Ctcf Haploinsufficiency Mediates Intron Retention in A Tissue-specific Manner

CCCTC binding-factor (CTCF) is a master regulator of gene transcription and chromatin organization with occupancy at tens of thousands of DNA target sites genome-wide. CTCF is essential for embryonic development and somatic cell viability and has been well-characterized as a haploinsufficient tumor suppressor. Increasing evidence demonstrates CTCF as a key player in several alternative splicing (AS) regulatory mechanisms, including transcription elongation, transcriptional regulation of splicing factors, DNA methylation, histone modification and chromatin architecture. However, the genome-wide impact of Ctcf haploinsufficiency on AS has not been investigated. We performed a transcriptomic analysis on multiple tissues from a Ctcf hemizygous (Ctcf+/-) mouse model to examine the effect of Ctcf haploinsufficiency on gene expression and AS. Distinct tissue-specific differences in gene expression were observed in Ctcf+/- mice compared to wildtype mice. While exon skipping was the most abundant form of AS in all tissues, we observed a surprisingly large number of increased intron retention (IR) events in Ctcf+/- liver and kidney. Increased IR in liver affected genes involved in cytoskeletal organization, splicing- and metabolic-related processes. This study provides further evidence for Ctcf dose-dependent and tissue-specific regulation of gene expression and AS. Our data provide a strong foundation for elucidating the mechanistic role of CTCF in AS regulation and its biological consequences. Transcriptomic analyses were performed on five tissues (brain, kidney, liver, muscle and spleen) from three wild type (C57BL/6) and three Ctcf haploinsufficient (Ctcf+/-) miceCCCTC结合因子（CCCTC binding-factor, CTCF）是基因转录与染色质组织的核心调控因子，可在全基因组范围内结合数以万计的DNA靶位点。CTCF对胚胎发育与体细胞存活至关重要，且已被充分表征为单倍剂量不足型肿瘤抑制因子（haploinsufficient tumor suppressor）。越来越多的证据表明，CTCF在多种可变剪接（alternative splicing, AS）调控机制中发挥关键作用，包括转录延伸、剪接因子的转录调控、DNA甲基化、组蛋白修饰以及染色质架构。然而，Ctcf单倍剂量不足对可变剪接的全基因组影响尚未得到研究。我们利用Ctcf半合子（Ctcf+/-）小鼠模型的多种组织开展转录组分析，以探究Ctcf单倍剂量不足对基因表达与可变剪接的影响。相较于野生型小鼠，Ctcf+/-小鼠的基因表达存在显著的组织特异性差异。尽管外显子跳跃是所有组织中最为常见的可变剪接形式，我们仍意外观察到Ctcf+/-小鼠的肝脏与肾脏中内含子保留（intron retention, IR）事件的数量大幅增多。肝脏中增多的内含子保留事件所影响的基因，参与细胞骨架组织、剪接相关及代谢相关的生物学过程。本研究进一步为Ctcf剂量依赖性与组织特异性的基因表达及可变剪接调控提供了证据。我们的数据为阐明CTCF在可变剪接调控中的机制性作用及其生物学后果提供了坚实的研究基础。本研究对3只野生型（C57BL/6）小鼠与3只Ctcf单倍剂量不足（Ctcf+/-）小鼠的5种组织（脑、肾脏、肝脏、肌肉与脾脏）完成了转录组分析。