histone h2b Search Results


anti h2bub1 antibody  (Cell Signaling Technology Inc)
95
Cell Signaling Technology Inc anti h2bub1 antibody
The core circadian component BMAL1 regulated histone H2B monoubiquitination levels (A) RNA-seq heatmap comparing the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 7th day of osteogenic differentiation. (B) GO analysis of the RNA-seq data between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups. Bar graph showing the p values of the enriched terms. (C) GSEA of the RNA-seq data between the Sh-NC and Sh-BMAL1, Sh-NC, and Sh-CLOCK groups. (D) <t>H2Bub1</t> and H2Aub1 levels in the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 10th day of osteogenic differentiation. H2B and H2A served as the internal controls. Bar graphs showing the relative levels. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (E) log 2 FC and −log 10 (q value) of differential RNF20/40 expression between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups as obtained from the RNA-seq data. (F) Circos plot showing the terms with enriched genes and log 2 FC and −log 10 (q value). TTK, the regulator of histone H2B monoubiquitination, is highlighted (G).
Anti H2bub1 Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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anti h2bub1 antibody - by Bioz Stars, 2026-08
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β actin  (Cell Signaling Technology Inc)
95
Cell Signaling Technology Inc β actin
The core circadian component BMAL1 regulated histone H2B monoubiquitination levels (A) RNA-seq heatmap comparing the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 7th day of osteogenic differentiation. (B) GO analysis of the RNA-seq data between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups. Bar graph showing the p values of the enriched terms. (C) GSEA of the RNA-seq data between the Sh-NC and Sh-BMAL1, Sh-NC, and Sh-CLOCK groups. (D) <t>H2Bub1</t> and H2Aub1 levels in the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 10th day of osteogenic differentiation. H2B and H2A served as the internal controls. Bar graphs showing the relative levels. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (E) log 2 FC and −log 10 (q value) of differential RNF20/40 expression between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups as obtained from the RNA-seq data. (F) Circos plot showing the terms with enriched genes and log 2 FC and −log 10 (q value). TTK, the regulator of histone H2B monoubiquitination, is highlighted (G).
β Actin, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/histone+h2b/pmc06880446-41-7-8?v=Cell+Signaling+Technology+Inc
Average 95 stars, based on 1 article reviews
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cell lysis buffer 10  (Cell Signaling Technology Inc)
93
Cell Signaling Technology Inc cell lysis buffer 10
The core circadian component BMAL1 regulated histone H2B monoubiquitination levels (A) RNA-seq heatmap comparing the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 7th day of osteogenic differentiation. (B) GO analysis of the RNA-seq data between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups. Bar graph showing the p values of the enriched terms. (C) GSEA of the RNA-seq data between the Sh-NC and Sh-BMAL1, Sh-NC, and Sh-CLOCK groups. (D) <t>H2Bub1</t> and H2Aub1 levels in the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 10th day of osteogenic differentiation. H2B and H2A served as the internal controls. Bar graphs showing the relative levels. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (E) log 2 FC and −log 10 (q value) of differential RNF20/40 expression between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups as obtained from the RNA-seq data. (F) Circos plot showing the terms with enriched genes and log 2 FC and −log 10 (q value). TTK, the regulator of histone H2B monoubiquitination, is highlighted (G).
Cell Lysis Buffer 10, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lysis buffer 10 - by Bioz Stars, 2026-08
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anti h2b antibody  (Proteintech)
94
Proteintech anti h2b antibody
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Anti H2b Antibody, supplied by Proteintech, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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histone h2b  (Santa Cruz Biotechnology)
94
Santa Cruz Biotechnology histone h2b
