INO80 remodelers differentially regulate the transcription termination

ABSTRACT: 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.xlsxP400 ChIP-MS：WH_20230628_789_P400.xlsxINO80 ChIP-MS：WH_20230628_456_INO80.xlsxSRCAP_ ChIP _MS_input：WH_20230628_1.rawSRCAP_ ChIP _MS_2_1：WH_20230628_2_1.rawSRCAP_ ChIP _MS_2_2: WH_20230628_2_2.rawSRCAP_ ChIP _MS_3_1：WH_20230628_3_1.rawSRCAP_ ChIP _MS_3_2: WH_20230628_3_2.rawINO80_ ChIP _MS_input：WH_20230628_4.rawINO80_ ChIP _MS_2_1：WH_20230628_5_1.rawINO80_ ChIP _MS_2_2: WH_20230628_5_2.rawINO80_ ChIP _MS_3_1：WH_20230628_6_1.rawINO80_ ChIP _MS_3_2: WH_20230628_6_2.rawP400_ ChIP _MS_input：WH_20230628_7.rawP400_ ChIP _MS_2_1：WH_20230628_8_1.rawP400_ ChIP _MS_2_2: WH_20230628_8_2.rawP400_ ChIP _MS_3_1：WH_20230628_9_1.rawP400_ ChIP _MS_3_2: WH_20230628_9_2.rawINO80_Ni_WCE_MS: WH_20230608_7_.xlsxSRCAP_Ni_WCE_MS: WH_20230608_1_.xlsxP400_Ni_WCE_MS: WH_20230822_1_.xlsxINO80_Ni_WCE_MS_1_1：WH_20230608_7_1INO80_Ni_WCE_MS_1_2: WH_20230608_7_2INO80_Ni_WCE_MS_2_1：WH_20230608_8_1INO80_Ni_WCE_MS_2_2: WH_20230608_8_2INO80_Ni_WCE_MS_3_1：WH_20230608_9_1INO80_Ni_WCE_MS_3_2: WH_20230608_9_2INO80_1h_WCE_MS_1_1：WH_20230608_10_1INO80_1h_WCE_MS_1_2: WH_20230608_10_2INO80_1h_WCE_MS_2_1：WH_20230608_11_1INO80_1h_WCE_MS_2_2: WH_20230608_11_2INO80_1h_WCE_MS_3_1：WH_20230608_12_1INO80_1h_WCE_MS_3_2: WH_20230608_12_2SRCAP_Ni_WCE_MS_1_1：WH_20230608_1_1SRCAP_Ni_WCE_MS_1_2: WH_20230608_1_2SRCAP_Ni_WCE_MS_2_1：WH_20230608_2_1SRCAP_Ni_WCE_MS_2_2: WH_20230608_2_2SRCAP_Ni_WCE_MS_3_1：WH_20230608_3_1SRCAP_Ni_WCE_MS_3_2: WH_20230608_3_2SRCAP_1h_WCE_MS_1_1：WH_20230608_4_1SRCAP _1h_WCE_MS_1_2: WH_20230608_4_2SRCAP _1h_WCE_MS_2_1：WH_20230608_5_1SRCAP _1h_WCE_MS_2_2: WH_20230608_5_2SRCAP _1h_WCE_MS_3_1：WH_20230608_6_1SRCAP _1h_WCE_MS_3_2: WH_20230608_6_2P400_Ni_WCE_MS_1_1：WH_20230822_1_1P400_Ni_WCE_MS_1_2: WH_20230822_1_2P400_Ni_WCE_MS_2_1：WH_20230822_2_1P400_Ni_WCE_MS_2_2: WH_20230822_2_2P400_Ni_WCE_MS_3_1：WH_20230822_3_1P400_Ni_WCE_MS_3_2: WH_20230822_3_2P400_1h_WCE_MS_1_1：WH_20230822_4_1P400 _1h_WCE_MS_1_2: WH_20230822_4_2P400 _1h_WCE_MS_2_1：WH_20230822_5_1P400 _1h_WCE_MS_2_2: WH_20230822_5_2P400 _1h_WCE_MS_3_1：WH_20230822_6_1P400 _1h_WCE_MS_3_2: WH_20230822_6_2INO80_Ni_chromatin_MS: WH_20230418_7_.xlsxP400_Ni_chromatin_MS: WH_20230418_13_.xlsxSRCAP_Ni_chromatin_MS: WH_20230418_1_.xlsxINO80_Ni_chromatin_MS_1_1: WH_20230418_7_1.rawINO80_Ni_chromatin_MS_1_2: WH_20230418_7_2.rawINO80_Ni_chromatin_MS_2_1: WH_20230418_8_1.rawINO80_Ni_chromatin_MS_2_2: WH_20230418_8_2.rawINO80_Ni_chromatin_MS_3_1: WH_20230418_9_1.rawINO80_Ni_chromatin_MS_3_2: WH_20230418_9_2.rawINO80_1h_chromatin_MS_1_1: WH_20230418_10_1.rawINO80_1h_chromatin_MS_1_2: WH_20230418_10_2.rawINO80_1h_chromatin_MS_2_1: WH_20230418_11_1.rawINO80_1h_chromatin_MS_2_2: WH_20230418_11_2.rawINO80_1h_chromatin_MS_3_1: WH_20230418_12_1.rawINO80_1h_chromatin_MS_3_2: WH_20230418_12_2.rawP400_Ni_chromatin_MS_1_1: WH_20230418_13_1.rawP400_Ni_chromatin_MS_1_2: WH_20230418_13_2.rawP400_Ni_chromatin_MS_2_1: WH_20230418_14_1.rawP400_Ni_chromatin_MS_2_2: WH_20230418_14_2.rawP400_Ni_chromatin_MS_3_1: WH_20230418_15_1.rawP400_Ni_chromatin_MS_3_2: WH_20230418_15_2.rawP400_1h_chromatin_MS_1_1: WH_20230418_16_1.rawP400_1h_chromatin_MS_1_2: WH_20230418_16_2.rawP400_1h_chromatin_MS_2_1: