INO80/SWR remodelers compose INO80, TIP60/P400, and SRCAP, which function in the dynamics of H2A.Z in cells. However, their immediate functions have not been clear. Here, we implied the auxin-inducible degradation to the largest subunits of the INO80/SWR remodelers in mESCs. Surprisingly, the H2A.Z occupancy and chromatin accessibility were not obviously changed after the acute loss of the remodelers. The Pol II ChIP-seq and transcriptome analyses indicate that INO80, TIP60/P400, or SRCAP degradation affects different gene expression and transcription processes. Pol II TurboID-mass spectrometry analyses revealed that RNA cleavage factors (such as CSTF and CPSF) preferentially decreased interactions with the Pol II. The chromatin environment and cis-regulatory elements of different genes underpin the differential transcriptional effects. Together, we proposed that INO80/SWR generally occupy active gene promoters but have different effects on different gene transcription via intrinsic combinations of chromatin environment and genomic sequences of different genes. Name correspondence table： SRCAP ChIP-MS：WH_20230628_123_SRCAP.xlsx P400 ChIP-MS：WH_20230628_789_P400.xlsx INO80 ChIP-MS：WH_20230628_456_INO80.xlsx SRCAP_ ChIP _MS_input：WH_20230628_1.raw SRCAP_ ChIP _MS_2_1：WH_20230628_2_1.raw SRCAP_ ChIP _MS_2_2: WH_20230628_2_2.raw SRCAP_ ChIP _MS_3_1：WH_20230628_3_1.raw SRCAP_ ChIP _MS_3_2: WH_20230628_3_2.raw INO80_ ChIP _MS_input：WH_20230628_4.raw INO80_ ChIP _MS_2_1：WH_20230628_5_1.raw INO80_ ChIP _MS_2_2: WH_20230628_5_2.raw INO80_ ChIP _MS_3_1：WH_20230628_6_1.raw INO80_ ChIP _MS_3_2: WH_20230628_6_2.raw P400_ ChIP _MS_input：WH_20230628_7.raw P400_ ChIP _MS_2_1：WH_20230628_8_1.raw P400_ ChIP _MS_2_2: WH_20230628_8_2.raw P400_ ChIP _MS_3_1：WH_20230628_9_1.raw P400_ ChIP _MS_3_2: WH_20230628_9_2.raw INO80_Ni_WCE_MS: WH_20230608_7_.xlsx SRCAP_Ni_WCE_MS: WH_20230608_1_.xlsx P400_Ni_WCE_MS: WH_20230822_1_.xlsx INO80_Ni_WCE_MS_1_1：WH_20230608_7_1 INO80_Ni_WCE_MS_1_2: WH_20230608_7_2 INO80_Ni_WCE_MS_2_1：WH_20230608_8_1 INO80_Ni_WCE_MS_2_2: WH_20230608_8_2 INO80_Ni_WCE_MS_3_1：WH_20230608_9_1 INO80_Ni_WCE_MS_3_2: WH_20230608_9_2 INO80_1h_WCE_MS_1_1：WH_20230608_10_1 INO80_1h_WCE_MS_1_2: WH_20230608_10_2 INO80_1h_WCE_MS_2_1：WH_20230608_11_1 INO80_1h_WCE_MS_2_2: WH_20230608_11_2 INO80_1h_WCE_MS_3_1：WH_20230608_12_1 INO80_1h_WCE_MS_3_2: WH_20230608_12_2 SRCAP_Ni_WCE_MS_1_1：WH_20230608_1_1 SRCAP_Ni_WCE_MS_1_2: WH_20230608_1_2 SRCAP_Ni_WCE_MS_2_1：WH_20230608_2_1 SRCAP_Ni_WCE_MS_2_2: WH_20230608_2_2 SRCAP_Ni_WCE_MS_3_1：WH_20230608_3_1 SRCAP_Ni_WCE_MS_3_2: WH_20230608_3_2 SRCAP_1h_WCE_MS_1_1：WH_20230608_4_1 SRCAP _1h_WCE_MS_1_2: WH_20230608_4_2 SRCAP _1h_WCE_MS_2_1：WH_20230608_5_1 SRCAP _1h_WCE_MS_2_2: WH_20230608_5_2 SRCAP _1h_WCE_MS_3_1：WH_20230608_6_1 SRCAP _1h_WCE_MS_3_2: WH_20230608_6_2 P400_Ni_WCE_MS_1_1：WH_20230822_1_1 P400_Ni_WCE_MS_1_2: WH_20230822_1_2 P400_Ni_WCE_MS_2_1：WH_20230822_2_1 P400_Ni_WCE_MS_2_2: WH_20230822_2_2 P400_Ni_WCE_MS_3_1：WH_20230822_3_1 P400_Ni_WCE_MS_3_2: WH_20230822_3_2 P400_1h_WCE_MS_1_1：WH_20230822_4_1 P400 _1h_WCE_MS_1_2: WH_20230822_4_2 P400 _1h_WCE_MS_2_1：WH_20230822_5_1 P400 _1h_WCE_MS_2_2: WH_20230822_5_2 P400 _1h_WCE_MS_3_1：WH_20230822_6_1 P400 _1h_WCE_MS_3_2: WH_20230822_6_2 INO80_Ni_chromatin_MS: WH_20230418_7_.xlsx P400_Ni_chromatin_MS: WH_20230418_13_.xlsx SRCAP_Ni_chromatin_MS: WH_20230418_1_.xlsx INO80_Ni_chromatin_MS_1_1: WH_20230418_7_1.raw INO80_Ni_chromatin_MS_1_2: WH_20230418_7_2.raw INO80_Ni_chromatin_MS_2_1: WH_20230418_8_1.raw INO80_Ni_chromatin_MS_2_2: WH_20230418_8_2.raw INO80_Ni_chromatin_MS_3_1: WH_20230418_9_1.raw INO80_Ni_chromatin_MS_3_2: WH_20230418_9_2.raw INO80_1h_chromatin_MS_1_1: WH_20230418_10_1.raw INO80_1h_chromatin_MS_1_2: WH_20230418_10_2.raw