kdm1a  (Cell Signaling Technology Inc)

Journal: bioRxiv

Article Title: Active repression of muscle fate preserves neural lineage identity during cerebellum development

doi: 10.64898/2026.05.13.725001

Figure Lengend Snippet: ( A to E ) Co-immunostaining of E16.5 and P7 WT cerebella for KDM1A, the granule neuron lineage marker PAX6, the glial lineage marker BLBP, and the Purkinje cell marker Calbindin. ( F to ) Co-immunostaining of P7 Kdm1a cKO cerebellum, showing loss of KDM1A immunosignal in PAX6 + cells. ( H and I ) The inverted and enlarged view of the TNNC2 channel from and , respectively. VZ, ventricular zone; EGL, external granule layer; uRL, upper rhombic lip.

Article Snippet: The Atoh1-Cre ( ) (strain #011104), Kdm1a F/F ( ) (#023969), and Myod1 −/− ( ) (#002523) lines were obtained from the Jackson Laboratory.

Techniques: Immunostaining, Marker

Journal: bioRxiv

Article Title: Active repression of muscle fate preserves neural lineage identity during cerebellum development

doi: 10.64898/2026.05.13.725001

Figure Lengend Snippet: ( A ) Co-immunoprecipitation (co-IP) of KDM1A by an anti-HA antibody from P7 Insm1 HA/HA , but not WT (negative control), cerebellar nuclear extracts. ( B ) Co-IP from P7 WT cerebellar nuclear extracts using either a nonspecific IgG (negative control) or an anti-TEAD1 antibody. ( C ) Co-IP from 293T cells transfected with the indicated TEAD1 and INSM1 constructs. Endogenous KDM1A was detected. ( D and E ) Nissl staining of P21 cerebellum vermis sections from control and Kdm1a cKO mice. ( F to G′ ) Co-immunostaining of P7 cerebella for PAX6, NeuN, and TNNC2. Boxed regions in F and G are shown at higher magnification in F′ and G′, respectively. ( H to J ) Quantifications of lobule VII TNNC2 + cells, PAX6 + cells located in the external granule layer (EGL), and NeuN + cells. Each data point represents an individual animal. Values are mean ± SEM. Unpaired two-tailed t -test; *, P < 0.05; ***, P < 0.001.

Article Snippet: The Atoh1-Cre ( ) (strain #011104), Kdm1a F/F ( ) (#023969), and Myod1 −/− ( ) (#002523) lines were obtained from the Jackson Laboratory.

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Negative Control, Transfection, Construct, Staining, Control, Immunostaining, Two Tailed Test

Journal: bioRxiv

Article Title: Cancer-associated KBTBD4 mutations induce differentiation defects and confer a unique therapeutic vulnerability

doi: 10.64898/2026.03.12.711277

Figure Lengend Snippet: (A) Volcano plot showing global protein expression in HL60 cells transduced with P311PP mutant. Blue and red dots show significantly decreased or increased proteins (adjusted p-value<0.05). CoREST components RREB1, RCOR1, KDM1A, RCOR3, and ZNF217 are highlighted in the volcano plot. The global proteome data was plotted after excluding PCDHGA11. (B) High throughput compound screening in HL60 cells stably expressing RCOR1-GFP treated with UM171 (200nM). Schematic of the screening rationale (top panel). The compounds were added at a final concentration of 1µM, and flow analysis was performed after 3 hours post treatment to measure the relative GFP expression (bottom panel). Red dots show the hits from the screen and the table on right-side shows the functional classification of the hits. (C) A dose-titration experiment showing the rescue of RCOR1-GFP by two class I specific HDAC inhibitors (mocetinostat and romidepsin) and three Pan HDAC inhibitors (belinostat, pracinostat and vorinostat). GFP mean fluorescence intensity of DMSO treatment was used as controls. Data from 3 replicates from 1 of 2 independent experiments with similar results are shown. (D) RCOR1 protein levels in P311PP expressing HL60 cells either treated with DMSO, belinostat (320nM) or mocetinostat (300nM) for 3 hours. (E) RCOR1 ELM2-GFP clones were expressed in HL60 cells and analyzed for the interaction with HDAC2 through immunoprecipitation. The degradation profiles of the corresponding alanine substitution clones to UM171 treatment are represented as a heat map. (F) Schematic representation of the mechanistic basis of HDAC inhibitors in preventing the CoREST degradation.

Article Snippet: The proteins were transferred to iBlot 2 PVDF membranes (#IB24001, Thermo Fisher Scientific) and probed with the following primary antibodies: RCOR1 (#14567), KDM1A (LSD1, #2184S), HDAC2 (#5113T, all from Cell Signaling Technology), GFP (#ab290, Abcam), and Actin (#612656, BD Biosciences).

