Journal: Nature

Article Title: Structural basis of human transcription-DNA repair coupling.

doi: 10.1038/s41586-021-03906-4

Figure Lengend Snippet: Fig. 1 | Structure of the Pol II–TCR complex. a, Cryo-EM density (left) and ribbon model (right) of the Pol II–CSB–CSA–DDB1–UVSSA complex. The scheme depicts the domain composition and colour code for proteins. The solid black lines mark residues included in the model.

Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used F-12 Pol II antibody, Santa Cruz Biotechnology, sc-55492; anti-mouse HRP conjugate, Abcam, ab5870 Validation Mouse monoclonal antibody to RNA polymerase II subunit A.

Techniques: Cryo-EM Sample Prep

Journal: Nature

Article Title: Structural basis of human transcription-DNA repair coupling.

doi: 10.1038/s41586-021-03906-4

Figure Lengend Snippet: Fig. 2 | Formation and structure of ECTCR. a, Electrophoretic mobility shift assay monitors replacement of DSIF by CSB on the Pol II elongation complex. The gel was scanned in three different channels to reveal the elongation complex (via DNA), DSIF and CSB through different fluorescent labels. The experiment was repeated three times. Asterisks indicate the attachment of

Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used F-12 Pol II antibody, Santa Cruz Biotechnology, sc-55492; anti-mouse HRP conjugate, Abcam, ab5870 Validation Mouse monoclonal antibody to RNA polymerase II subunit A.

Techniques: Electrophoretic Mobility Shift Assay

Journal: Nature

Article Title: Structural basis of human transcription-DNA repair coupling.

doi: 10.1038/s41586-021-03906-4

Figure Lengend Snippet: Fig. 3 | Complete Pol II–TCR complex and ubiquitylation by CRL4CSA. a, In vitro ubiquitylation of the complete Pol II–TCR complex by CRL4CSA. The experiment was repeated two times. For gel source data, see Supplementary Fig. 1. b, Tandem mass spectrometry fragment spectrum of the RPB1 peptide

Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used F-12 Pol II antibody, Santa Cruz Biotechnology, sc-55492; anti-mouse HRP conjugate, Abcam, ab5870 Validation Mouse monoclonal antibody to RNA polymerase II subunit A.

Techniques: In Vitro, Mass Spectrometry

Journal: Nature

Article Title: DAXX represents a new type of protein-folding enabler.

doi: 10.1038/s41586-021-03824-5

Figure Lengend Snippet: Fig. 1 | DAXX prevents protein misfolding and aggregation. a, b, Heat-induced luciferase inactivation (a, 5 nM) and aggregation (b, 200 nM) in presence or absence of GST, DAXX and HSP70–HSP40 at 200 nM (a) or at the indicated molar ratios (b). c, Aggregation of ATXN1(82Q) (50 nM) in the presence or absence of glutathione S-transferase (GST) or DAXX (200 nM each). Raw data for this and other gels are found in Supplementary Fig 1. PE, pelletable aggregates that were soluble with SDS; SN, supernatant. d–f, Fibrillization of α-Syn (70 μM) in the presence GST, HSP70–HSP40, HSPs (HSP70–HSP40–HSP104(A503S)) (200 nM each) and DAXX (100–400 nM) was assayed by ThT-binding (d), electron microscopy (e; red arrows, fibrils; blue arrows, large oligomers; scale bar, 100 nm), and sedimentation followed by dot blot for SDS-soluble and SDS-resistant (SR) aggregates and total α-Syn and by disuccinimidyl suberate (DSS) cross-linking for soluble oligomers (f). IB, immunoblot. g–i, Fibrillization of Aβ42 monomers (10 μM) in the absence or presence of DAXX (50–600 nM) (g, h), and viability of SH-SY5Y cells treated with Aβ42 pre-incubated with or without DAXX (i). An ATP-regeneration system was included with heat-shock proteins but not DAXX (all subsequent experiments with heat-shock proteins, but not experiments with DAXX, also contained an ATP-regeneration system). Data are mean or mean ± s.d. (n = 4 for i, and 3 for the rest) and are representative of three independent experiments. *P < 0.05, NS, not significant; unpaired Student’s t-test.

Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology Animals and other organisms Human research participants Clinical data Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used Antibodies against the following proteins/epitopes were purchased from the indicated sources: GAPDH (sc-47724,Mouse, WB, IP, IF and IHC(P)), His (sc-8036, Mouse, IP, WB, IHC(P), ELISA, IF, FCM), GST (sc-138, Mouse, IP, WB, IHC(P), ELISA, IF, FCM), p53DO1 (sc-126, Mouse, WB, IP, IF, IHC(P) and FCM), Mdm2 (sc-965, Mouse, WB, IP, IF and IHC(P)), DAXX (sc-8043, Mouse IP,WB, IHC(P), ELISA, IF, FCM), α-synuclein syn211 (sc-12767, Mouse, IP, WB, IHC(P), ELISA, IF, and FCM) (Santa Cruz Biotechnology); Flag (#14793, Rabbit, WB, IP, IHC, ChIP, IF, FCM, ELISA) and DAXX (#4533S, Rabbit, WB, IP, IHC, ChIP, IF, FCM, ELISA) (Cell Signaling Technology); p53 (PAb1620, #OP33, Mouse, WB, IP, IF; PAb240, #OP29, Mouse, WB, IP), and Mdm2 (#OP46, Mouse, WB, IP) (Calbiochem); and HA (ab137838, Rabbit, WB, ICC/IF, IP) and Luciferase (ab21176, Rabbit, ICC/IF, WB) (Abcam); βAmyloid 1-42 (#805509) (BioLegend, Mouse, WB, IHC(P), ELISA).

Techniques: Luciferase, Binding Assay, Electron Microscopy, Sedimentation, Dot Blot, Western Blot, Incubation