INO80_1h_chromatin_MS_2_1: WH_20230418_11_1.raw INO80_1h_chromatin_MS_2_2: WH_20230418_11_2.raw INO80_1h_chromatin_MS_3_1: WH_20230418_12_1.raw INO80_1h_chromatin_MS_3_2: WH_20230418_12_2.raw P400_Ni_chromatin_MS_1_1: WH_20230418_13_1.raw P400_Ni_chromatin_MS_1_2: WH_20230418_13_2.raw P400_Ni_chromatin_MS_2_1: WH_20230418_14_1.raw P400_Ni_chromatin_MS_2_2: WH_20230418_14_2.raw P400_Ni_chromatin_MS_3_1: WH_20230418_15_1.raw P400_Ni_chromatin_MS_3_2: WH_20230418_15_2.raw P400_1h_chromatin_MS_1_1: WH_20230418_16_1.raw P400_1h_chromatin_MS_1_2: WH_20230418_16_2.raw P400_1h_chromatin_MS_2_1: WH_20230418_17_1.raw P400_1h_chromatin_MS_2_2: WH_20230418_17_2.raw P400_1h_chromatin_MS_3_1: WH_20230418_18_1.raw P400_1h_chromatin_MS_3_2: WH_20230418_18_2.raw SRCAP_Ni_chromatin_MS_1_1: WH_20230418_1_1.raw SRCAP_Ni_chromatin_MS_1_2: WH_20230418_1_2.raw SRCAP_Ni_chromatin_MS_2_1: WH_20230418_2_1.raw SRCAP _Ni_chromatin_MS_2_2: WH_20230418_2_2.raw SRCAP _Ni_chromatin_MS_3_1: WH_20230418_3_1.raw SRCAP _Ni_chromatin_MS_3_2: WH_20230418_3_2.raw SRCAP _1h_chromatin_MS_1_1: WH_20230418_4_1.raw SRCAP _1h_chromatin_MS_1_2: WH_20230418_4_2.raw SRCAP _1h_chromatin_MS_2_1: WH_20230418_5_1.raw SRCAP _1h_chromatin_MS_2_2: WH_20230418_5_2.raw SRCAP _1h_chromatin_MS_3_1: WH_20230418_6_1.raw SRCAP _1h_chromatin_MS_3_2: WH_20230418_6_2.raw INO80_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20221202_Ni_1_1.raw INO80_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20221202_Ni_1_2.raw INO80_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20221202_Ni_2_1.raw INO80_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20221202_Ni_2_2.raw INO80_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20221202_Ni_3_1.raw INO80_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20221202_Ni_3_2.raw INO80_1h_ RPB1_TurboID_IP_MS_1_1: WH_20221202_auxin_1_1.raw INO80_1h_ RPB1_TurboID_IP_MS_1_2: WH_20221202_auxin_1_2.raw INO80_1h_ RPB1_TurboID_IP_MS_2_1: WH_20221202_auxin_2_1.raw INO80_1h_ RPB1_TurboID_IP_MS_2_2: WH_20221202_auxin_2_2.raw INO80_1h_ RPB1_TurboID_IP_MS_3_1: WH_20221202_auxin_3_1.raw INO80_1h_ RPB1_TurboID_IP_MS_3_2: WH_20221202_auxin_3_2.raw P400_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20230215_Ni_1_1.raw P400_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20230215_Ni_1_2.raw P400_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20230215_Ni_2_1.raw P400_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20230215_Ni_2_2.raw P400_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20230215_Ni_3_1.raw P400_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20230215_Ni_3_2.raw P400_1h_ RPB1_TurboID_IP_MS_1_1: WH_20230215_auxin_1_1.raw P400_1h_ RPB1_TurboID_IP_MS_1_2: WH_20230215_auxin_1_2.raw P400_1h_ RPB1_TurboID_IP_MS_2_1: WH_20230215_auxin_2_1.raw P400_1h_ RPB1_TurboID_IP_MS_2_2: WH_20230215_auxin_2_2.raw P400_1h_ RPB1_TurboID_IP_MS_3_1: WH_20230215_auxin_3_1.raw P400_1h_ RPB1_TurboID_IP_MS_3_2: WH_20230215_auxin_3_2.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20221028_Ni_1_1.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20221028_Ni_1_2.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20221028_Ni_2_1.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20221028_Ni_2_2.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20221028_Ni_3_1.raw SRCAP_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20221028_Ni_3_2.raw SRCAP_1h_ RPB1_TurboID_IP_MS_1_1: WH_20221028_auxin_1_1.raw SRCAP_1h_ RPB1_TurboID_IP_MS_1_2: WH_20221028_auxin_1_2.raw SRCAP_1h_ RPB1_TurboID_IP_MS_2_1: WH_20221028_auxin_2_1.raw SRCAP_1h_ RPB1_TurboID_IP_MS_2_2: WH_20221028_auxin_2_2.raw SRCAP_1h_ RPB1_TurboID_IP_MS_3_1: WH_20221028_auxin_3_1.raw SRCAP_1h_ RPB1_TurboID_IP_MS_3_2: WH_20221028_auxin_3_2.raw