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. 2022 Jun 6;24(6):872–884. doi: 10.1038/s41556-022-00925-9

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© The Author(s) 2022

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, Proteins that interact with NLS1–HK2, as determined by BioID coupled with mass spectrometry; n = 3 biological repeats. b, Intensity of the PLA signal of endogenous HK2 and MAX, SIRT1, IWS1, CTR9 and SPIN1 in NB4 cells. A.u., arbitrary units; n = 278 cells from three biological repeats. c, Chromatin accessibility, measured through ATAC-seq, following overexpression of NLS1–HK2 in NB4 cells; n = 3 biological repeats. d, LSC⁺ and LSC⁻ signatures in EV control NB4 cells. LSC⁻: minimum, 5.15; maximum, 12.81; and median, 8.27. LSC⁺: minimum, 5.990; maximum, 12.030; and median, 9.325. e, LSC⁺ and LSC⁻ signatures in NLS1–HK2 NB4 cells. LSC⁻: minimum, 6.840; maximum, 13.010; and median, 9.020. LSC⁺: minimum, 7.300; maximum, 12.340; and median, 9.895. f, ATAC-seq pathway enrichment analysis in EV control and NLS1–HK2 NB4 cells. The size of the pie chart slices is proportional to the FDR score, −log₁₀(FDR), for each of the gene lists. Blue and pink lines pinpoint to pathways that overlap significantly with the HSC and granulocyte (GRAN) gene lists at FDR < 0.05 according to a Fisher’s exact test. g, Enhanced enrichment of the pathways in NLS1–HK2 and NLS2–HK2 ChIP–seq compared with EV control ChIP–seq in NB4 cells. h, Consensus motif identified by HOMER DNA-binding-motif analysis significantly enriched in NLS1– and NLS2–HK2 peaks at FDR < 0.05. The P value shows significant enrichment of bHLH motifs, determined using a Fisher’s exact test. The boxes with the dashed lines represent sequence similarity overlap. i, Enrichment of the consensus motif CACGTG in sequences of peaks associated with the selected pathways. The hypergeometric P value estimated using the Fisher’s exact test indicate the significance of the enrichment of the motif when compared with random sequences. c–e, Statistical analyses were performed using a two-tailed unpaired Student’s t-test. Data represent the mean ± s.e.m. d,e, In the box-and-whisker plots, the horizontal lines mark the median, the box limits indicate the 25th and 75th percentiles, and the whiskers extend to 1.5× the interquartile range from the 25th and 75th percentiles.

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