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: Molecular and cellular endocrinology

Article Title: SDHB and SDHD silenced pheochromocytoma spheroids respond differently to tumour microenvironment and their aggressiveness is inhibited by impairing stroma metabolism.

doi: 10.1016/j.mce.2022.111594

Figure Lengend Snippet: Fig. 1. Characterization of stable SDHB and SDHD silenced cell lines. (A) Representative blots of the expression of mitochondrial SDHA, B and D subunits. (B) Densitometric analysis of western blot bands, performed by Bio-Rad imaging and analysis software (Quantity One), showed significant differences in the SDHB and SDHD subunit expression levels in SDHB (light grey) and in SDHD silenced cells (dark grey) respectively, compared to Wt (black). Bars are the means of three independent preparations ± SD, ***p < 0.001. (C) Representative traces of SDH enzymatic activity measured in cell homogenates. The silenced SDHB and SDHD cells (dotted and continuous lines, respectively) showed a similar decrease of the SDH activity, significantly different compared with Wt (dashed line). (D) Histogram represents the SDH activity expressed as the percentages. SDHB and SDHD silenced cells (light and dark grey, respectively) showed a significantly decreased of SDH activity compared to Wt (black). Bars are the means of three independent experiments (each of them conducted in duplicate samples) ± SD, ***p < 0.01. (E) The bar graph represents the means of intracellular succinate/fumarate ratio ± SD, measured by GC/MS, in three independent experiments with two replicates. SDHB silenced cells (light grey) showed a significant increase of the metabolites ratio compared with both Wt (black) and to SDHD silenced cells (dark grey), *p < 0.05, **p < 0.01. (F) Representative immunoblot of HIF1α expression in Wt, SDHB and SDHD silenced cells. (G) Optical density analysis of western blot bands. Actin im munoblots was used as loading control. For all the analyses One-way ANOVA post-test Bonferroni was used.

Article Snippet: Bound antibodies were detected using ECL reagents (Immobilon) and analysed with a Bio-Rad ChemiDoc Imaging System (Quantity One) for dedicated chemiluminescent image acquisition.

Techniques: Expressing, Western Blot, Imaging, Software, Activity Assay, Gas Chromatography-Mass Spectrometry, Control