A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

The genome is extensively transcribed into long intergenic non-coding RNAs (lincRNAs), many of which are implicated in gene silencing (1,2). Potential roles of lincRNAs in gene activation are much less understood (3-5). Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control (6). Some locus control elements and enhancers transcribe lincRNAs (7-10), hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3' to 5'of the cluster (11). Here we identify HOTTIP, alincRNA transcribed from the 5' tip of the HOXA locus that coordinates the activation of several 5' HOXA genes in vivo. Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation.
We examined chromosome structure and histone modifications in human primary fibroblasts derived from several anatomic sites (12), and found distinctive differences in the HOXA locus. High throughput chromosome conformation capture [...]