Journal: Frontiers in Neural Circuits

Article Title: Activity-Dependent Remodeling of Synaptic Protein Organization Revealed by High Throughput Analysis of STED Nanoscopy Images

doi: 10.3389/fncir.2020.00057

Figure Lengend Snippet: Primary and secondary antibodies used for STED imaging.

Article Snippet: Rabbit anti-RIM1/2 , Synaptic Systems , 140203 , 1 : 500 , AA 1 to 466 from rat Rim2 , Dani et al. ( ); Tang et al. ( ) .

Techniques: Imaging, Purification, Recombinant

Journal: Frontiers in Neural Circuits

Article Title: Activity-Dependent Remodeling of Synaptic Protein Organization Revealed by High Throughput Analysis of STED Nanoscopy Images

doi: 10.3389/fncir.2020.00057

Figure Lengend Snippet: Coupling properties of synaptic scaffold protein pairs at low neuronal activity measured with pySODA. (A) Schematic representation of the axial positions of the four synaptic scaffold proteins analyzed in this work. (B) Two examples of representative confocal and STED images of synaptic scaffold pairs. (C) Coupling probability and distance histograms measured for coupled cluster pairs of Bassoon - RIM1/2 (red, n = 16), PSD95 - Homer1c (yellow, n = 6), Bassoon - PSD95 (green, n = 18), Bassoon - Homer1c (blue, n = 17). Each 15 nm bin represents the average coupling probability calculated from the individual images of independent neurons with standard error. (D) Cumulative frequency plots of coupling distance (left) and coupling probability (right) for each synaptic element pair with standard error (shaded area). (C,D) n = number of neurons from 2 independent cultures. Statistical difference between scaffold protein pairs was assessed using a randomization test (see section Materials and Methods and ). Scale bar 250 nm.

Article Snippet: Rabbit anti-RIM1/2 , Synaptic Systems , 140203 , 1 : 500 , AA 1 to 466 from rat Rim2 , Dani et al. ( ); Tang et al. ( ) .

Techniques: Activity Assay

Journal: Frontiers in Neural Circuits

Article Title: Activity-Dependent Remodeling of Synaptic Protein Organization Revealed by High Throughput Analysis of STED Nanoscopy Images

doi: 10.3389/fncir.2020.00057

Figure Lengend Snippet: Activity-dependent re-organization of pre- and postsynaptic scaffolding protein pairs measured with the pySODA analysis framework. (A,E,I,M) Representative two-color STED images of synaptic protein pairs for the activity reducing high Mg 2+ /low Ca 2+ condition (left) or synaptic stimulation 0Mg 2+ /Gly/Bic (right) . Cumulative frequency graphs of the coupling distance (B,F,J,N) and of the coupling probability (C,G,K,O) measured for coupled protein pairs. (D,H,L,P) Histograms of the mean coupling probability per neuron at a given distance. Measurements were performed on two-color STED images of (A–D) the presynaptic protein pair Bassoon - RIM1/2 (High Mg 2+ / low Ca 2+ (gray): n = 16 and 0Mg 2+ /Gly/Bic (red): n = 21); (E–H) the postsynaptic protein pair PSD95 - Homer1c (high Mg 2+ / low Ca 2+ (gray): n = 9 and 0Mg 2+ /Gly/Bic (orange): n = 12); (I–L) the transsynaptic pair Bassoon - PSD95 (High Mg 2+ / low Ca 2+ (gray): n = 18 and 0Mg 2+ /Gly/Bic (green): n = 24) and (M–P) the transsynaptic pair Bassoon - Homer1c (High Mg 2+ / low Ca 2+ (gray): n = 17 and 0Mg 2+ /Gly/Bic (blue): n = 17). Shown are the means (plain lines) with standard error (shaded area). n = number of neurons from 3 independent cultures. Statistical difference was assessed using a randomization test (see section Materials and Methods and ). Exact p -values are reported in , with * p < 0.05, ** p < 0.01, and *** p < 0.001. Scale bar 250 nm.

Article Snippet: Rabbit anti-RIM1/2 , Synaptic Systems , 140203 , 1 : 500 , AA 1 to 466 from rat Rim2 , Dani et al. ( ); Tang et al. ( ) .

