Journal: iScience

Article Title: A mechanism of target mRNA selection and activity regulation in meiosis-related RBM46-MEIOC-YTHDC2 complex

doi: 10.1016/j.isci.2026.116234

Figure Lengend Snippet: XRN2 is a new partner of MEIOC and involved in RMY-dependent RNA repression (A) Immunoprecipitated MEIOC complexes were separated by SDS-PAGE and the protein in the gel was stained with silver prior to mass spectrometry (MS). (B) Related proteins in MEIOC complex were identified by MS. (C) Cytoplasm and nuclei were separated from HEK293T cells transfected with MEIOC and YTHDC2 (M + Y). Lamin B1 was used as a nuclear marker and GADPH as a cytoplasmic marker, N = 3. (D) XRN2 protein was co-immunoprecipitated with MEIOC. IgG was used as a negative control. N = 3. (E) Western blot analysis of MEIOC and XNR2 protein. A lentivirus containing HIS-MEIOC infected HEK293T cells. The cells were lysed with RIPA buffer and then coIP assay was performed with anti-XRN2 antibody. IgG was used as a negative control. N = 3. (F) Western blot analysis of XRN2 and β-Actin from HEK293T cells transfected with XRN2 siRNAs and control siRNA, N = 3. (G) RT-qPCR analysis showing relative mRNA levels of XRN2 in HEK293T cells transfected with XRN2 siRNAs and control siRNA, N = 3. (H) Relative luciferase activities of F-Luc-Rad21 3′UTR in HEK293T cells after knockdown of XRN2 only or combined with the expression of RBM46, MEIOC and YTHDC2 (RMY). N = 3. Data are presented as mean ± SEM. p values were determined by unpaired t test with Welch’s correction (C–E) or by one-way ANOVA with Benjamini-Hochberg correction (F–H). (I) A model of RMY complex assembly and target mRNA degradation.

Article Snippet: SDS-PAGE running buffer powder , Servicebio , Cat#G2018-1L.

Techniques: Immunoprecipitation, SDS Page, Staining, Mass Spectrometry, Transfection, Marker, Negative Control, Western Blot, Infection, Co-Immunoprecipitation Assay, Control, Quantitative RT-PCR, Luciferase, Knockdown, Expressing

Journal: bioRxiv

Article Title: Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex

doi: 10.64898/2026.06.05.730395

Figure Lengend Snippet: a , Domain architecture of RAP80 and ARISC constructs. FL, full-length; SIM, small ubiquitin-like modifier (SUMO)-interacting motif; UIM, ubiquitin-interacting motif; AIR, Abraxas1-interacting region; ZnF, zinc finger; MPN, Mpr1, Pad1 N-terminal; CC, coiled coil; UEV, ubiquitin E2 variant; vWFA, von Willebrand factor type A ( left ). Schematics of indicated complexes ( right ). b , SDS-PAGE analysis of ARISC, ARISC–RAP80, and ARISC–RAP80 AIR. c , K63-linked ubiquitin chains (1 µM) were incubated with ARISC or ARISC–RAP80 (5 nM) for the indicated time points. Cleavage activity was analysed by SDS-PAGE and silver staining. Data are representative of two independent experiments. d , K63-Ub2, -Ub4, and - Ub7 chains (1 µM) were incubated with ARISC, ARISC–RAP80, or ARISC–RAP80 AIR (5 nM) for the indicated time points. Cleavage activity was analysed as in c . Data are representative of three independent experiments. e , Schematics ( left ) and SDS-PAGE analysis ( right ) of indicated complexes. dStrepII, double StrepII tag. * indicates Abraxas1 degradation product. f , Alexa-Fluor 488 (AF488) labelled distally (AF488- Cys Ub4 K63R ) blocked K63-Ub4 chains (1.5 µM) were incubated with ARISC–RAP80, ARISC–RAP80 ΔUIMs, or ARISC–RAP80 ΔZnF (10 nM) for the indicated time points. Cleavage activity was analysed by SDS-PAGE and fluorescence scanning ( left ; see Methods ). The disappearance of the K63-Ub4 parent band was quantified using densitometry, and plotted as fraction of substrate consumed (%). Data points are mean ± SEM of two independent experiments ( right ). g , Cyclical and linear K63-Ub5 chains (2 µM) were incubated with ARISC or ARISC–RAP80 (10 nM) for the indicated time points. Cleavage activity was analysed by SDS-PAGE and Oriole staining. Data are representative of two independent experiments. Ub, ubiquitin; DUB, deubiquitylating enzyme. * indicates lower molecular weight ubiquitin species.