WH_20230418_17_1.rawP400_1h_chromatin_MS_2_2: WH_20230418_17_2.rawP400_1h_chromatin_MS_3_1: WH_20230418_18_1.rawP400_1h_chromatin_MS_3_2: WH_20230418_18_2.rawSRCAP_Ni_chromatin_MS_1_1: WH_20230418_1_1.rawSRCAP_Ni_chromatin_MS_1_2: WH_20230418_1_2.rawSRCAP_Ni_chromatin_MS_2_1: WH_20230418_2_1.rawSRCAP _Ni_chromatin_MS_2_2: WH_20230418_2_2.rawSRCAP _Ni_chromatin_MS_3_1: WH_20230418_3_1.rawSRCAP _Ni_chromatin_MS_3_2: WH_20230418_3_2.rawSRCAP _1h_chromatin_MS_1_1: WH_20230418_4_1.rawSRCAP _1h_chromatin_MS_1_2: WH_20230418_4_2.rawSRCAP _1h_chromatin_MS_2_1: WH_20230418_5_1.rawSRCAP _1h_chromatin_MS_2_2: WH_20230418_5_2.rawSRCAP _1h_chromatin_MS_3_1: WH_20230418_6_1.rawSRCAP _1h_chromatin_MS_3_2: WH_20230418_6_2.rawINO80_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20221202_Ni_1_1.rawINO80_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20221202_Ni_1_2.rawINO80_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20221202_Ni_2_1.rawINO80_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20221202_Ni_2_2.rawINO80_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20221202_Ni_3_1.rawINO80_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20221202_Ni_3_2.rawINO80_1h_ RPB1_TurboID_IP_MS_1_1: WH_20221202_auxin_1_1.rawINO80_1h_ RPB1_TurboID_IP_MS_1_2: WH_20221202_auxin_1_2.rawINO80_1h_ RPB1_TurboID_IP_MS_2_1: WH_20221202_auxin_2_1.rawINO80_1h_ RPB1_TurboID_IP_MS_2_2: WH_20221202_auxin_2_2.rawINO80_1h_ RPB1_TurboID_IP_MS_3_1: WH_20221202_auxin_3_1.rawINO80_1h_ RPB1_TurboID_IP_MS_3_2: WH_20221202_auxin_3_2.rawP400_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20230215_Ni_1_1.rawP400_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20230215_Ni_1_2.rawP400_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20230215_Ni_2_1.rawP400_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20230215_Ni_2_2.rawP400_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20230215_Ni_3_1.rawP400_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20230215_Ni_3_2.rawP400_1h_ RPB1_TurboID_IP_MS_1_1: WH_20230215_auxin_1_1.rawP400_1h_ RPB1_TurboID_IP_MS_1_2: WH_20230215_auxin_1_2.rawP400_1h_ RPB1_TurboID_IP_MS_2_1: WH_20230215_auxin_2_1.rawP400_1h_ RPB1_TurboID_IP_MS_2_2: WH_20230215_auxin_2_2.rawP400_1h_ RPB1_TurboID_IP_MS_3_1: WH_20230215_auxin_3_1.rawP400_1h_ RPB1_TurboID_IP_MS_3_2: WH_20230215_auxin_3_2.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_1_1: WH_20221028_Ni_1_1.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_1_2: WH_20221028_Ni_1_2.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_2_1: WH_20221028_Ni_2_1.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_2_2: WH_20221028_Ni_2_2.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_3_1: WH_20221028_Ni_3_1.rawSRCAP_Ni_ RPB1_TurboID_IP_MS_3_2: WH_20221028_Ni_3_2.rawSRCAP_1h_ RPB1_TurboID_IP_MS_1_1: WH_20221028_auxin_1_1.rawSRCAP_1h_ RPB1_TurboID_IP_MS_1_2: WH_20221028_auxin_1_2.rawSRCAP_1h_ RPB1_TurboID_IP_MS_2_1: WH_20221028_auxin_2_1.rawSRCAP_1h_ RPB1_TurboID_IP_MS_2_2: WH_20221028_auxin_2_2.rawSRCAP_1h_ RPB1_TurboID_IP_MS_3_1: WH_20221028_auxin_3_1.rawSRCAP_1h_ RPB1_TurboID_IP_MS_3_2: WH_20221028_auxin_3_2.raw

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Meitong Liu  

LAB HEAD: Meitong Liu

PROVIDER: PXD045590 | Pride | 2025-09-02

REPOSITORIES: Pride