Techniques: Activity Assay, Scaffolding

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet: TeNT-LC or BoNT/B overexpression does not promote axon growth in adult DRG neurons (A) Immunoblot of VAMP2 and Tuj1 in L3–L5 DRG extracts 3 weeks after AAV-TeNT-LC-P2A-mCherry or AAV-tdTomato injection into wild-type mice. (B) Quantification of (A). Values are plotted as mean ± SEM; ∗∗∗ p < 0.001 by Student’s t test; n = 3 independent experiments. (C) Representative fluorescence images of Tuj1 (cyan) and TeNT-LC-P2A-mCherry/tdTomato (red) immunolabeled DRG neurons 3 weeks after AAV administration and plated for 15–16 h. Scale bar, 100 μm. (D and E) Length of the longest axon (D) and branching frequency (E) of (C). Values are plotted as mean ± SEM; n = 3–4 independent experiments with 145 tdTomato + neurons, 133 TeNT-LC-P2A-mCherry + neurons. (F) Immunoblot of VAMP2 and Tuj1 in L3–L5 DRG extracts 3 weeks after AAV-Cre-GFP injection into iBOT and wild-type control mice. (G) Quantification of (F). Values are plotted as mean ± SEM; ∗ p < 0.05 by Student’s t test. n = 3 independent experiments. (H) Representative fluorescence images of Tuj1 (red) and Cre-GFP (cyan) immunolabeled DRG neurons 3 weeks after AAV-Cre-GFP administration and plated for 15–16 h. Scale bar, 100 μm. (I and J) Length of the longest axon (I) and branching frequency (J) of (H). Values are plotted as mean ± SEM; n = 3 independent experiments with 100 Cre-GFP + wild-type neurons, 164 Cre-GFP + iBOT neurons. (K) Multiphoton tile scan of GFP + sensory axons (yellow) and GFAP + astrocytes (blue) in the unsectioned spinal cord after complete dorsal column SCI in the given conditions. R, rostral; C, caudal. Asterisks indicate lesion centers. Scale bar, 200 μm. (L) Quantification of (K). Scatterplot with means. n = 7 WT mice and 9 iBOT mice.

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Over Expression, Western Blot, Injection, Fluorescence, Immunolabeling

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet:

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Recombinant, Protease Inhibitor, Software, Microscopy, Plasmid Preparation, Fluorescence, Incubation, Imaging

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet: Munc13-1 suppresses axon growth in adult DRG neurons (A) Normalized expression values of Munc13-1 in DRG at E12.5, E17.5, and adult from 6 to 36 h in culture. ∗∗ p < 0.01 6 versus 24 h, ∗∗ p < 0.01 6 versus 36 h in culture by one-way ANOVA followed by Tukey’s post hoc test; n = 3 technical replicates per condition. (B) Immunoblot of Munc13-1 and Tuj1 in L3-L5 DRG extracts after 6 or 24 h in culture. (C) Quantification of (B). Values are plotted as mean ± SEM; ∗ p < 0.05 by Student’s t test; n = 3 independent experiments. (D) Representative fluorescence images of adult DRG neurons cultured for 6 or 24 h and stained with Munc13-1 and Tuj1 antibodies. Scale bars, 10 μm in outset and 3 μm in inset. (E) Quantification of (D). Values are plotted as mean ± SEM; ∗∗ p < 0.01 by Student’s t test; n = 21 neurons at 6 h, 18 neurons at 24 h from 3 independent experiments. (F) Immunoblot of Munc13-1 and Tuj1 in L3-L5 DRG extracts electroporated with Munc13-1 or tdTomato-expressing plasmids and cultured for 24 h. (G) Quantification of (F). Values are plotted as mean ± SEM; ∗∗∗ p < 0.001 by Student’s t test. n = 3 independent experiments. (H) Representative fluorescence images of uninjured/naive or conditioned/PNL DRG neurons electroporated with Munc13-1-DDK or tdTomato-expressing plasmids. Scale bar, 100 μm. (I and J) Length of the longest axon (I) and branching frequency (J) of (H). Values are plotted as mean ± SEM; ∗∗ p < 0.01 naive tdTomato versus naive Munc13-1-DDK and PNL tdTomato versus PNL Munc13-1-DDK by Student’s t test in (I) and ∗∗ p < 0.01 naive tdTomato versus naive Munc13-1-DDK and PNL tdTomato versus PNL Munc13-1-DDK by Student’s t test in (J); n = 3 independent experiments with 94 naive tdTomato + neurons, 224 naive Munc13-1-DDK + neurons, 125 PNL tdTomato + neurons, 145 PNL Munc13-1-DDK + neurons. (K) XY plot of Munc13-1-DDK mean intensity (arbitrary units) and length of the longest axon for all Munc13-1-DDK + neurons analyzed in (H)–(J). Red line shows linear regression (p < 0.0001).

