Deregulation of 3D genome structure in models of memory and learning disability

染色质调节因子在伴有神经损伤的发育障碍中经常发生突变。例如，智力残疾与具有不同功能的染色质蛋白（如CTCF、ATRX和SATB 2）的突变有关。在基于恐惧的实验中，使用条件性敲除（cKO）小鼠模型，有丝分裂后锥体神经元中的任一因子的耗尽导致电生理功能障碍并损害与大脑相关的学习和长期记忆。然而，CTCF，SATB 2和ATRX损失对染色质调控和受影响的基因的直接影响仍有待调查。在这里，我们建议解剖的后果CTCF，ATRX或SATB 2损失在体内，直接在成熟的小鼠海马锥体神经元。我们将使用最先进的方法，基因组结构映射（GAM），映射3D染色质结构，和10 x Genomics multiome，在单细胞中分析基因表达和染色质可及性。我们将提供一个所有海马细胞的cKO影响的调控区域的图谱，以及改变染色质接触的景观。我们将在3D基因组组织的不同水平上绘制全基因组染色质结构的变化，以及改变基因表达和3D基因组折叠的转录因子和染色质调控途径。我们将重点关注三种突变体共同的染色质结构和基因表达的变化，以确定参与学习和记忆功能障碍的候选途径。我们将验证所有cKO中受影响的基因，因为这些基因为干预改善学习障碍提供了潜在的候选靶点。最终，我们的目标也是推进我们的知识染色质调控专门的有丝分裂后神经元。我们的假设是，学习障碍中海马功能障碍的发生根源于染色质功能障碍机制，并期望开发一个可用于加速评估人类患者样本的框架。

Chromatin regulators are often mutated in developmental disorders accompanied by neurological impairments. For example, intellectual disability is associated with mutations in chromatin proteins with diverse functions, such as CTCF, ATRX and SATB2. Depletion of either factor in post-mitotic pyramidal neurons, using conditional knockout (cKO) mouse models, results in eletrophysiological dysfunction and impairs hippocampal-related learning and long-term memory in fear-based experiments. However, the direct effects of CTCF, SATB2 and ATRX loss on chromatin regulation and the affected genes remain to be investigated.Here, we propose to dissect the consequences CTCF, ATRX or SATB2 loss in vivo, directly in pyramidal glutamatergic neurons of the mature murine hippocampus. We will use state-of-the-art methodologies, Genome Architecture Mapping (GAM), to map 3D chromatin structure, and 10x Genomics multiome, to profile both gene expression and chromatin accessibility in single cells. We will deliver an atlas of cKO-affected regulatory regions for all hippocampal cells, and the landscape of altered chromatin contacts. We will map the changes in chromatin structure genome-wide at different levels of 3D genome organization, and the transcription factors and chromatin regulatory pathways underlying the altered gene expression and 3D genome folding. We will focus on changes in chromatin structure and gene expression common to the three mutants, to identify candidate pathways involved in the learning and memory dysfunctions. We will validate genes affected in all cKOs, as these provide candidate targets with potential for intervention to ameliorate learning disabilities. Ultimately, we also aim to advance our knowledge of chromatin regulation in specialized post-mitotic neurons. Our hypothesis is that the inception of hippocampal dysfunction in learning disabilities is rooted in chromatin dysfunction mechanisms, and expect to develop a framework that can be adopted to accelerate the evaluation human patient samples.