Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

LIM domain-binding protein 1 (LDB1) is a highly conserved and widely expressed chromatin looping protein that connects enhancer-promoter genes through LIM and LIM homologous domains in various cell types. LDB1 has been confirmed to play a crucial role in various physiological and pathological processes. In our study, we aim to investigate the function and mechanisms of LDB1 in the context of T-cell acute lymphoblastic leukemia (T-ALL). RNA-seq was conducted and the differently expressed genes were revealed in the LDB1-knockdown 6T-CEM and J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of LDB1 with several master transcription factors on chromatin in 6T-CEM cells. mRNA profiles of 6T-CEM and J.gamma1 cells transfected with control shRNA (sh-NC) or sh-LDB1 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

LIM结构域结合蛋白1（LIM domain-binding protein 1, LDB1）是一类高度保守且广泛表达的染色质环化蛋白，可在各类细胞中通过LIM结构域及LIM同源结构域介导增强子与启动子基因的连接。LDB1已被证实于多种生理及病理过程中发挥关键作用。本研究旨在探究LDB1在T细胞急性淋巴细胞白血病（T-cell acute lymphoblastic leukemia, T-ALL）背景下的功能与作用机制。研究通过RNA测序（RNA-seq），对比分析了LDB1敲低的6T-CEM细胞、J.gamma1细胞与对照组的差异表达基因。靶向切割与标签化（Cleavage Under Targets and Tagmentation, CUT&Tag）实验显示，在6T-CEM细胞的染色质上，LDB1与多种核心转录因子存在共定位现象。本数据集采用Illumina NovaSeq6000平台进行双重复RNA测序，获取了转染阴性对照短发卡RNA（sh-NC）或sh-LDB1的6T-CEM与J.gamma1细胞的mRNA表达谱。