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Expressing, Western Blot, Fluorescence, Cell Culture, Staining

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet: Munc13 deletion promotes axon growth in adult DRG neurons (A) Scheme of Munc13’s function. (B) Representative images of cultured DRG neurons after AAV-Cre-GFP administration into Munc13-1 fl/fl Munc13-2 KO/KO Munc13-3 KO/KO mice. Cyan arrowheads point to Cre-GFP + neurons, and the white arrowhead points to Cre-GFP – neuron. Scale bar, 15 μm. (C) Quantification of (B). Values are plotted as mean ± SEM; ∗∗ p < 0.01 by Student’s t test; n = 3 independent experiments, 18 GFP + neurons, 22 Cre-GFP + neurons. (D) Immunoblot of Munc13-1 and Tuj1 in L3-L5 DRG extracts 3 weeks after AAV-Cre-GFP injection into Munc13-1 fl/fl Munc13-2 KO/KO Munc13-3 KO/KO mice. (E) Quantification of (D). Values are plotted as mean ± SEM; ∗ p = 0.0192 by Student’s t test; n = 3 independent experiments. (F) Representative fluorescence images of Tuj1 (red) and GFP/Cre-GFP (cyan)-immunolabeled DRG neurons 3 weeks after AAV-GFP or AAV-Cre-GFP administration and plated for 15–16 h. Cyan arrowhead points to Cre-GFP + neuron and white arrowhead points to Cre-GFP – neuron. Scale bar, 200 μm. (G and H) Length of the longest axon (G) and branching frequency (H) of (F). Values are plotted as mean ± SEM; ∗∗∗ p < 0.001 by Student’s t test. n = 3 independent experiments, 102 GFP neurons, 125 Cre-GFP neurons, 116 GFP + PNL neurons. (I) Representative fluorescence images of Tuj1, GFP/Cre-GFP/Cre-RFP, and tdTomato/Munc13-1-DDK/Munc13-1-DN/Munc13-1-H567K/Munc13-1-W464R immunolabeled DRG neurons from Munc13-1 fl/fl Munc13-2 KO/KO Munc13-3 KO/KO mice administered AAV-GFP, AAV-Cre-GFP or AAV-Cre-RFP, transfected with plasmids and cultured for 16–18 h. Scale bar, 200 μm. (J and K) Length of the longest axon (J) and branching frequency (K) of (I). Values are plotted as mean ± SEM; ∗∗∗ p < 0.0001 by one-way ANOVA followed by Tukey’s post hoc test; n = 80 GFP + tdTomato neurons from 5 independent experiments, 64 Cre-GFP + tdTomato neurons from 6 independent experiments, 78 Cre-GFP + Munc13-1 (DDK) neurons from 6 independent experiments, 71 Cre-RFP + Munc13-1-DN neurons from 4 independent experiments, 80 Cre-RFP + Munc13-1-H567K neurons from 5 independent experiments, 81 Cre-RFP + Munc13-1-W464R neurons from 5 independent experiments.

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Cell Culture, Western Blot, Injection, Fluorescence, Immunolabeling, Transfection

