Journal: bioRxiv

Article Title: Bone morphogenetic protein 4 reduces global H3K4me3 to inhibit proliferation and promote differentiation of human neural stem cells

doi: 10.1101/2020.01.22.915934

Figure Lengend Snippet: A. Gross anatomy of partial fetal SVZ architecture and localization of H3K4me3 positive cells. View of fetal brain in the area of the lateral ventricle (LV), showing the SVZ with H3K4me3 positive cells. Top panel: H&E staining (LV and SVZ are separated by a green dashed line). Bottom panel: immunostaining with H3K4me3 antibody (LV and SVZ are separated by a red dashed line). B. Immunofluorescence of human StemPro® NSC neurospheres positive for NESTIN, SOX2, CD133 and OCT4 and differentiated cells positive for MUSHASHI, GFAP, TUJ1 and O4. C. Real-time PCR showing hSETD1A and WDR82 expression in spheres and differentiated human StemPro® NSCs. D. Western blots using total protein extracts and histone from un- (UD) and -differentiated (Diff) cells. Error bars show the standard error of three independent experiments (** p<0.01).

Article Snippet: Human short interference RNA (siRNA) against human SETD1A (Gene ID 9739, Cat# SR306505), short hairpin RNA (shRNA) against WDR82 (Gene ID 80335, Cat#TG301034), and scrambled control shRNA cassette in pGFP-V-RS Vector (Cat#TR30013) were purchased from Origene (Rockville, MD, USA).

Techniques: Staining, Immunostaining, Immunofluorescence, Real-time Polymerase Chain Reaction, Expressing, Western Blot

Journal: bioRxiv

Article Title: Bone morphogenetic protein 4 reduces global H3K4me3 to inhibit proliferation and promote differentiation of human neural stem cells

doi: 10.1101/2020.01.22.915934

Figure Lengend Snippet: A. Western blots shows WDR82 and human SETD1A/B expression following 100ng/ml BMP4 treatment. B. Representative images and quantitative graphs showing sphere formation in human StemPro® NSCs following treatment with siRNA for hSETD1A (siSETD1A) or shRNA for WDR82 (shWDR82) vectors versus controls (control siRNA, siCtrl and scrambled shRNA, scrCtrl). C and D. Real-time PCR (C) and western blots (D) showing expression of hSETD1A, WDR82, OCT4, CCND1 and NESTIN, following treatments as in B. E. Real-time PCR using DNA from ChIP with rabbit IgG and H3K4me3 and detected with promoter primers for OCT4, CCND1 and NESTIN following treatment with siSETD1A, shWDR82 or siCtrl, scrCtrl, in StemPro® NSCs. Error bars show the standard error of three independent experiments. (* p<0.05, ** p<0.01)

Article Snippet: Human short interference RNA (siRNA) against human SETD1A (Gene ID 9739, Cat# SR306505), short hairpin RNA (shRNA) against WDR82 (Gene ID 80335, Cat#TG301034), and scrambled control shRNA cassette in pGFP-V-RS Vector (Cat#TR30013) were purchased from Origene (Rockville, MD, USA).

Techniques: Western Blot, Expressing, shRNA, Control, Real-time Polymerase Chain Reaction

Journal: bioRxiv

Article Title: Bone morphogenetic protein 4 reduces global H3K4me3 to inhibit proliferation and promote differentiation of human neural stem cells

doi: 10.1101/2020.01.22.915934

Figure Lengend Snippet: A. Representative images and quantitative graphs show sphere formation from HAs following transfection with WDR82 (pcDNA3-WDR82) or human SETD1A (pET28-hSETD1A-MHL) expression plasmids, in comparison to controls (pcDNA3 and pET28- MHL). B and C. Real-time PCR (B) and western blots (C) show expression of hSETD1A, WDR82, OCT4, CCND1 and NESTIN. D. ChIP with rabbit IgG and H3K4me3 combined with real-time PCR using promoter primers for OCT4, CCND1 and NESTIN following HA transfection. Error bars show the standard deviation of three independent experiments. (* p<0.05, ** p<0.01)

Article Snippet: Human short interference RNA (siRNA) against human SETD1A (Gene ID 9739, Cat# SR306505), short hairpin RNA (shRNA) against WDR82 (Gene ID 80335, Cat#TG301034), and scrambled control shRNA cassette in pGFP-V-RS Vector (Cat#TR30013) were purchased from Origene (Rockville, MD, USA).

Techniques: Transfection, Expressing, Comparison, Real-time Polymerase Chain Reaction, Western Blot, Standard Deviation

Journal: bioRxiv

Article Title: Bone morphogenetic protein 4 reduces global H3K4me3 to inhibit proliferation and promote differentiation of human neural stem cells

doi: 10.1101/2020.01.22.915934

Figure Lengend Snippet: Schematic diagram showing that BMP4 decreases levels of H3K4me3 mediated by hSETD1A-WDR82 at promoters of key regulators to promote differentiation and inhibit proliferation of human neural stem cells (NSCs).

Article Snippet: Human short interference RNA (siRNA) against human SETD1A (Gene ID 9739, Cat# SR306505), short hairpin RNA (shRNA) against WDR82 (Gene ID 80335, Cat#TG301034), and scrambled control shRNA cassette in pGFP-V-RS Vector (Cat#TR30013) were purchased from Origene (Rockville, MD, USA).