Techniques: Expressing, Transduction, Mutagenesis, High Throughput Screening Assay, Stable Transfection, Concentration Assay, Functional Assay, Titration, Fluorescence, Clone Assay, Immunoprecipitation

Journal: bioRxiv

Article Title: Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation

doi: 10.64898/2026.02.27.708571

Figure Lengend Snippet: ( A ) WB analysis of histone modifications in Akata (EBV+) cells following HNRNPA2B1 depletion and IgG-crosslinking-induced lytic reactivation. Whole-cell lysates were collected at the indicated time points and probed for H3K4Me3, H3K27Ac, total H3, H2AK5Ac, and total H2A. β-actin serves as a loading control. ( B ) ChIP-qPCR analysis of H3K4Me3 enrichment at EBV ZTAp and RTAp in control (sg-NC) and HNRNPA2B1-depleted (sg2-A2B1) Akata (EBV+) cells. Data are shown as relative to 2% of input. Data are presented as mean ± SD from three biological replicates. ***p<0.001. ( C ) Plasmids expressing Halo-HA-KDMs and Halo-V5-HNRNPA2B1 were co-transfected into HEK-293T cells as indicated. Cell lysates containing the indicated tagged proteins were IP-ed with anti-HA antibody-conjugated beads and analyzed by WB with anti-V5 and anti-HA antibodies. Co-IP analysis showing stronger interaction between HNRNPA2B1 and KDM1A. β-actin serves as a loading control. ( D-F ) WB analysis of EBV lytic protein ZTA and KDM1A ( D ), KDM5A ( E ), or KDM5D ( F ) expression in KDM1A-, KDM5A-, or KDM5D-depleted SNU-719 cells following lytic induction by TPA treatment. β-actin serves as a loading control. ( G ) Co-IP analysis validating the interaction between HNRNPA2B1 and KDM1A. HEK-293T cells were transfected with Halo-HA-KDM1A and Halo-V5-HNRNPA2B1 as indicated. Cell lysates were treated with or without benzonase, followed by IP using anti-HA antibody-conjugated beads. IP and input samples were analyzed by WB with anti-V5 and anti-HA antibodies. β-actin serves as a loading control. ( H ) Proximity ligation assay (PLA) demonstrating the interaction between HNRNPA2B1 and KDM1A in situ . Akata (EBV+) cells were blocked with 3% bovine serum albumin (BSA) in phosphate-buffered saline (PBS) for 1 h at room temperature. Subsequently, the cells were incubated with either PBS control or a combination of mouse anti-KDM1A and rabbit anti-HNRNPA2B1 antibodies. Probes were then added for ligation and amplification. Cell nuclei were visualized using Nikon AXR after staining with 4′,6-diamidino-2-phenylindole (DAPI). The interaction between HNRNPA2B1 and KDM1A in situ was indicated by red dot representing PLA signals. Scale bars, 10 µm.

Article Snippet: DNA-protein complex were immunoprecipitated with anti-RNA polymerase II (Cat. #05-623-25UG, Milipore Sigma), anti-HNRNPA2B1 (Cat. # 67445-1-Ig, Proteintech), anti-H3K4Me3 (Cat. # 9751S, Cell Signaling Technology), anti-KDM1A (Cat. #2139S, Cell Signaling Technology), rabbit IgG control (Cat. #2729, Cell Signaling Technology), and mouse IgG control (Cat. #sc-2025, Santa Cruz).

Techniques: Control, ChIP-qPCR, Expressing, Transfection, Co-Immunoprecipitation Assay, Proximity Ligation Assay, In Situ, Saline, Incubation, Ligation, Amplification, Staining

Journal: bioRxiv

Article Title: Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation

doi: 10.64898/2026.02.27.708571

Figure Lengend Snippet: ( A ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata (EBV+) cells transduced with non-targeting control (sg-NC) or HNRNPA2B1-targeting sgRNA (sg2-A2B1). Anti-KDM1A was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. *p<0.05; **p<0.01. ( B ) Akata (EBV+) cells carrying control sg-NC or HNRNPA2B1-targeting sgRNA (sg2-A2B1) were treated with anti-human IgG for the indicated times. Protein levels of HNRNPA2B1 and KDM1A were analyzed by WB. β-actin serves as a loading control. ( C ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata-BX1 cells expressing control sg-NC or HNRNPA2B1-targeting sgRNA (sg2-A2B1). Anti-KDM1A was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. ***p<0.001. ( D ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata-BX1 sgA2B1 cells reconstituted with vector control or HNRNPA2B1 (pLenti-A2B1). Anti-KDM1A antibody was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. *p<0.05; ***p<0.001.

Article Snippet: DNA-protein complex were immunoprecipitated with anti-RNA polymerase II (Cat. #05-623-25UG, Milipore Sigma), anti-HNRNPA2B1 (Cat. # 67445-1-Ig, Proteintech), anti-H3K4Me3 (Cat. # 9751S, Cell Signaling Technology), anti-KDM1A (Cat. #2139S, Cell Signaling Technology), rabbit IgG control (Cat. #2729, Cell Signaling Technology), and mouse IgG control (Cat. #sc-2025, Santa Cruz).