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet: Munc13 deletion promotes axon regeneration following adult CNS injury (A) Multiphoton tile scan of GFP + sensory axons (yellow) and GFAP + astrocytes (blue) in the unsectioned spinal cord after complete dorsal column SCI in the given conditions. R, rostral; C, caudal. Asterisks indicate lesion centers. Scale bar, 200 μm. (B) Quantification of (A). Scatterplot with means; ∗∗∗ p < 0.001, ∗∗ p < 0.01 by permutation test. n = 11 animals per group. (C) Scheme of VGCC activation, presynaptic Ca 2+ influx, and vesicle release. (D) Representative fluorescence images of Tuj1 (red) and GFP/Cre-GFP (cyan) immunolabeled DRG neurons from Munc13-1 fl/fl Munc13-2 KO/KO Munc13-3 KO/KO mice administered AAV-GFP or AAV-Cre-GFP and cultured for 24 h in the presence of DMSO, KCl (40 mM), Roscovotine (20 μM), or GV-58 (20 μM). Scale bar, 200 μm. (E and F) Length of the longest axon (E) and branching frequency (F) of AAV-GFP + neurons in (D). Values are plotted as mean ± SEM; ∗∗∗ p < 0.001 GFP DMSO versus GFP KCl, GFP Roscovotine, GFP GV-58 in (E) and ∗∗ p < 0.01 GFP DMSO versus GFP KCl, ∗ p < 0.05 GFP DMSO versus GFP Roscovotine, GFP DMSO versus GFP GV-58 in (F) by one-way ANOVA followed by Tukey’s post hoc test; n = 72 GFP DMSO, 86 GFP GV-58, 37 GFP KCl, 53 GFP Roscovotine-treated neurons from 3 independent experiments. (G and H) Length of the longest axon (G) and branching frequency (H) of AAV-Cre-GFP + neurons in (D). Values are plotted as mean ± SEM n = 82 Cre-GFP DMSO, 92 Cre-GFP GV-58, 48 Cre-GFP KCl, 23 Cre-GFP Roscovotine-treated neurons from 3 independent experiments.

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Activation Assay, Fluorescence, Immunolabeling, Cell Culture

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet: Baclofen promotes axon regeneration following spinal cord injury (A) Whole-cell recording of voltage-activated calcium currents in a cultured DRG neuron one day in vitro . The holding potential was −60 mV, and the calcium current was evoked by 100 ms voltage steps from −60 to 50 mV in 10 mV increments. (B) Raw traces of calcium currents in cultured DRG neurons before and after bath application of Baclofen (100 μM). (C) Plot of all DRG neurons indicating the reduction of the voltage-activated calcium current in response to Baclofen administration. (D) Quantification of (C). Values are plotted as mean ± SEM; ∗∗∗ p = 0.001 by Wilcoxon matched-pairs signed-rank test; n = 11 neurons. (E) Representative fluorescence images of Tuj1 (red) and GFP/Cre-GFP (cyan)-immunolabeled DRG neurons from Munc13-1 fl/fl Munc13-2 KO/KO Munc13-3 KO/KO mice administered AAV-GFP or AAV-Cre-GFP and cultured for 15–16 h in the presence of vehicle or Baclofen (100 μM). Scale bar, 100 μm. (F and G) Length of the longest axon (F) and branching frequency (G) of DRG neurons cultured for 15–16 h in the presence of vehicle or Baclofen (10 μM, 100 μM, or 500 μM). Values are plotted as mean ± SEM; ∗ p < 0.05 vehicle versus 10 μM, ∗∗ p < 0.01 vehicle versus 100 μM, vehicle versus 500 μM by one-way ANOVA followed by Tukey’s post hoc test in (F); ∗∗ p < 0.01 vehicle versus 10 μM, ∗∗∗ p < 0.001 vehicle versus 100 μM, vehicle versus 500 μM by one-way ANOVA followed by Tukey’s post hoc test in (G); n = 235 vehicle, 136 10 μM, 122 100 μM, 156 500 μM Baclofen-treated neurons from 3–4 independent experiments. (H and I) Length of the longest axon (H) and branching frequency (I) of (E). Values are plotted as mean ± SEM; ∗ p < 0.05 GFP + vehicle versus GFP + Baclofen, ∗∗ p < 0.01 GFP + Baclofen versus Cre-GFP + vehicle, p = 0.9024 Cre-GFP + vehicle versus Cre-GFP + Baclofen in (H), ∗∗∗ p < 0.0001 GFP + vehicle versus GFP + Baclofen, ∗ p < 0.05 GFP + Baclofen versus Cre-GFP + vehicle in (I) by one-way ANOVA followed by Tukey’s post hoc test; n = 68 GFP + vehicle, 73 GFP + Baclofen, 62 Cre-GFP + vehicle, 58 Cre-GFP + Baclofen neurons from 3 independent experiments. (J) Multiphoton tile scan of GFP + sensory axons (yellow) and GFAP + astrocytes (blue) in the unsectioned spinal cord after complete dorsal column SCI in the given conditions. R, rostral; C, caudal. Asterisks indicate lesion centers. Scale bar, 200 μm. (K) Quantification of (J). Scatterplot with means; ∗∗ p < 0.01, ∗ p < 0.05, # p < 0.1 by permutation test. n = 8 animals per group. See also Figure S5 .

