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. 2022 Dec 20;29:107. doi: 10.1186/s12929-022-00892-1

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© The Author(s) 2022

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. 3 — SCA7 downregulated genes have low RNAPII pausing. A Violin plots showing the decrease of RNAPII densities on TSS ± 300 bp regions of non-deregulated and downregulated genes in SCA7 retina, compared to WT. B ChIP-qPCR analysis showing the decrease of RNAPII occupancies (% of the input) on the TSS region of representative downregulated and non-deregulated genes in SCA7 retina compared to WT. Silent regions are used as controls. C Comparison of genomic distribution of RNAPII peaks in WT and SCA7 retina. Data are displayed as percentage of peaks annotated to each region relative to total number of peaks. Distant promoter (− 20 kb to − 1 kb relative to the TSS), promoter-TSS (− 1 kb to + 100 bp at the TSS), and TTS (− 100 bp to + 1 kb relative to the TTS). D Graph representing the ratio of RNAPII peak distribution in different genic and intergenic regions in SCA7 and WT retina. E Graph showing the comparison of RNAPII pausing index in WT and SCA7 retina for all expressed protein coding genes. F Graph showing the comparison of RNAPII pausing index at basal level in WT retina for non-deregulated gene sets and SCA7 downregulated genes with different fold change (FC). Data in A, E and F were analyzed using Mann–Whitney test. Data in B are normalized as percentage of input DNA signal, expressed as mean ± SEM (n = 3 mice/genotype) and analyzed using two-tailed Student’s t-test. *p < 0.05; **p < 0.01; ***p < 0.001, ****p < 0.0001