate of replicative senescence		Detection: qRT-PCR after releasing G1-arrested cells into the cell cycle Interaction: DRIP with S9.6, EMSA	Interacts with telomeric DNA forming R-loops that promotes homology directed repair at very short telomeres by excluding Rif2 mediated RNase H2 recruitment	[141,142,143]; [144]