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Histone H2b, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/histone+h2b/pmc09012021-64-11-21?v=Santa+Cruz+Biotechnology
Average 94 stars, based on 1 article reviews
histone h2b - by Bioz Stars, 2026-08
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histone h2b  (Novus Biologicals)
86
Novus Biologicals histone h2b
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Histone H2b, supplied by Novus Biologicals, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/histone+h2b/pmc03062408-63-18-20?v=Novus+Biologicals
Average 86 stars, based on 1 article reviews
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anti acetyl histone h2b  (Cell Signaling Technology Inc)
91
Cell Signaling Technology Inc anti acetyl histone h2b
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Anti Acetyl Histone H2b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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anti acetylated lysine monoclonal antibody  (Cell Signaling Technology Inc)
85
Cell Signaling Technology Inc anti acetylated lysine monoclonal antibody
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Anti Acetylated Lysine Monoclonal Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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anti acetylated lysine monoclonal antibody - by Bioz Stars, 2026-08
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chromotek histone label atto488  (Proteintech)
90
Proteintech chromotek histone label atto488
a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and <t>H2B)</t> and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of <t>H2B,</t> H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.
Chromotek Histone Label Atto488, supplied by Proteintech, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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acetyl histone h2b  (Cell Signaling Technology Inc)
94
Cell Signaling Technology Inc acetyl histone h2b
FIGURE 5 Hydroxamic acid derivatives 7d and 7p induce inhibition of histone deacetylase (HDAC) class I and II enzyme activity in THP‐1 cells. (a) The inhibitory effects of vorinostat 1, 7d, and 7p on the enzyme activity of HDAC class I and II were determined using the HDAC‐Glo™ I/II Assay. The results are expressed as the mean ± SD of three independent experiments. The levels of histone H2A, <t>H2B,</t> H3, or H4 acetylation after (b) 24 h or (c) 48 h of treatment with vorinostat 1, 7d, and 7p were determined by immunoblot analysis using appropriate antibodies. Representative immunoblots of one of three experiments are shown. CTRL is a drug‐free control.
Acetyl Histone H2b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell signaling technology 8135  (Cell Signaling Technology Inc)
93
Cell Signaling Technology Inc cell signaling technology 8135
FIGURE 5 Hydroxamic acid derivatives 7d and 7p induce inhibition of histone deacetylase (HDAC) class I and II enzyme activity in THP‐1 cells. (a) The inhibitory effects of vorinostat 1, 7d, and 7p on the enzyme activity of HDAC class I and II were determined using the HDAC‐Glo™ I/II Assay. The results are expressed as the mean ± SD of three independent experiments. The levels of histone H2A, <t>H2B,</t> H3, or H4 acetylation after (b) 24 h or (c) 48 h of treatment with vorinostat 1, 7d, and 7p were determined by immunoblot analysis using appropriate antibodies. Representative immunoblots of one of three experiments are shown. CTRL is a drug‐free control.
Cell Signaling Technology 8135, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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anti h2b 2934s  (Cell Signaling Technology Inc)
93
Cell Signaling Technology Inc anti h2b 2934s
FIGURE 5 Hydroxamic acid derivatives 7d and 7p induce inhibition of histone deacetylase (HDAC) class I and II enzyme activity in THP‐1 cells. (a) The inhibitory effects of vorinostat 1, 7d, and 7p on the enzyme activity of HDAC class I and II were determined using the HDAC‐Glo™ I/II Assay. The results are expressed as the mean ± SD of three independent experiments. The levels of histone H2A, <t>H2B,</t> H3, or H4 acetylation after (b) 24 h or (c) 48 h of treatment with vorinostat 1, 7d, and 7p were determined by immunoblot analysis using appropriate antibodies. Representative immunoblots of one of three experiments are shown. CTRL is a drug‐free control.
Anti H2b 2934s, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


