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HIST1H2BG, NT (HIST1H2BC, H2BFL, Histone H2B type 1-C/E/F/G/I, Histone H2B.1 A, Histone H2B.a, Histone H2B.g, Histone H2B.h, Histone H2B.k, Histone H2B.l) (Biotin) Catalog number 036594-Biotin Supplier United States Biological Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq]. Applications Suitable for use in Western Blot, ELISA Recommended Dilution ELISA: 1:1,000 Western Blot: 1:100-500 Storage and Stability Store product at 4°C if to be used immediately within two weeks. For long-term storage, aliquot to avoid repeated freezing and thawing and store at -20°C. Aliquots are stable at -20°C for 12 months after receipt. Dilute required amount only prior to immediate use. Further dilutions can be made in assay buffer. For maximum recovery of product, centrifuge the original vial after thawing and prior to removing the cap. Note Applications are based on unconjugated antibody. Immunogen HIST1H2BG antibody is generated from rabbits immunized with a KLH conjugated synthetic peptide between 1-30 amino acids from the N-terminal region of human HIST1H2BG. Formulation Supplied as a liquid in PBS, pH 7.2. No preservative added. Labeled with Biotin. Purity Purified by Protein A affinity chromatography. Specificity Human Product Type Pab Source human Isotype IgG Grade Affinity Purified Applications E WB Crossreactivity Hu Storage -20°C Detection Method Biotin Reference Kim, S.C., et al. Mol. Cell 23(4):607-618(2006) Beck, H.C., et al. Mol. Cell Proteomics 5(7):1314-1325(2006) Pavri, R., et al. Cell 125(4):703-717(2006) Bonenfant, D., et al. Mol. Cell Proteomics 5(3):541-552(2006) Zhu, B., et al. Mol. Cell 20(4):601-611(2005) Powered by TCPDF (www.tcpdf.org).

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Supplementary Figure S1. Results of flow cytometry analysis, performed to estimate CD34 positivity, after immunomagnetic separation in two different experiments. As monoclonal antibody for labeling the sample, the fluorescein isothiocyanate (FITC)- conjugated mouse anti-human CD34 MoAb (Mylteni) was used. Briefly, cell samples were incubated in the presence of the indicated MoAbs, at the proper dilution, in PBS containing 5% FCS and 1% Fc receptor (FcR) blocking reagent (Miltenyi) for 30 min at 4 C. Cells were then washed twice, resuspended with PBS and analyzed by a Coulter Epics XL (Coulter Electronics Inc., Hialeah, FL, USA) flow cytometer. only use Non-commercial 1 Supplementary Table S1. Complete list of the datasets used in this study and their sources. GEO Total samples Geo selected GEO accession of used Platform Reference series in series samples samples GSM142565 GSM142566 GSM142567 GSM142568 GSE6146 HG-U133A 14 8 - GSM142569 GSM142571 GSM142572 GSM142574 GSM51391 GSM51392 GSE2666 HG-U133A 36 4 1 GSM51393 GSM51394 only GSM321583 GSE12803 HG-U133A 20 3 GSM321584 2 GSM321585 use Promyelocytes_1 Promyelocytes_2 Promyelocytes_3 Promyelocytes_4 HG-U133A 8 8 3 GSE64282 Promyelocytes_5 Promyelocytes_6 Promyelocytes_7 Promyelocytes_8 Non-commercial 2 Supplementary Table S2. Chromosomal regions up-regulated in CD34+ samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/)
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MYC-Containing Amplicons in Acute Myeloid Leukemia: Genomic Structures, Evolution, and Transcriptional Consequences
Leukemia (2018) 32:2152–2166 https://doi.org/10.1038/s41375-018-0033-0 ARTICLE Acute myeloid leukemia Corrected: Correction MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences 1 1 2 2 1 Alberto L’Abbate ● Doron Tolomeo ● Ingrid Cifola ● Marco Severgnini ● Antonella Turchiano ● 3 3 1 1 1 Bartolomeo Augello ● Gabriella Squeo ● Pietro D’Addabbo ● Debora Traversa ● Giulia Daniele ● 1 1 3 3 4 Angelo Lonoce ● Mariella Pafundi ● Massimo Carella ● Orazio Palumbo ● Anna Dolnik ● 5 5 6 2 7 Dominique Muehlematter ● Jacqueline Schoumans ● Nadine Van Roy ● Gianluca De Bellis ● Giovanni Martinelli ● 3 4 8 1 Giuseppe Merla ● Lars Bullinger ● Claudia Haferlach ● Clelia Tiziana Storlazzi Received: 4 August 2017 / Revised: 27 October 2017 / Accepted: 13 November 2017 / Published online: 22 February 2018 © The Author(s) 2018. This article is published with open access Abstract Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene ampliﬁcation in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This 1234567890();,: revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres.
