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. 2020 Nov 3;21:269. doi: 10.1186/s13059-020-02186-x

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — HOXA9/HOXA10 binds to the upstream enhancer of SEELA to reprogram the enhancer-related histone mark. a A schematic diagram shows the genomic location and the H3K27ac enrichment of ELA-enhancer 1/2/3 (located at the region 20.5 kb, 38.2 kb, and 59.3 kb upstream of SEELA1, respectively). ChIP-qPCR assays of HOXA9 (middle) and HOXA10 (bottom) showed that HOXA9/HOXA10 bound to ELA-enhancer 1 instead of ELA-enhancer 2/3; Error bars reflect ± SD (*P < 0.05; ***P < 0.001; ns, no significant) in three independent experiments. An IgG antibody was used as negative controls in the ChIP assay. b, c A schematic diagram shows the normal and mutant DNA sequences that are predicted in HOXA9 located (b). EMSA experiments validated the binding motif of HOXA9/10, which was a 14 bp motif (GGTAATTAATTACG) (c). d ChIP-qPCR assay results of H3K27ac and H3K4me1 after knocking down HOXA9 and HOXA10, the enrichment of enhancer histone marks in the SEELA locus were decreased. Error bars reflect ± SEM (*P < 0.05, **P < 0.01, and ***P < 0.001) in three independent experiments. An IgG antibody was used as a negative control in the ChIP assay. e, f qPCR and western blotting showed that the mRNA and protein levels of SEELA and SERINC2 were reduced after knocking down HOXA9 (e) or HOXA10 (f). Error bars reflect ± SD (*P < 0.05, **P < 0.01, and ***P < 0.001) in three independent experiments. g Analysis of the chip-seq data showed that 16 of 18 i-BET responding lnc-eRNAs loci were marked by HOXA9