The core circadian component BMAL1 regulated histone H2B monoubiquitination levels (A) RNA-seq heatmap comparing the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 7th day of osteogenic differentiation. (B) GO analysis of the RNA-seq data between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups. Bar graph showing the p values of the enriched terms. (C) GSEA of the RNA-seq data between the Sh-NC and Sh-BMAL1, Sh-NC, and Sh-CLOCK groups. (D) H2Bub1 and H2Aub1 levels in the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 10th day of osteogenic differentiation. H2B and H2A served as the internal controls. Bar graphs showing the relative levels. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (E) log 2 FC and −log 10 (q value) of differential RNF20/40 expression between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups as obtained from the RNA-seq data. (F) Circos plot showing the terms with enriched genes and log 2 FC and −log 10 (q value). TTK, the regulator of histone H2B monoubiquitination, is highlighted (G).

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: The core circadian component BMAL1 regulated histone H2B monoubiquitination levels (A) RNA-seq heatmap comparing the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 7th day of osteogenic differentiation. (B) GO analysis of the RNA-seq data between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups. Bar graph showing the p values of the enriched terms. (C) GSEA of the RNA-seq data between the Sh-NC and Sh-BMAL1, Sh-NC, and Sh-CLOCK groups. (D) H2Bub1 and H2Aub1 levels in the MSCs infected with Sh-NC, Sh-BMAL1, or Sh-CLOCK lentiviruses on the 10th day of osteogenic differentiation. H2B and H2A served as the internal controls. Bar graphs showing the relative levels. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (E) log 2 FC and −log 10 (q value) of differential RNF20/40 expression between the Sh-NC and Sh-BMAL1 groups and the Sh-NC and Sh-CLOCK groups as obtained from the RNA-seq data. (F) Circos plot showing the terms with enriched genes and log 2 FC and −log 10 (q value). TTK, the regulator of histone H2B monoubiquitination, is highlighted (G).

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: RNA Sequencing, Infection, Expressing

BMAL1 targeted the circadian-controlled gene TTK to regulate H2Bub1 levels to affect the osteogenic capacity of MSCs (A and B) Relative mRNA (A) and protein (B) expression of TTK in the MSCs infected with Sh-NC, Sh-BMAL1, OE-NC, or OE-BMAL1 lentiviruses on the 10th day of osteogenic differentiation. (C) The putative E-boxes in the TTK promoter region. (D) CUT&Tag-qPCR showed the percentage of BMAL1 occupancy on the TTK promoter. Data are shown as the proportion of input level and normalized to the IgG control. (E) CUT&Tag-qPCR analysis showing the H2Bub1 occupancy on RUNX2 and OSX in the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC or Sh-BMAL1 and OE-TTK lentiviruses that were undergoing osteogenic differentiation. (F and G) Relative mRNA expression (F) and protein expression (G) of RUNX2 and OSX in MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses that were undergoing osteogenic differentiation. Bar graphs showing the relative expression. (H) ARS and ALP staining of the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses on the 14th day of osteogenic differentiation. (I) HE and Masson staining and Col I immunohistochemistry of transplanted HA/TCP embedded with the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses. All data are presented as mean ± SD; n = 3; ∗p < 0.05.

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: BMAL1 targeted the circadian-controlled gene TTK to regulate H2Bub1 levels to affect the osteogenic capacity of MSCs (A and B) Relative mRNA (A) and protein (B) expression of TTK in the MSCs infected with Sh-NC, Sh-BMAL1, OE-NC, or OE-BMAL1 lentiviruses on the 10th day of osteogenic differentiation. (C) The putative E-boxes in the TTK promoter region. (D) CUT&Tag-qPCR showed the percentage of BMAL1 occupancy on the TTK promoter. Data are shown as the proportion of input level and normalized to the IgG control. (E) CUT&Tag-qPCR analysis showing the H2Bub1 occupancy on RUNX2 and OSX in the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC or Sh-BMAL1 and OE-TTK lentiviruses that were undergoing osteogenic differentiation. (F and G) Relative mRNA expression (F) and protein expression (G) of RUNX2 and OSX in MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses that were undergoing osteogenic differentiation. Bar graphs showing the relative expression. (H) ARS and ALP staining of the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses on the 14th day of osteogenic differentiation. (I) HE and Masson staining and Col I immunohistochemistry of transplanted HA/TCP embedded with the MSCs infected with Sh-NC and OE-NC, Sh-BMAL1 and OE-NC, or Sh-BMAL1 and OE-TTK lentiviruses. All data are presented as mean ± SD; n = 3; ∗p < 0.05.