Techniques:

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A) Permutation tests (n=20,000, randomization method: circularRandomizeRegions) indicate there is significant overlaps between conserved and chromatin accessible Setd1a ChIP-Seq peaks (P = 0.0055, Z-score = 2.9) and established SCZ-GWAS loci identified. X-axis is the number of overlaps, Y-axis is the density of expected number of overlaps determined by permutation. EVperm, Expected average number of overlaps by permutation, EVobs, actual observed number of overlaps. Permutation P value threshold = 0.05.

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: ChIP-sequencing

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A) Representative ChIP-Seq locus (Kmt2a gene). Normalized reads per genomic coverage from PFC ChIP-Seq for Setd1a (black) and chromatin marks (H3K4me1, red; H3K4me2, orange; H3K4me3, blue; H3K27ac, green) are shown. Black boxes below the Setd1a track depict significant peaks that passed all quality checks (see Methods).

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: ChIP-sequencing

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A-B) Volcano plots of differentially expressed genes in whole-PFC RNA-Seq of Setd1a+/− mice are depicted in (A). 342 differentially expressed genes (FDR<5%) are shown in red, while non-significant changes are shown in grey (left panel). Of the 342 differentially expressed genes, 271 are Setd1a targets (orange and blue, right panel). We partitioned these genes in 4 categories based on the binding regions of Setd1a in the PFC. We defined ‘Setd1a bound promoters up-regulated genes’ and ‘Setd1a bound promoters down-regulated genes’ as genes in which promoters are bound by Setd1a. We defined ‘Setd1a bound enhancers up-regulated genes’ and ‘Setd1a bound enhancers down-regulated genes’ as genes in which enhancers, but not promoters, are bound by Setd1a. Genes with Setd1a binding at both promoters and enhancers, were partitioned into the “Setd1a-promoter bound” classes. A summary of the number of genes in each category is shown in (B).

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: RNA Sequencing Assay, Binding Assay

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A) Restoration of knockout-first allele after TAM treatment. For the rescue experiments, Setd1a+/− mice were crossed to R26FlpoER mice. FLP (Flpo) induced globally by TAM converts the “knockout-first” allele to a conditional allele, restoring gene activity.

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: Knock-Out, Activity Assay

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A) Neurod6 locus. ChIP-Seq of LSD1 (grey), Setd1a (black), Mef2 (dark blue), H3K27ac (green), H3K4me3 (light blue) is shown. Grey, black and dark blue boxes below Lsd1, Setd1a and Mef2 tracks respectively represent significant peaks that passed all quality checks (see methods).

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: ChIP-sequencing

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Setd1a CDS vector , Origene , Cat# MR215352.

Techniques: Virus, Recombinant, Luciferase, Plasmid Preparation, Software

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: A. A volcano plot is used to depict RNA-seq data. Three independent samples on Setd1a+/+ and Setd1aΔ/Δ leukemia cells were analyzed. Significantly downregulated DNA repair genes classified by GO analysis (see also Figure S4A) are shown as red dots.

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: RNA Sequencing

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: A. The human SETD1A deletion mutant constructs are shown as schematic illustrations.

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: Mutagenesis, Construct

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: A. Relative expression level of Setd1a in MLL-AF9 leukemia cells was quantified by qRT-PCR at 4 days post-tamoxifen treatment. This experiment was repeated 3 times with 3 biological replicates in each experiment.

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: Expressing, Quantitative RT-PCR

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: A. SETD1A-binding proteins were identified by Co-IP MS. Proteins were visualized by silver stain (left) and excised from the gel. 68 proteins were identified as SETD1A-binding proteins (right box outlined in grey) and 11 proteins were classified as DNA damage response-associated proteins in GO analysis (red circle). The ranks of signal intensity are shown in brackets.

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: Binding Assay, Co-Immunoprecipitation Assay, Silver Staining

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: A. Density of ChIP-seq reads for SETD1A (red) and RNAP2 (blue) of SETD1A positive TSS (n=18396) from Ren shRNA or Setd1a shRNA–expressing NIH3T3 cells are shown. Regions are ranked according to log2 fold change of SETD1A signal intensity between Ren and Setd1a shRNA.

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: ChIP-sequencing, shRNA, Expressing

Journal: Cell

Article Title: A non-catalytic function of SETD1A regulates Cyclin-K and the DNA damage response

doi: 10.1016/j.cell.2018.01.032

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Myc- and DDK-tagged human SETD1A ( {"type":"entrez-nucleotide","attrs":{"text":"NM_014712","term_id":"1519314153","term_text":"NM_014712"}} NM_014712 ) and SETD1B ( {"type":"entrez-nucleotide","attrs":{"text":"NM_015048","term_id":"210032579","term_text":"NM_015048"}} NM_015048 ) cDNA were obtained from Origene and DDK-tagged human CCNK ( {"type":"entrez-nucleotide","attrs":{"text":"NM_001099402","term_id":"1653961938","term_text":"NM_001099402"}} NM_001099402 ) cDNA was obtained from GenScript.

Techniques: Mass Spectrometry, Knock-In, shRNA, Recombinant, Plasmid Preparation, Software