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. 2022 Sep 17;12:15636. doi: 10.1038/s41598-022-19654-y

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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 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/.

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Corresponding epigenetic changes and differential gene expression resulting from CHD2 haploinsufficiency in hcINs. (A) Intersection of H3K27ac differentially bound regions (DBRs) and DEGs in the WT versus CHD2^+/− comparisons, and of CHD2 binding events in hcINs. DBRs and DEGs were required to change in the same direction in CHD2^+/− versus WT hcINs. (B) Temporal kinetics of CHD2 binding at H3K27ac DBRs associated with a DEG. The relative frequency with which DBR and DEG associated peaks were bound by CHD2 throughout differentiation (“All”) was compared was compared with the fraction of DBR- and DEG-associated peaks bound by CHD2 only at later stages of development (either at both the hMGE and hcIN stages or uniquely in hcINs). (C, D) Gene ontology (GO) enrichment analysis of DEGs associated with H3K27ac DBRs that were (C) down-regulated or (D) up-regulated in CHD2^+/− hcINs, by comparison with WT. Top GO terms and their -log10 p-values are shown. (E, F) Gene ontology (GO) term analysis of DEGs associated with H3K27ac DBRs that were also CHD2 bound in hcINs, where the DEGs and DBRs were either (E) down-regulated or (F) up-regulated in the CHD2^+/− versus WT hcINs. (G, H) Examples of H3K27ac DBRs that were associated with DEGs and with CHD2 binding in hcINs were obtained from analysis of genes associated with significant GO terms and include (G) GMMN (down-regulated DBR and DEG in the CHD2^+/− vs. WT comparison) or (H) SYN5 (up-regulated DBR and DEG in the CHD2^+/− vs. WT comparison). (I, J) Analysis of enriched transcription factor binding sites under DBRs that are also CHD2 bound peaks and are associated with DEGs in hcINs, with analysis considering either sequences under peaks that were (I) down-regulated or (J) up-regulated DBRs and DEGs in CHD2^+/− versus WT hcINs.