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: Expressing, Infection, Control, Staining, Immunohistochemistry

H2Bub1 positively modulated the expression of BMAL1 at the transcript level (A) Signal traces of ChIP-seq data showing H2Bub1 and Pol II occupancy on BMAL1 in hFOB1.19 cells on day 0 or 7 of osteogenic differentiation. (B and C) Relative mRNA expression (B) and protein expression (C) of BMAL1 in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. Bar graphs showing the relative expression. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (D) CUT&Tag-seq average binding profiles and heatmaps depicting occupancy of H2Bub1 and Pol II in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. (E) GO biological process analyses of the CUT&Tag-seq data comparing between the Sh-NC and Sh-RNF40 groups and the Sh-NC and Sh-WAC groups. Bar graph showing the p values of the enriched terms. (F) Signal traces of CUT&Tag-seq data showing H2Bub1 and Pol II occupancy on BMAL1 in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. The colorful shadows showing regions with difference (G) CUT&Tag-qPCR analysis showing the H2Bub1 and Pol II occupancy on BMAL1 sites A–F in the MSCs infected with Sh-NC, Sh-RNF40 or Sh-WAC lentiviruses. Data are presented as mean ± SD; n = 3; ∗p < 0.05.

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: H2Bub1 positively modulated the expression of BMAL1 at the transcript level (A) Signal traces of ChIP-seq data showing H2Bub1 and Pol II occupancy on BMAL1 in hFOB1.19 cells on day 0 or 7 of osteogenic differentiation. (B and C) Relative mRNA expression (B) and protein expression (C) of BMAL1 in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. Bar graphs showing the relative expression. Data are presented as mean ± SD; n = 3; ∗p < 0.05. (D) CUT&Tag-seq average binding profiles and heatmaps depicting occupancy of H2Bub1 and Pol II in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. (E) GO biological process analyses of the CUT&Tag-seq data comparing between the Sh-NC and Sh-RNF40 groups and the Sh-NC and Sh-WAC groups. Bar graph showing the p values of the enriched terms. (F) Signal traces of CUT&Tag-seq data showing H2Bub1 and Pol II occupancy on BMAL1 in the MSCs infected with Sh-NC, Sh-RNF40, or Sh-WAC lentiviruses. The colorful shadows showing regions with difference (G) CUT&Tag-qPCR analysis showing the H2Bub1 and Pol II occupancy on BMAL1 sites A–F in the MSCs infected with Sh-NC, Sh-RNF40 or Sh-WAC lentiviruses. Data are presented as mean ± SD; n = 3; ∗p < 0.05.

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: Expressing, ChIP-sequencing, Infection, Binding Assay

TTK expression and H2Bub1 levels were decreased in BM-MSCs in senile osteoporosis (A and B) Western blot analysis of the levels of TTK and H2Bub1 in BM-MSCs from 2-month-old and 20-month-old mice, patients with traffic injuries and patients with senile osteoporosis. (C and D) Immunofluorescence staining (scale bar, 100 μm) showed Ttk expression and H2Bub1 levels in the Ocn + osteoblast lineage in 2-month-old and 20-month-old mice (white arrows). (E and F) Immunofluorescence staining (scale bar, 100 μm) showed TTK expression and H2Bub1 levels in the OCN + osteoblast lineage in young patients with traffic injuries and patients with senile osteoporosis (white arrows). All data are presented as mean ± SD; n = 3; ∗p < 0.05.

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: TTK expression and H2Bub1 levels were decreased in BM-MSCs in senile osteoporosis (A and B) Western blot analysis of the levels of TTK and H2Bub1 in BM-MSCs from 2-month-old and 20-month-old mice, patients with traffic injuries and patients with senile osteoporosis. (C and D) Immunofluorescence staining (scale bar, 100 μm) showed Ttk expression and H2Bub1 levels in the Ocn + osteoblast lineage in 2-month-old and 20-month-old mice (white arrows). (E and F) Immunofluorescence staining (scale bar, 100 μm) showed TTK expression and H2Bub1 levels in the OCN + osteoblast lineage in young patients with traffic injuries and patients with senile osteoporosis (white arrows). All data are presented as mean ± SD; n = 3; ∗p < 0.05.

