Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation.
Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation.
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DOI：
10.1039/d1mo00236h
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发表时间：
2022-01-17
期刊：
影响因子：
2.9
通讯作者：
Cowley SM
中科院分区：
文献类型：
--
作者：
Barnes CE;English DM;Broderick M;Collins MO;Cowley SM
赖氨酸特异性去甲基酶1(LSD1)与组蛋白脱乙酰基酶1(HDAC1)一起调节基因的表达，是COREST复合体的一部分。Corest通过核心成分以及与染色质相关因子和转录因子的大量瞬时相互作用被招募到特定的基因组位点。我们假设，使用传统的免疫共沉淀方法可能很难识别其中许多较弱的和短暂的关联。因此，我们在三种不同的细胞类型中，对核心复合体的四个不同成员进行了邻近依赖的生物素识别(BioID)，以确定LSD1/核心相关蛋白的全面网络。在HEK293T细胞中，我们鉴定了302个核心相关蛋白。在这一组中，有18个已知核心成分中的16个和众多小说关联，包括读者(CHD3、4、6、7和8)、作者(KMT2b和KMT2D)和组蛋白甲基化的擦除器(Kdm2b)。然而，其他含HDAC1的络合物(如SIN3)的成分基本上不存在。为了研究原代细胞类型中核心相互作用组的动态性质，我们在胚胎干细胞(ES)中用BIRA*-LSD1替换了内源性LSD1，并在多潜能、早分化和晚分化环境中进行了BioID。我们鉴定了156个LSD1相关蛋白，其中67个在所有三个时间点(43%)都是成分相关的，包括与MMB和ChAHP复合体的新关联，这意味着大多数相互作用是动态的和细胞类型依赖的。总体而言，我们在三种不同的细胞类型中为LSD1进行了16次独立的BioID实验，产生了LSD1相关蛋白的最终网络，这应该会为该领域提供主要资源。Bio-ID识别与干细胞分化过程中的LSD1-核心复合体相关的不同蛋白质亚集。
Lysine specific demethylase 1 (LSD1) regulates gene expression as part of the CoREST complex, along with co-repressor of REST (CoREST) and histone deacetylase 1 (HDAC1). CoREST is recruited to specific genomic loci by core components and numerous transient interactions with chromatin-associated factors and transcription factors. We hypothesise that many of these weaker and transient associations may be difficult to identify using traditional co-immunoprecipitation methods. We have therefore employed proximity-dependent biotin-identification (BioID) with four different members of the CoREST complex, in three different cell types, to identify a comprehensive network of LSD1/CoREST associated proteins. In HEK293T cells, we identified 302 CoREST-associated proteins. Among this group were 16 of 18 known CoREST components and numerous novel associations, including readers (CHD3, 4, 6, 7 and 8), writers (KMT2B and KMT2D) and erasers (KDM2B) of histone methylation. However, components of other HDAC1 containing complexes (e.g. Sin3) were largely absent. To examine the dynamic nature of the CoREST interactome in a primary cell type, we replaced endogenous LSD1 with BirA*-LSD1 in embryonic stem (ES) cells and performed BioID in pluripotent, early- and late-differentiating environments. We identified 156 LSD1-associated proteins of which 67 were constitutively associated across all three time-points (43%), including novel associations with the MMB and ChAHP complexes, implying that the majority of interactors are both dynamic and cell type dependent. In total, we have performed 16 independent BioID experiments for LSD1 in three different cell types, producing a definitive network of LSD1-assoicated proteins that should provide a major resource for the field. BIO-ID identifies different subsets of proteins associated with the LSD1-CoREST complex during stem cell differentiation.
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影响因子：
6
作者：
Bochyńska A;Lüscher-Firzlaff J;Lüscher B
通讯作者：
Lüscher B
影响因子：
64.5
作者：
Klose, Robert J.;Yan, Qin;Kaelin, William G., Jr.
通讯作者：
Kaelin, William G., Jr.
影响因子：
16.6
作者：
Kalin JH;Wu M;Gomez AV;Song Y;Das J;Hayward D;Adejola N;Wu M;Panova I;Chung HJ;Kim E;Roberts HJ;Roberts JM;Prusevich P;Jeliazkov JR;Roy Burman SS;Fairall L;Milano C;Eroglu A;Proby CM;Dinkova-Kostova AT;Hancock WW;Gray JJ;Bradner JE;Valente S;Mai A;Anders NM;Rudek MA;Hu Y;Ryu B;Schwabe JWR;Mattevi A;Alani RM;Cole PA
通讯作者：
Cole PA
DOI：
10.1073/pnas.96.17.9873
发表时间：
1999-08-17
影响因子：
11.1
作者：
Andrés, ME;Burger, C;Mandel, G
通讯作者：
Mandel, G
影响因子：
64.8
作者：
Lee, MG;Wynder, C;Shiekhattar, R
通讯作者：
Shiekhattar, R