a301 092a  (Bethyl)

Journal: EMBO Reports

Article Title: NELF prevents transcriptional readthrough into DNA replication zones in cancer cells

doi: 10.1038/s44319-026-00700-z

Figure Lengend Snippet: ( A ) Schematic diagram of Pol II elongation index (EI) analysis. Pol II EI is determined as TT/POINT. 4sU (Green circle), Pol II (blue oval). ( B ) Pol II EI for all expressed pc genes across normalized transcription units in NELF-C-AID DLD-1 cells treated for 4 h with DMSO or IAA. Last exon (LE)-0.5 kb ~ +2.5 kb window is highlighted in gray. ( C ) Pol II EI for non-overlapping pc genes across LE. ( D ) Metagene of CSTF64 and XRN2 ChIP-seq for non-overlapping pc genes across normalized transcription units (top) and LE (bottom) in NELF-C-AID DLD-1 cells treated for 4 h with DMSO or IAA. Last exon (LE)-0.5 kb ~ +2.5 kb window is highlighted in gray. ( E ) Quantification of CSTF64 and XRN2 ChIP-seq signals (IAA/DMSO) in 2.5 kb DoG regions of non-overlapping pc genes. Statistical test: Kruskal–Wallis test. **** P < 0.0001. Violin plot: minimal-to-maximal value, box center line: median.

Article Snippet: Rabbit polyclonal anti CSTF64 , Bethyl , Cat# A301-092A.

Techniques: ChIP-sequencing

Journal: bioRxiv

Article Title: U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

doi: 10.1101/2023.02.24.529985

Figure Lengend Snippet: (A) Meta-gene plots of CPSF160, WDR33 and CSTF77 ChIP-seq reads in control and U1 AMO treated HeLa cells for all actively expressed genes (n=13217), intronic PCPAed genes (n=5937), and other non-intronic PCPAed genes (n=7280). For intronic PCPAed genes, a second meta-gene plot was made for each ChIP-seq by replacing the default TES (transcription end sites) with intronic PCPA site. If multiple PCPA sites were detected for a given gene, the one showing the most significant PCPA was chosen to create the plot. (B) Meta-gene plots of WDR33 and CSTF64 iCLIP-seq reads in control and U1 AMO treated HeLa cells for all actively expressed genes (n=13217), intronic PCPAed genes (n=5937), and other non-intronic PCPAed genes (n=7280). For intronic PCPAed genes, a second meta-gene plot was made for each ChIP-seq by replacing the default TES (transcription end sites) with intronic PCPA site. (C) IGV track screen shots showing CPSF160/WDR33/CSTF77 ChIP-seq(s), WDR33/CSTF64 iCLIP-seq(s) and 3’-seq results for basp1 gene in control and U1 AMO treated HeLa cells. (D) IGV track screen shots showing CSTF64 iCLIP-seq and 3’-seq results for eed gene in control and U1 AMO treated HeLa cells. (E) Gel mobility shift assay using recombinant GST-CSTF64-RRM (RNA recognition motif) (0, 1, 2, 5, 10, 15, 20 μM) and indicated PAS RNAs (detectable amount, approximately 0.1 uM). The PAS RNA sequences are listed in Supplemental Table 7. (F) Measurement of the processing efficiencies of eed intronic PAS RNAs and two mutants using pPASPORT system. Experiments were performed three times and the standard deviations are shown in error bars. Student’s t-test was performed to examine the significance of the difference. *P<0.05.

Article Snippet: The primary antibodies [WDR33 (A301-152A) and CstF64 (A301-092A)] were purchased from Bethyl.

Techniques: ChIP-sequencing, Mobility Shift, Recombinant