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: Expressing, Western Blot, Immunofluorescence, Staining

Bone-targeted Bmal1 or Ttk rescue-treated senile osteoporosis (A) Diagram showing the workflow of rAAV9 injection in 18-month-old mice with calvarial and femoral defects and bone section analysis. (B) Immunoblot analysis showing mNeonGreen expression in different organs of the mice injected with rAAV9. (C) Fluorescence images of different organs of mice injected with rAAV9. (D) Immunofluorescence staining (scale bar, 100 μm) showing mNeonGreen-expressing osteoblasts in the femurs of the mice injected with rAAV9. (E) Immunofluorescence staining (scale bar, 100 μm) showing Bmal1 expression in the Ocn + osteoblast lineage in the mice injected with rAAV9-control or rAAV9-Bmal1 (white arrows). (F) Immunofluorescence staining (scale bar, 100 μm) showing Ttk expression in the Ocn + osteoblast lineage in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk (white arrows). (G) Immunofluorescence staining (scale bar, 100 μm) showing H2Bub1 levels in the Ocn + osteoblast lineage in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk (white arrows). Data are presented as mean ± SD; n = 3; ∗p < 0.05. (H) Micro-CT analysis comparing the healing rates of calvarial and femoral defects in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk. (I) Representative micro-CT images showing the trabecular bone of mice with senile osteoporosis injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk. Bone morphometric analysis, including the analysis of BV/TV, Tb.Th, Tb.N, Tb.Sp, and Ct.Th., was performed. Data are presented as mean ± SD; n = 5; ∗p < 0.05.

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: Bone-targeted Bmal1 or Ttk rescue-treated senile osteoporosis (A) Diagram showing the workflow of rAAV9 injection in 18-month-old mice with calvarial and femoral defects and bone section analysis. (B) Immunoblot analysis showing mNeonGreen expression in different organs of the mice injected with rAAV9. (C) Fluorescence images of different organs of mice injected with rAAV9. (D) Immunofluorescence staining (scale bar, 100 μm) showing mNeonGreen-expressing osteoblasts in the femurs of the mice injected with rAAV9. (E) Immunofluorescence staining (scale bar, 100 μm) showing Bmal1 expression in the Ocn + osteoblast lineage in the mice injected with rAAV9-control or rAAV9-Bmal1 (white arrows). (F) Immunofluorescence staining (scale bar, 100 μm) showing Ttk expression in the Ocn + osteoblast lineage in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk (white arrows). (G) Immunofluorescence staining (scale bar, 100 μm) showing H2Bub1 levels in the Ocn + osteoblast lineage in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk (white arrows). Data are presented as mean ± SD; n = 3; ∗p < 0.05. (H) Micro-CT analysis comparing the healing rates of calvarial and femoral defects in the mice injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk. (I) Representative micro-CT images showing the trabecular bone of mice with senile osteoporosis injected with rAAV9-control, rAAV9-Bmal1, or rAAV9-Ttk. Bone morphometric analysis, including the analysis of BV/TV, Tb.Th, Tb.N, Tb.Sp, and Ct.Th., was performed. Data are presented as mean ± SD; n = 5; ∗p < 0.05.

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: Injection, Western Blot, Expressing, Fluorescence, Immunofluorescence, Staining, Control, Micro-CT

Model showing that the disruption of the BMAL1-TTK-MDM2-H2Bub1 positive loop led to the impaired osteogenic capacity of BM-MSCs in senile osteoporosis

Journal: Molecular Therapy. Nucleic Acids

Article Title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

doi: 10.1016/j.omtn.2023.02.014

Figure Lengend Snippet: Model showing that the disruption of the BMAL1-TTK-MDM2-H2Bub1 positive loop led to the impaired osteogenic capacity of BM-MSCs in senile osteoporosis

