(A) Overview of genes and transcript numbers in the human genome (GENCODE v35). Circle area represents relative quantities. (B) Schematics of three possible functional properties of lncRNA loci.
In addition, lncRNA TSS, exon and/or pA site more often associate with transposable elements (TEs), while TEs contribute mostly to UTRs and/or introns of mRNAs. In addition, mRNAs are more efficiently spliced.
(A) Transcriptional activity modulates DNA methylation and thereby alters occupation of DNA binding factors within the gene body, for example CTCF. The POL2 complex is indicated in violet. Black drumsticks indicate methylated CpGs, white drumstick non-methylated CpGs. (B) LncRNA expression alters promoter (Prom.) activity by modifying e.g. acetylation of histones at TSS sites. (C) Transcription elongation can activate poised enhancers within their gene body (only acetylation shown).
DNA:DNA contacts can change upon transcriptional activity of nearby, cis located lncRNA genes.