Techniques: ChIP-qPCR, Transduction, Control, Negative Control, Expressing, Plasmid Preparation

Journal: bioRxiv

Article Title: Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation

doi: 10.64898/2026.02.27.708571

Figure Lengend Snippet: ( A ) WB analysis of histone modifications in Akata (EBV+) cells following HNRNPA2B1 depletion and IgG-crosslinking-induced lytic reactivation. Whole-cell lysates were collected at the indicated time points and probed for H3K4Me3, H3K27Ac, total H3, H2AK5Ac, and total H2A. β-actin serves as a loading control. ( B ) ChIP-qPCR analysis of H3K4Me3 enrichment at EBV ZTAp and RTAp in control (sg-NC) and HNRNPA2B1-depleted (sg2-A2B1) Akata (EBV+) cells. Data are shown as relative to 2% of input. Data are presented as mean ± SD from three biological replicates. ***p<0.001. ( C ) Plasmids expressing Halo-HA-KDMs and Halo-V5-HNRNPA2B1 were co-transfected into HEK-293T cells as indicated. Cell lysates containing the indicated tagged proteins were IP-ed with anti-HA antibody-conjugated beads and analyzed by WB with anti-V5 and anti-HA antibodies. Co-IP analysis showing stronger interaction between HNRNPA2B1 and KDM1A. β-actin serves as a loading control. ( D-F ) WB analysis of EBV lytic protein ZTA and KDM1A ( D ), KDM5A ( E ), or KDM5D ( F ) expression in KDM1A-, KDM5A-, or KDM5D-depleted SNU-719 cells following lytic induction by TPA treatment. β-actin serves as a loading control. ( G ) Co-IP analysis validating the interaction between HNRNPA2B1 and KDM1A. HEK-293T cells were transfected with Halo-HA-KDM1A and Halo-V5-HNRNPA2B1 as indicated. Cell lysates were treated with or without benzonase, followed by IP using anti-HA antibody-conjugated beads. IP and input samples were analyzed by WB with anti-V5 and anti-HA antibodies. β-actin serves as a loading control. ( H ) Proximity ligation assay (PLA) demonstrating the interaction between HNRNPA2B1 and KDM1A in situ . Akata (EBV+) cells were blocked with 3% bovine serum albumin (BSA) in phosphate-buffered saline (PBS) for 1 h at room temperature. Subsequently, the cells were incubated with either PBS control or a combination of mouse anti-KDM1A and rabbit anti-HNRNPA2B1 antibodies. Probes were then added for ligation and amplification. Cell nuclei were visualized using Nikon AXR after staining with 4′,6-diamidino-2-phenylindole (DAPI). The interaction between HNRNPA2B1 and KDM1A in situ was indicated by red dot representing PLA signals. Scale bars, 10 µm.

Article Snippet: Briefly, Akata (EBV+) cells were blocked with 3% BSA in PBS for 1 hour at room temperature, then incubated overnight at 4□°C with either PBS control or a mixture of rabbit anti-HNRNPA2B1 (Cat. #14813-1-AP, Proteintech) and mouse anti-KDM1A (Cat. #67037-1-Ig, Proteintech) antibodies (1:50 in 3% BSA).

Techniques: Control, ChIP-qPCR, Expressing, Transfection, Co-Immunoprecipitation Assay, Proximity Ligation Assay, In Situ, Saline, Incubation, Ligation, Amplification, Staining

Journal: bioRxiv

Article Title: Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation

doi: 10.64898/2026.02.27.708571

Figure Lengend Snippet: ( A ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata (EBV+) cells transduced with non-targeting control (sg-NC) or HNRNPA2B1-targeting sgRNA (sg2-A2B1). Anti-KDM1A was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. *p<0.05; **p<0.01. ( B ) Akata (EBV+) cells carrying control sg-NC or HNRNPA2B1-targeting sgRNA (sg2-A2B1) were treated with anti-human IgG for the indicated times. Protein levels of HNRNPA2B1 and KDM1A were analyzed by WB. β-actin serves as a loading control. ( C ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata-BX1 cells expressing control sg-NC or HNRNPA2B1-targeting sgRNA (sg2-A2B1). Anti-KDM1A was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. ***p<0.001. ( D ) ChIP-qPCR analysis of KDM1A occupancy at ZTAp and RTAp in Akata-BX1 sgA2B1 cells reconstituted with vector control or HNRNPA2B1 (pLenti-A2B1). Anti-KDM1A antibody was used for KDM1A ChIP and IgG served as a negative control. Data are normalized to 2% input and shown as mean ± SD from three biological replicates. *p<0.05; ***p<0.001.

Article Snippet: Briefly, Akata (EBV+) cells were blocked with 3% BSA in PBS for 1 hour at room temperature, then incubated overnight at 4□°C with either PBS control or a mixture of rabbit anti-HNRNPA2B1 (Cat. #14813-1-AP, Proteintech) and mouse anti-KDM1A (Cat. #67037-1-Ig, Proteintech) antibodies (1:50 in 3% BSA).

Techniques: ChIP-qPCR, Transduction, Control, Negative Control, Expressing, Plasmid Preparation