Article Snippet: The following primary antibodies were used: anti-BMAL1 antibody (catalog no. 14020; Cell Signaling Technology), anti-TTK antibody (catalog no. ab11108; Abcam), anti-CLOCK antibody (catalog no. ab3517; Abcam), anti-OCN antibody (catalog no. 29560; Sab), anti-GAPDH (catalog no. 5174S; Cell Signaling Technology), anti-RUNX2 (catalog no. 12556S; Cell Signaling Technology), anti-OSX (catalog no. ab209484; Abcam), anti-β-tubulin (catalog no. 2128; Cell Signaling Technology), anti-OPN antibody (catalog no. 42036; Sab), anti-RNF20 antibody (catalog no. ab181104; Abcam), anti-RNF40 antibody (catalog no. ab191309; Abcam), anti-WAC antibody (catalog no. ab109486; Abcam), anti-H2B antibody (catalog no. 12364; Cell Signaling Technology), anti-H2Bub1 antibody (catalog no. 5546; Cell Signaling Technology), anti-H2A antibody (catalog no. 12349; Cell Signaling Technology) anti-H2Aub1 antibody (catalog no. 8240; Cell Signaling Technology), anti-MDM2 antibody (catalog no. ab226939; Abcam), and anti-pan phosphoserine/threonine antibody (catalog no. AP1067; Abclonal).

Techniques: Disruption

a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and H2B) and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of H2B, H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.

Journal: bioRxiv

Article Title: ZCCHC4 Promotes Translation of Replication-dependent Histone mRNAs by Recruiting Cytoplasmic eIF3 complex

doi: 10.1101/2025.06.21.660898

Figure Lengend Snippet: a, Venn diagram showed the overlap of ZCCHC4 PAR-CLIP-seq target genes between two biological replicates. b, Distribution plots (up) and sequence motif enrichment analysis (down) of ZCCHC4-bound histone mRNAs. ZCCHC4-binding motifs were identified by HOMER findMotifsGenome.pl from the PAR-CLIP-seq peaks of two biological replicates. The motif length was restricted to 4-8 nucleotides. The P -value was calculated from the random background sequences with a ZOOPS score. c, RIP/qPCR analyses showed the binding of ZCCHC4 and potential targets in wild-type HeLa cells. d, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by Ribo-seq in ZCCHC4 KO cells compared with WT cells. e, Integrated Genome Viewer (IGV) showing the mapped reads of the binding peaks identified by ribosome-bound fragments identified by Ribo-seq of H2BC6 after ZCCHC4 knockout. The histograms represent the sum of mapped reads along the genome. The mapped reads of Ribo-seq were normalized by the sequencing depth. f, Volcano plot depicting down-regulated (blue) and up-regulated (red) genes identified by TMT in ZCCHC4 KO cells compared with WT cells. g, Cumulative distribution of translation efficiency with histone mRNA (red) and non-histone (blue) mRNA by TMT (up) and Ribo-seq (down). h, Volcano plot depicting replication-dependent (blue, RD-Histone) and replication-independent (red, RI-Histone) histone identified by Ribo-seq (left) and TMT (right) in ZCCHC4 KO cells compared with WT cells. i, Western blot analysis to validate the expression of RD-histone (H2A and H2B) and RI-histone (H2AZ) in ZCCHC4 knockout and control cells. β-actin was used as internal control. j, The broken line chart showed the relative distribution of the mRNA level of H2B, H2AC and H4A in the different fractions isolated by the sucrose gradient. The same volume (50 µL) of the fractions was loaded to perform RT-qPCR. k, RT-qPCR analysis of polysome-or monosome (80S)-bound histone mRNA in WT (left) ZCCHC4 knockout (right) HeLa cells. Note: c , k Two-tailed unpaired Student’s t tests. Data were presented as mean ± SD (n=3). * P <0.05, * * P <0.01, ** * P <0.001, **** P <0.0001. ns: not significant.

