Non-coding RNAs as direct and indirect modulators of epigenetic regulation

Figures & data

Table 1. Classification of lncRNAs.

lncRNA subtype	Origin	Function
Natural Antisense Transcript (NAT)	cis-NAT: sequence complementarity to a coding RNA at the same locus	Regulates expression of sense partner transcript
	trans-NAT: sequence complementarity to a coding RNA at a distal genomic locus	Likely regulates expression of sense partner transcript, may have other functions
Long Intergenic Noncoding RNA (lincRNA)	Encoded between known protein coding genes or within introns. macroRNA or vlincRNA = very long intergenic RNA	Functions not fully characterized, likely include regulation of transcription, RNA stability, recruitment of protein complexes and other subcellular elements
Sense Overlapping	Transcribed from same strand of DNA as another transcript
Sense Intronic	Originate from introns of coding genes; do not overlap with exons
Processed Transcript	RNA transcript that is spliced and/or polyadenylated

LncRNAs, which are all non-coding transcripts longer than 200 nucleotides, can vary greatly in their genomic origin, relationship to coding genes, and level of processing. While definitions continue to evolve, we present several of the terms currently in use.

Figure 1. Environmentally sensitive, dynamic regulation of gene expression by long and short ncRNAs occurs through direct and indirect interaction with classical epigenetic mechanisms, forming a larger epigenetic network. ncRNAs are known to bind and recruit histone modifying complexes to either add (A) or remove (B) methyl and acetyl groups. These transcripts also modulate DNA methyltransferases (C), thereby facilitating or suppressing DNA methylation. Loci that are targeted by each of these mechanisms can encode protein coding and/or noncoding RNA transcripts (D). ncRNAs in turn can affect gene expression by interacting with mRNA, or through feedback into the previously discussed pathways (E).