Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 1 | PGR interacts with TRIM28 to regulate decidualization in HESCs. a PR interacting proteins in decidual HESCs by RIME. b Immunofluorescence (IF) of TRIM28 (magenta) and PR (green) in pre-decidual and decidual HESCs. c TRIM28 and PR proximity (red dots, arrow pointed) in siNT and siTRIM28 treated pre-decidual and decidual HESCs by Proximity Ligation Assay.

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques: Proximity Ligation Assay

Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 2 | TRIM28 knockdown disrupt PR signaling in HESCs. a Edu labeled cell proliferation, migrated cells in the transwell assay, and brightfield images of pre- decidual and decidual HESCs. Yellow line circles the cells. b Comparison of siPGR and siTRIM28 mediated transcriptomic changes in the hormone stimulated decid- ual HESCs. c The heatmap of PR and TRIM28 binding peaks in decidual HESCs by CUT&RUN. d The overlapped peaks of TRIM28 and PR, the associated common DEGs altered by TRIM28 and PGR knockdown in the decidual HESCs. Genome

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques: Knockdown, Labeling, Transwell Assay, Comparison, Binding Assay

Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 3 | TRIM28 deletion impaired decidualization and steroid signaling in mouse uterus. a The representative pictures and immunofluorescence of FOXO1, GJB2, and COX2 at D4.5 uterus. Red arrows pointed to the embryo implantation sites. b The representative uterine pictures and Immunohistochemistry (IHC) of KI67 and HAND2 of decidual uterus upon artificial decidualization. Blue arrow pointed to the decidual horn. c The Immunohistochemistry of proliferative marker KI67 and

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques: Immunohistochemistry, Marker

Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 5 | TRIM28 deletion inhibited ERα activity. a Immunofluorescence (IF) of PR and ERα. b The overlapped binding peaks of TRIM28 and ERα, the associated common DEGs and top altered pathways between TRIM28d/d mice and E2 treated ovariectomized wildtype mouse uterus. c The genome browser of ERα, TRIM28 and H3K27AC binding peaks at Pgr. Blue line is the Chromatin loops predicted by HiC.

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques: Activity Assay, Binding Assay

Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 7 | Abnormally accumulation of TRIM28 positive alone cells in the TRIM28d/d uterus. a Immunofluorescence (IF) of TRIM28 and PR in the TRIM28f/f

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques:

Journal: Nature communications

Article Title: TRIM28 modulates nuclear receptor signaling to regulate uterine function.

doi: 10.1038/s41467-023-40395-7

Figure Lengend Snippet: Fig. 8 | Epithelial TRIM28 deletion reduced Ihh expression and promoted progenitor cell accumulations at luminal epithelium. a The immuno- fluorescence (IF) of TRIM28 and PR, TRIM28 and Pgrcre-GFP at D2.5, D3.5, and D4.5 of the TRIM28f/f, eTRIM28d/d and TRIM28d/d mouse uterus. Arrow points to the TRIM28 positive cells in the luminal epithelium of the TRIM28d/d and eTRIM28d/d

Article Snippet: GFP tagged TRIM28 plasmid was purchased from Addgene (Plasmid #6539776).

Techniques: Expressing

Journal: DNA Repair

Article Title: ASCIZ/ATMIN is dispensable for ATM signaling in response to replication stress

doi: 10.1016/j.dnarep.2017.06.022

Figure Lengend Snippet: Aphidicolin-induced ATM signaling in immortalized MEFs. (A) Cells (WT, MJI-53; KO, MJI-1) were treated for 24 h using 0 or 3 μM aphidicolin. (B) Cells (lane 1–3, WT, MJI-91; lanes 4–6, KO, MJI-186; lanes 7–9, WT, MJI-105; lanes 1–12, KO, MJI-84) were treated for 24 h using 0, 1 or 3 μM aphidicolin. Actin and 53BP1 serve as loading controls. DYNLL1 is used as a surrogate marker for loss of ASCIZ. (C) Quantification of western blot band intensities. An arbitrary unit of 100 represents the average band intensity for the respective phospho-protein in the 3 μM aphidicolin-treated wildtype samples on each membrane. Graphs indicate the mean ± standard error, n = 3. Additional loading controls for total KAP1, p53 and H2AX are shown in Supplementary Fig. S1A and B.

Article Snippet: The following antibodies were used for western blots: Actin (EMD Millipore/Merck, MAB1501), ATM (Abcam, 5C2, ab2618), DYNLL1 (Abcam, ab51603), FANCD2 (Abcam, ab178705), 53BP1 (Novus, NB100-304, lot A3), γH2AX (EMD Millipore/Merck, 05-636), H2AX (Abcam, ab20669), KAP1 (Proteintech, 15202-1-AP), M601 (Abcam, ab110411), p53 (Cell Signaling Technology, 1C12; for mouse samples), p53 (Santa Cruz Biotechnology, DO-1, sc-126; for human samples), phospho-CRMP2 (Ser522; ECM Biosciences, CP2191), phospho-ATM (Ser1981; Cell Signaling Technology, 10H11.E12), phospho-KAP1 (Ser824; Bethyl, A300-767A); phospho-p53 (Ser-15; Cell Signaling Technology, 9284); α-tubulin (Sigma-Aldrich, T9026).

