Proposed unique features that make lncRNA a versatile factor in controlling chromatin structure.
(a) lncRNA may work in cis by staying attached to the transcribing RNA polymerase. Nascent lncRNA provides a binding site for RNA binding proteins. RNA-binding proteins interact with lncRNA by a sequence- or structure-specific mechanism.
(b) lncRNA may work in trans by combining nucleotide sequence and complex three-dimensional structure. Sequence complementarity may facilitate lncRNA binding to specific loci in the genome. A complex three-dimensional structure may allow interaction with proteins that are recruited to chromatin or mediate chromosome looping.