Article Snippet: Reactions were stopped with the addition of 3 μL 4x SDS-PAGE loading dye [240 mM Tris-HCl pH 6.8, 40% (v/v) glycerol, 8% (w/v) SDS, 0.04% (w/v) bromophenol blue, and 5% (v/v) β-Mercaptoethanol], and products were separated on 4-12% or 12% Nu-PAGE Bis-Tris gels (Invitrogen).

Techniques: Construct, Ubiquitin Proteomics, Variant Assay, SDS Page, Incubation, Activity Assay, Silver Staining, Fluorescence, Staining, Molecular Weight

Journal: bioRxiv

Article Title: Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex

doi: 10.64898/2026.06.05.730395

Figure Lengend Snippet: a , K63-Ub2, -Ub4, and -Ub7 chains (1 µM) were incubated with ARISC WT or the indicated ARISC variants (5 nM) for 60 minutes. Cleavage activity was analysed by SDS-PAGE and silver staining. Data are representative of two independent experiments. b, SDS-PAGE analysis of ARISC(E33A)–RAP80, ARISC(E33A) BRCC36(S98K) –RAP80, ARISC(E33A) Abraxas1(Δ42-55) –RAP80, and ARISC(E33A) BRCC45(ΔLoop) –RAP80. dStrepII, double StrepII tag. * indicates Abraxas1 degradation product. c, Spectral shift assays measuring binding of labelled ARISC(E33A)–RAP80 or the indicated mutant complexes (40 nM) to cyclical K63-Ub6 chains (20 µM-0 µM). Data points are mean ± SEM of two independent experiments carried out in technical duplicates. Dissociation constants (K d ) are indicated; CI, confidence interval. d, Representative images of WT or mutants BRCC36 IRIF in HT-29 cells 4 h post irradiation (10 Gy). Scale bar is 10 µm. e, Western blots showing BRCC36 protein levels in HT-29 cells reconstituted with WT or mutants BRCC36 as indicated (l eft ). Scatter plot showing quantification of the BRCC36 IRIF described in d . Data represent mean ± SEM derived from n ≥ 300 nuclei examined over two independent experiments; p values are indicated, unpaired two-tailed t test ( right ). f, K63-Ub2, -Ub4, and -Ub7 chains (1 µM) were incubated with ARISC WT or ARISC Δ42-55 (Abraxas1 Δ42-55) (5 nM) for up to 60 minutes. Cleavage activity was analysed as in a . Data are representative of two independent experiments. DUB, deubiquitylating enzyme; WT, wild type; Ub, ubiquitin.

Article Snippet: Reactions were stopped with the addition of 3 μL 4x SDS-PAGE loading dye [240 mM Tris-HCl pH 6.8, 40% (v/v) glycerol, 8% (w/v) SDS, 0.04% (w/v) bromophenol blue, and 5% (v/v) β-Mercaptoethanol], and products were separated on 4-12% or 12% Nu-PAGE Bis-Tris gels (Invitrogen).

Techniques: Incubation, Activity Assay, SDS Page, Silver Staining, Binding Assay, Mutagenesis, Irradiation, Western Blot, Derivative Assay, Two Tailed Test, Ubiquitin Proteomics