Center for Biomarker Research and Precision Medicine.
Department of Pharmacotherapy and Outcomes Science.
Hum Mol Genet. 2018 Sep 15;27(18):3246-3256. doi: 10.1093/hmg/ddy222.
The transcription factor 4 (TCF4) locus is a robust association finding with schizophrenia (SCZ), but little is known about the genes regulated by the encoded transcription factor. Therefore, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) of TCF4 in neural-derived (SH-SY5Y) cells to identify genome-wide TCF4 binding sites, followed by data integration with SCZ association findings. We identified 11 322 TCF4 binding sites overlapping in two ChIP-seq experiments. These sites are significantly enriched for the TCF4 Ebox binding motif (>85% having ≥1 Ebox) and implicate a gene set enriched for genes downregulated in TCF4 small-interfering RNA (siRNA) knockdown experiments, indicating the validity of our findings. The TCF4 gene set was also enriched among (1) gene ontology categories such as axon/neuronal development, (2) genes preferentially expressed in brain, in particular pyramidal neurons of the somatosensory cortex and (3) genes downregulated in postmortem brain tissue from SCZ patients (odds ratio, OR = 2.8, permutation P < 4x10-5). Considering genomic alignments, TCF4 binding sites significantly overlapped those for neural DNA-binding proteins such as FOXP2 and the SCZ-associated EP300. TCF4 binding sites were modestly enriched among SCZ risk loci from the Psychiatric Genomic Consortium (OR = 1.56, P = 0.03). In total, 130 TCF4 binding sites occurred in 39 of the 108 regions published in 2014. Thirteen genes within the 108 loci had both a TCF4 binding site ±10kb and were differentially expressed in siRNA knockdown experiments of TCF4, suggesting direct TCF4 regulation. These findings confirm TCF4 as an important regulator of neural genes and point toward functional interactions with potential relevance for SCZ.
转录因子 4 (TCF4) 基因座与精神分裂症 (SCZ) 有很强的关联，但对于该编码转录因子调控的基因知之甚少。因此，我们对神经源性 (SH-SY5Y) 细胞中的 TCF4 进行了染色质免疫沉淀测序 (ChIP-seq)，以鉴定全基因组 TCF4 结合位点，并将这些数据与 SCZ 关联研究结果进行整合。我们在两项 ChIP-seq 实验中鉴定出 11322 个 TCF4 结合位点。这些位点显著富集 TCF4 Ebox 结合基序 (>85%至少有 1 个 Ebox)，并暗示了一组在 TCF4 小干扰 RNA (siRNA) 敲低实验中下调的基因，表明我们的发现是有效的。TCF4 基因集也在以下方面富集：(1) 基因本体论类别，如轴突/神经元发育；(2) 在大脑中优先表达的基因，特别是体感皮层的锥体神经元；(3) 在 SCZ 患者死后脑组织中下调的基因 (比值比，OR=2.8，置换 P<4x10-5)。考虑到基因组比对，TCF4 结合位点与神经 DNA 结合蛋白如 FOXP2 和与 SCZ 相关的 EP300 显著重叠。TCF4 结合位点在精神病基因组学联盟 (Psychiatric Genomic Consortium) 的 SCZ 风险基因座中适度富集 (OR=1.56，P=0.03)。总的来说，在 2014 年发表的 108 个区域中，有 39 个区域的 130 个 TCF4 结合位点发生了作用。在 108 个基因座中，有 13 个基因在 TCF4 的 siRNA 敲低实验中，其 TCF4 结合位点±10kb 处的表达既不同又有差异，这表明它们受到 TCF4 的直接调控。这些发现证实了 TCF4 是神经基因的重要调控因子，并指出了与 SCZ 具有潜在相关性的功能相互作用。
