Fig. 3: NKAPL co-localizes with HDAC3/SOX30 on the genome and regulates the HDAC3/SOX30-DNA interaction. | Nature Communications

Fig. 3: NKAPL co-localizes with HDAC3/SOX30 on the genome and regulates the HDAC3/SOX30-DNA interaction.

From: NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit

Fig. 3

a Annotations of NKAPL ChIP-seq peaks across different genomic regions in P21 wild-type testes. ChIP experiments were performed in biologically duplicates. b Caculated NKAPL ChIP-seq tags’ densities on UCSC mm10 RefSeq gene bodies (n = 20,460), and the genomic regions from -2 kb to +2 kb surrounding the TSS of genes were shown. c Heat map of NKAPL, SOX30 and HDAC3 ChIP-seq signals in P21 wild type testes depicting their co-localization at many binding sites. Regions from -5 kb to +5 kb surrounding the center of SOX30 sites were plotted in heatmap views. d The top-ranked motif in the binding sites of NKAPL with p values using Homer motif search. Sequences within ± 200 bp from the centers of all the binding sites were used for de novo motif analysis. p values = 1E-16. The top enriched motif at SOX30 binding sites in mouse testis was also shown. Hypergenomic Distribution Test, p values = 1E-132. e Position and distance between SOX30 and NKAPL average ChIP-seq signals. Average ChIP-seq signals of SOX30 and NKAPL, represented by counts per million, from -2 kb to +2 kb surrounding the TSS of genes were shown. f FLAG tagged HDAC3 was co-expressed with full-length HA-NKAPL or HA tagged NKAPL mutants with deleted fragments. Immunoprecipitation assay was performed with anti-FLAG antibody before western blot analysis with HA and FLAG antibodies. Representative images from biological duplicates were shown. g Testes protein lysates were immunoprecipitated either with HDAC3 or normal IgG antibodies followed by immunoblot analysis. h Co-immunoprecipitation of HDAC3 from wild-type and Nkapl KO testes at P21 and western blot with SOX30 antibodies. Protein lysates were prepared at P21. n = 3 for each genotype. Experiments were performed with biological triplicates. i, j Heat map of SOX30 (i) and HDAC3 (j) signals in Nkapl null testes at P21 from -5 kb to +5 kb surrounding the center of SOX30 sites. k Average SOX30 ChIP-seq signals across ±3 kb flanking TSS in Nkapl knockout versus their wild-types. CPM, counts per million. l Average HDAC3 ChIP-seq signals across ±3 kb flanking TSS in Nkapl knockout versus their wild-types.

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