Super-enhancers are characterized by high levels of Mediator binding and are 
major contributors to the expression of their associated genes. They exhibit 
high levels of local chromatin interactions and a higher order of local 
chromatin organization. On the other hand, lncRNAs can localize to specific DNA 
sites by forming a RNA:DNA:DNA triplex, which in turn can contribute to local 
chromatin organization. In this paper, we characterize a new class of lncRNAs 
called super-lncRNAs that target super-enhancers and which can contribute to the 
local chromatin organization of the super-enhancers. Using a logistic regression 
model based on the number of RNA:DNA:DNA triplex sites a lncRNA forms within the 
super-enhancer, we identify 442 unique super-lncRNA transcripts in 27 different 
human cell and tissue types; 70% of these super-lncRNAs were tissue restricted. 
They primarily harbor a single triplex-forming repeat domain, which forms an 
RNA:DNA:DNA triplex with multiple anchor DNA sites (originating from 
transposable elements) within the super-enhancers. Super-lncRNAs can be grouped 
into 17 different clusters based on the tissue or cell lines they target. 
Super-lncRNAs in a particular cluster share common short structural motifs and 
their corresponding super-enhancer targets are associated with gene ontology 
terms pertaining to the tissue or cell line. Super-lncRNAs may use these 
structural motifs to recruit and transport necessary regulators (such as 
transcription factors and Mediator complexes) to super-enhancers, influence 
chromatin organization, and act as spatial amplifiers for key tissue-specific 
genes associated with super-enhancers.