Techniques: Marker, Western Blot, Membrane

Journal: DNA Repair

Article Title: ASCIZ/ATMIN is dispensable for ATM signaling in response to replication stress

doi: 10.1016/j.dnarep.2017.06.022

Figure Lengend Snippet: Aphidicolin-induced ATM signaling in primary MEFs. Freshly prepared primary MEFs from a wildtype and an Asciz −/− embryo were treated for 24 h with 0, 1 or 3 μM aphidicolin. For comparison, cultures from the same embryos were also irradiated with 2-Gy and allowed to recover for 30 min. Similar results for another independent pair of wildtype and Asciz −/− primary MEFs are shown in Supplementary Fig. S1C, and additional loading controls for total KAP1, p53 and H2AX are shown in Supplementary Fig. S1D.

Article Snippet: The following antibodies were used for western blots: Actin (EMD Millipore/Merck, MAB1501), ATM (Abcam, 5C2, ab2618), DYNLL1 (Abcam, ab51603), FANCD2 (Abcam, ab178705), 53BP1 (Novus, NB100-304, lot A3), γH2AX (EMD Millipore/Merck, 05-636), H2AX (Abcam, ab20669), KAP1 (Proteintech, 15202-1-AP), M601 (Abcam, ab110411), p53 (Cell Signaling Technology, 1C12; for mouse samples), p53 (Santa Cruz Biotechnology, DO-1, sc-126; for human samples), phospho-CRMP2 (Ser522; ECM Biosciences, CP2191), phospho-ATM (Ser1981; Cell Signaling Technology, 10H11.E12), phospho-KAP1 (Ser824; Bethyl, A300-767A); phospho-p53 (Ser-15; Cell Signaling Technology, 9284); α-tubulin (Sigma-Aldrich, T9026).

Techniques: Comparison, Irradiation

Journal: DNA Repair

Article Title: ASCIZ/ATMIN is dispensable for ATM signaling in response to replication stress

doi: 10.1016/j.dnarep.2017.06.022

Figure Lengend Snippet: Aphidicolin-induced ATM signaling in human ASCIZ/ATMIN knockout cells. (A, B) BL30 cells were cultured as indicated in the presence or absence of doxycycline to induce a non-targeting control guide RNA or the guide RNA against ASCIZ , and aphidicolin to elicit prolonged DNA replication stress as indicated. For comparison, control guide RNA transduced cells were also irradiated for canonical ATM activation without doxycycline or aphidicolin treatment in panel A. Panel B shows a blot of the same samples except the irradiated control. Additional loading controls for total ATM, KAP1 and p53 are shown in Supplementary Fig. S1E.

Article Snippet: The following antibodies were used for western blots: Actin (EMD Millipore/Merck, MAB1501), ATM (Abcam, 5C2, ab2618), DYNLL1 (Abcam, ab51603), FANCD2 (Abcam, ab178705), 53BP1 (Novus, NB100-304, lot A3), γH2AX (EMD Millipore/Merck, 05-636), H2AX (Abcam, ab20669), KAP1 (Proteintech, 15202-1-AP), M601 (Abcam, ab110411), p53 (Cell Signaling Technology, 1C12; for mouse samples), p53 (Santa Cruz Biotechnology, DO-1, sc-126; for human samples), phospho-CRMP2 (Ser522; ECM Biosciences, CP2191), phospho-ATM (Ser1981; Cell Signaling Technology, 10H11.E12), phospho-KAP1 (Ser824; Bethyl, A300-767A); phospho-p53 (Ser-15; Cell Signaling Technology, 9284); α-tubulin (Sigma-Aldrich, T9026).

Techniques: Knock-Out, Cell Culture, Control, Comparison, Irradiation, Activation Assay

Journal: Cell

Article Title: B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

doi: 10.1016/j.cell.2021.02.015

Figure Lengend Snippet: A. RNA-seq tracks of TLR7 gene at Xi (blue) and Xa (yellow) between control, TRIM28 KO and sgXIST group.

Article Snippet: Lentiviral vectors that carry full length TRIM28 and RING domain or PB (PHD-Bromodomain) domain deletion mutants conjugated to eGFP fused with a 2A peptide were cloned using Gibson Assembly from the PCR product of the plasmid containing TRIM28 cDNA (Addgene #124960).

Techniques: RNA Sequencing Assay

Journal: Cell

Article Title: B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

doi: 10.1016/j.cell.2021.02.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Lentiviral vectors that carry full length TRIM28 and RING domain or PB (PHD-Bromodomain) domain deletion mutants conjugated to eGFP fused with a 2A peptide were cloned using Gibson Assembly from the PCR product of the plasmid containing TRIM28 cDNA (Addgene #124960).

Techniques: Recombinant, Sequencing, Mass Spectrometry, Software