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Cell Culture, In Vitro, Fluorescence, Immunolabeling

Journal: Neuron

Article Title: An active vesicle priming machinery suppresses axon regeneration upon adult CNS injury

doi: 10.1016/j.neuron.2021.10.007

Figure Lengend Snippet:

Article Snippet: The following primary antibodies were used: anti-VAMP2 (1:1000, Synaptic Systems #104 211, mouse monoclonal), anti-Munc13-1 (1:2000, Synaptic Systems #126 103, rabbit polyclonal), anti-RIM1 (1:500; Synaptic Systems #140 003, rabbit polyclonal), anti-RIM2 (1:500; Synaptic Systems #140 103, rabbit polyclonal), anti-tuj1 (1:10000, Sigma #T2200, rabbit polyclonal).

Techniques: Recombinant, Protease Inhibitor, Software, Microscopy, Plasmid Preparation, Fluorescence, Incubation, Imaging

Journal: Molecular cell

Article Title: Molecular basis for control of diverse genome stability factors by the multi-BRCT scaffold Rtt107

doi: 10.1016/j.molcel.2019.05.035

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Yeast strains are listed in the . table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-HA mouse monoclonal IgG2a (Clone: F-7) Santa Cruz Biotech Cat# sc-7392, RRID: AB_627809 Anti-Myc mouse monoclonal IgG1 (Clone: 9E10) Bio X Cell Cat# BE0238, RRID: AB_2687720 Anti-Flag mouse monoclonal IgG1 (Clone: M2) Sigma-Aldrich Cat# F1804, RRID: AB_262044 Anti-TAP rabbit antibody Sigma-Aldrich Cat# P1291, RRID: AB_1079562 Anti-Pgk1 mouse monoclonal IgG1 (Clone: 22C5D8) Invitrogen Cat# 459250, RRID: AB_2532235 Anti-Histone H3 rabbit antibody Abcam Cat# ab46765, RRID: AB_880439 Anti-mouse HRP-linked antibody GE Healthcare Cat# NA 931V, RRID: AB_772210 Anti-rabbit HRP-linked antibody GE Healthcare Cat# NA 934V, RRID: AB_772206 Bacterial Strains TOP10 Chemically Competent Cells Invitrogen Cat# C4040-10 BL21(DE3) Competent Cells - Novagen EMD Millipore Cat# 69450-4 Chemicals, Peptides, and Recombinant Proteins 2-nitrophenyl β-D-galactopyranoside (ONPG) Sigma-Aldrich Cat# N1127-5G ULP1 Protease Home-made N/A PreScission (3C) Protease GE Healthcare Cat# 27084301 Deposited Data Structure of Rtt107 NTD (tetra-BRCT) This paper PDB: 6J0V Structure of Rtt107 NTD -Nse6 RIM This paper PDB: 6J0W Structure of Rtt107 NTD -Mms22 RIM This paper PDB: 6J0X Structure of Rtt107 NTD -Slx4 RIM2 This paper PDB: 6J0Y Mendeley Dataset This paper http://dx.doi.org/null/bj532s6vd4.1 Recombinant DNA pRS315-YEL072W:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1378 pRS315-YEL068C:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1379 pFA6a-4GS-6HA::NAT (for yeast gene tagging PCR) This paper pXZ1043 pBTM116-Rtt107 NTD (2-513a.a.)

Techniques: Recombinant, Expressing, Software

Journal: Molecular cell

Article Title: Molecular basis for control of diverse genome stability factors by the multi-BRCT scaffold Rtt107

doi: 10.1016/j.molcel.2019.05.035

Figure Lengend Snippet: (A) Schematic of Rtt107 domains and interacting proteins.

