HOXs and lincRNAs: Two sides of the same coin

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Science Advances  29 Jan 2016:
Vol. 2, no. 1, e1501402
DOI: 10.1126/sciadv.1501402


  • Fig. 1 Functions of Hox cluster lincRNAs and Mirs in cis and trans.

    Cis function is defined as the functional impact of a lincRNA and Mirs on Hox genes from the same cluster.

  • Fig. 2 Comparative alignment of human and mouse coding and noncoding transcripts originating from the four Hox clusters.

    Each Hox cluster is scaled on the basis of human coordinates with the gene name listed below. Relative positions of mouse (green) and human (red) noncoding transcripts are shown on the basis of human coding genes as landmark. Arrows indicate the direction of transcription.

  • Fig. 3 Models for activities of lincRNAs from Hox clusters.

    (A) Regulation of Hoxa1 by Halr1 in mouse ES cells. Isoforms of Halr1 and Halr1os1 from the Heater region expressed in ES cells are indicated below the locus in blue. RA treatment changes the repertoire of transcripts, depicted as a shift in color from black to blue. The positions of various RAREs are also indicated. (B) A distal element–RARE (DE-RARE) enhancer is shared between Hoxb4, Hoxb5, Hobbit1, and Mir10a. Arrows indicate the regulatory influences of the ENE (early neural enhancer), B4U, and DE-RAREs on Hoxb4, Hoxb5, Mir10, and Hobbit1. (C) Long-range interaction between enhancers, the Hog and Tog noncoding RNAs, and Hoxd3-d11 genes. The shaded yellow area depicts topologically active domains (TADs). Red solid boxes indicate enhancers. Long-range interactions between Hog, Tog, and HoxD3-11 are noted by brown arrows. In the cecum, Hoxd1, Hoxd12, and Hoxd13 (blue-shaded area) are outside the TAD region.

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