Article Snippet: The corresponding antibodies included anti-ZCCHC4 antibody with 1:1000 dilution (Abcam, ab209901), anti-RPS6 antibody with 1:1000 dilution (Proteintech, 66886-1-Ig), anti-RPL14 antibody with 1:1000 dilution (Proteintech, 14991-1-AP), anti-CDKN1A antibody with 1:1000 dilution (Proteintech, 10355-1-AP), anti-puromycin antibody with 1:1000 dilution (ABclonal, A21205), anti-H2B antibody with 1:2000 dilution (PTM-1007), anti-H2A antibody with 1:2000 dilution (ABclonal, A3692), anti-H2AZ antibody with 1:2000 dilution (Proteintech, 16441-1-AP), anti-HistoneH1.2 antibody with 1:1000 dilution (Proteintech, 19649-1-AP), anti HistoneH3 antibody with 1:2000 dilution (ABclonal, A22348), anti-α-Tubulin antibody with 1:3000 dilution (Proteintech, 80762-1-RR), anti-EIF3H antibody with 1:1000 dilution (Proteintech, 11310-1-AP), anti-EIF3A antibody with 1:1000 dilution (Proteintech, 26178-1-AP), anti-PDCD4 antibody with 1:1000 dilution (Proteintech, 12587-1-AP), anti-CyclinB1 antibody with 1:1000 dilution (ABclonal, A19037), anti-GAPDH antibody with 1:5000 dilution (Proteintech, 10494-1-AP), anti-β-actin antibody with 1:3000 dilution (SAB Signalway Antibody, 52901), and anti-Flag antibody with 1:2000 dilution (Sigma, F1804).

Techniques: Sequencing, Binding Assay, Knock-Out, Western Blot, Expressing, Control, Isolation, Quantitative RT-PCR, Two Tailed Test

FIGURE 5 Hydroxamic acid derivatives 7d and 7p induce inhibition of histone deacetylase (HDAC) class I and II enzyme activity in THP‐1 cells. (a) The inhibitory effects of vorinostat 1, 7d, and 7p on the enzyme activity of HDAC class I and II were determined using the HDAC‐Glo™ I/II Assay. The results are expressed as the mean ± SD of three independent experiments. The levels of histone H2A, H2B, H3, or H4 acetylation after (b) 24 h or (c) 48 h of treatment with vorinostat 1, 7d, and 7p were determined by immunoblot analysis using appropriate antibodies. Representative immunoblots of one of three experiments are shown. CTRL is a drug‐free control.

Journal: Archiv der Pharmazie

Article Title: New potent N-hydroxycinnamamide-based histone deacetylase inhibitors suppress proliferation and trigger apoptosis in THP-1 leukaemia cells.

doi: 10.1002/ardp.202400889

Figure Lengend Snippet: FIGURE 5 Hydroxamic acid derivatives 7d and 7p induce inhibition of histone deacetylase (HDAC) class I and II enzyme activity in THP‐1 cells. (a) The inhibitory effects of vorinostat 1, 7d, and 7p on the enzyme activity of HDAC class I and II were determined using the HDAC‐Glo™ I/II Assay. The results are expressed as the mean ± SD of three independent experiments. The levels of histone H2A, H2B, H3, or H4 acetylation after (b) 24 h or (c) 48 h of treatment with vorinostat 1, 7d, and 7p were determined by immunoblot analysis using appropriate antibodies. Representative immunoblots of one of three experiments are shown. CTRL is a drug‐free control.

Article Snippet: [82,86] Membranes were stained overnight at 4°C with appropriate primary antibodies: anti‐β‐actin antibody (Santa Cruz Biotechnology), antibodies against cyclin E1 (Clone: HE12, Cat. #: sc‐ 247), p‐Rb [Ser 807/811] (sc‐16670‐R), cleaved PARP (D64E10, 5625), acetyl‐histone H2A [Lys5] (2576), acetyl‐histone H2B [Lys5] (D5H1S, 12799), acetyl‐histone H3 [Lys9] (C5B11, 9649) and acetyl‐ histone H4 [Lys8] (2594) were purchased Cell Signalling Technology.

Techniques: Inhibition, Histone Deacetylase Assay, Activity Assay, Ii Assay, Western Blot, Control