Article Snippet: Yeast strains are listed in the . table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-HA mouse monoclonal IgG2a (Clone: F-7) Santa Cruz Biotech Cat# sc-7392, RRID: AB_627809 Anti-Myc mouse monoclonal IgG1 (Clone: 9E10) Bio X Cell Cat# BE0238, RRID: AB_2687720 Anti-Flag mouse monoclonal IgG1 (Clone: M2) Sigma-Aldrich Cat# F1804, RRID: AB_262044 Anti-TAP rabbit antibody Sigma-Aldrich Cat# P1291, RRID: AB_1079562 Anti-Pgk1 mouse monoclonal IgG1 (Clone: 22C5D8) Invitrogen Cat# 459250, RRID: AB_2532235 Anti-Histone H3 rabbit antibody Abcam Cat# ab46765, RRID: AB_880439 Anti-mouse HRP-linked antibody GE Healthcare Cat# NA 931V, RRID: AB_772210 Anti-rabbit HRP-linked antibody GE Healthcare Cat# NA 934V, RRID: AB_772206 Bacterial Strains TOP10 Chemically Competent Cells Invitrogen Cat# C4040-10 BL21(DE3) Competent Cells - Novagen EMD Millipore Cat# 69450-4 Chemicals, Peptides, and Recombinant Proteins 2-nitrophenyl β-D-galactopyranoside (ONPG) Sigma-Aldrich Cat# N1127-5G ULP1 Protease Home-made N/A PreScission (3C) Protease GE Healthcare Cat# 27084301 Deposited Data Structure of Rtt107 NTD (tetra-BRCT) This paper PDB: 6J0V Structure of Rtt107 NTD -Nse6 RIM This paper PDB: 6J0W Structure of Rtt107 NTD -Mms22 RIM This paper PDB: 6J0X Structure of Rtt107 NTD -Slx4 RIM2 This paper PDB: 6J0Y Mendeley Dataset This paper http://dx.doi.org/null/bj532s6vd4.1 Recombinant DNA pRS315-YEL072W:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1378 pRS315-YEL068C:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1379 pFA6a-4GS-6HA::NAT (for yeast gene tagging PCR) This paper pXZ1043 pBTM116-Rtt107 NTD (2-513a.a.)

Techniques:

Journal: Molecular cell

Article Title: Molecular basis for control of diverse genome stability factors by the multi-BRCT scaffold Rtt107

doi: 10.1016/j.molcel.2019.05.035

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Yeast strains are listed in the . table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-HA mouse monoclonal IgG2a (Clone: F-7) Santa Cruz Biotech Cat# sc-7392, RRID: AB_627809 Anti-Myc mouse monoclonal IgG1 (Clone: 9E10) Bio X Cell Cat# BE0238, RRID: AB_2687720 Anti-Flag mouse monoclonal IgG1 (Clone: M2) Sigma-Aldrich Cat# F1804, RRID: AB_262044 Anti-TAP rabbit antibody Sigma-Aldrich Cat# P1291, RRID: AB_1079562 Anti-Pgk1 mouse monoclonal IgG1 (Clone: 22C5D8) Invitrogen Cat# 459250, RRID: AB_2532235 Anti-Histone H3 rabbit antibody Abcam Cat# ab46765, RRID: AB_880439 Anti-mouse HRP-linked antibody GE Healthcare Cat# NA 931V, RRID: AB_772210 Anti-rabbit HRP-linked antibody GE Healthcare Cat# NA 934V, RRID: AB_772206 Bacterial Strains TOP10 Chemically Competent Cells Invitrogen Cat# C4040-10 BL21(DE3) Competent Cells - Novagen EMD Millipore Cat# 69450-4 Chemicals, Peptides, and Recombinant Proteins 2-nitrophenyl β-D-galactopyranoside (ONPG) Sigma-Aldrich Cat# N1127-5G ULP1 Protease Home-made N/A PreScission (3C) Protease GE Healthcare Cat# 27084301 Deposited Data Structure of Rtt107 NTD (tetra-BRCT) This paper PDB: 6J0V Structure of Rtt107 NTD -Nse6 RIM This paper PDB: 6J0W Structure of Rtt107 NTD -Mms22 RIM This paper PDB: 6J0X Structure of Rtt107 NTD -Slx4 RIM2 This paper PDB: 6J0Y Mendeley Dataset This paper http://dx.doi.org/null/bj532s6vd4.1 Recombinant DNA pRS315-YEL072W:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1378 pRS315-YEL068C:: URA3/CAN1 (for W303 GCR strain) R. Kolodner pRDK1379 pFA6a-4GS-6HA::NAT (for yeast gene tagging PCR) This paper pXZ1043 pBTM116-Rtt107 NTD (2-513a.a.)

Techniques: Recombinant, Expressing, Software