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Mutational Landscape of Uterine and Ovarian Carcinosarcomas Implicates Histone Genes in Epithelial–Mesenchymal Transition
Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition Siming Zhaoa,b, Stefania Bellonec, Salvatore Lopezc, Durga Thakrala,b, Carlton Schwabc, Diana P. Englishc, Jonathan Blackc, Emiliano Coccoc, Jungmin Choia,b, Luca Zammataroc, Federica Predolinic, Elena Bonazzolic, Mark Bia,b, Natalia Buzad, Pei Huid, Serena Wongd, Maysa Abu-Khalafe, Antonella Ravaggif, Eliana Bignottif, Elisabetta Bandieraf, Chiara Romanif, Paola Todeschinif, Renata Tassif, Laura Zanottif, Franco Odicinof, Sergio Pecorellif, Carla Donzellig, Laura Ardighierig, Fabio Facchettig, Marcella Falchettig, Dan-Arin Silasic, Elena Ratnerc, Masoud Azodic, Peter E. Schwartzc, Shrikant Manea,b, Roberto Angiolih, Corrado Terranovah, Charles Matthew Quicki, Babak Edrakij, Kaya Bilgüvara,b, Moses Leek, Murim Choik, Amy L. Stieglerl, Titus J. Boggonl, Joseph Schlessingerl, Richard P. Liftona,b,m,1, and Alessandro D. Santinc aDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510; bHoward Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510; cDepartment of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510; dDepartment of Pathology, Yale University School of Medicine, New Haven, CT 06510; eInternal Medicine & Oncology, Yale University School of Medicine, New Haven, CT 06510; f“Angelo Nocivelli” Institute of Molecular Medicine, Department of Obstetrics & Gynecology, University of Brescia, 25100 Brescia, Italy;
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A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context.
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DIPPER, a Spatiotemporal Proteomics Atlas of Human Intervertebral Discs
TOOLS AND RESOURCES DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics Vivian Tam1,2†, Peikai Chen1†‡, Anita Yee1, Nestor Solis3, Theo Klein3§, Mateusz Kudelko1, Rakesh Sharma4, Wilson CW Chan1,2,5, Christopher M Overall3, Lisbet Haglund6, Pak C Sham7, Kathryn Song Eng Cheah1, Danny Chan1,2* 1School of Biomedical Sciences, , The University of Hong Kong, Hong Kong; 2The University of Hong Kong Shenzhen of Research Institute and Innovation (HKU-SIRI), Shenzhen, China; 3Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, Canada; 4Proteomics and Metabolomics Core Facility, The University of Hong Kong, Hong Kong; 5Department of Orthopaedics Surgery and Traumatology, HKU-Shenzhen Hospital, Shenzhen, China; 6Department of Surgery, McGill University, Montreal, Canada; 7Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Hong Kong Abstract The spatiotemporal proteome of the intervertebral disc (IVD) underpins its integrity *For correspondence: and function. We present DIPPER, a deep and comprehensive IVD proteomic resource comprising [email protected] 94 genome-wide profiles from 17 individuals. To begin with, protein modules defining key †These authors contributed directional trends spanning the lateral and anteroposterior axes were derived from high-resolution equally to this work spatial proteomes of intact young cadaveric lumbar IVDs. They revealed novel region-specific Present address: ‡Department profiles of regulatory activities
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Associated R-Loops at Near-Nucleotide Resolution Using Bisdrip-Seq Jason G Dumelie, Samie R Jaffrey*
TOOLS AND RESOURCES Defining the location of promoter- associated R-loops at near-nucleotide resolution using bisDRIP-seq Jason G Dumelie, Samie R Jaffrey* Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, United States Abstract R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP- seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron- containing genes, R-loops are bounded between the transcription start site and the first exon- intron junction. In intronless genes, the 3’ boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation. DOI: https://doi.org/10.7554/eLife.28306.001 *For correspondence: Introduction [email protected] R-loops are nucleic acid structures in which a strand of RNA is hybridized to a strand of DNA, while Competing interests: The the other strand of DNA is looped out. Recent techniques for genome-wide mapping of R-loops authors declare that no revealed that promoter regions are enriched in R-loops (Ginno et al., 2012).
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Table 3: Average Gene Expression Profiles by Chromosome
Supplemental Data Table 1: Experimental Setup Correlation Array Reverse Fluor Array Extraction Coefficient Print Batch (Y/N) mean (range) DLD1-I.1 I A N DLD1-I.2 I B N 0.86 DLD1-I.3 I C N (0.79-0.90) DLD1-I.4 I C Y DLD1 DLD1-II.1 II D N DLD1-II.2 II E N 0.86 DLD1-II.3 II F N (0.74-0.94) DLD1-II.4 II F Y DLD1+3-II.1 II A N DLD1+3-II.2 II A N 0.85 DLD1 + 3 DLD1+3-II.3 II B N (0.64-0.95) DLD1+3-II.4 II B Y DLD1+7-I.1 I A N DLD1+7-I.2 I A N 0.79 DLD1 + 7 DLD1+7-I.3 I B N (0.68-0.90) DLD1+7-I.4 I B Y DLD1+13-I.1 I A N DLD1+13-I.2 I A N 0.88 DLD1 + 13 DLD1+13-I.3 I B N (0.84-0.91) DLD1+13-I.4 I B Y hTERT-HME-I.1 I A N hTERT-HME-I.2 I B N 0.85 hTERT-HME hTERT-HME-I.3 I C N (0.80-0.92) hTERT-HME-I.4 I C Y hTERT-HME+3-I.1 I A N hTERT-HME+3-I.2 I B N 0.84 hTERT-HME + 3 hTERT-HME+3-I.3 I C N (0.74-0.90) hTERT-HME+3-I.4 I C Y Supplemental Data Table 2: Average gene expression profiles by chromosome arm DLD1 hTERT-HME Ratio.7 Ratio.1 Ratio.3 Ratio.3 Chrom.
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A Multiprotein Occupancy Map of the Mrnp on the 3 End of Histone
Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press A multiprotein occupancy map of the mRNP on the 3′ end of histone mRNAs LIONEL BROOKS III,1 SHAWN M. LYONS,2 J. MATTHEW MAHONEY,1 JOSHUA D. WELCH,3 ZHONGLE LIU,1 WILLIAM F. MARZLUFF,2 and MICHAEL L. WHITFIELD1 1Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA 2Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA 3Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599, USA ABSTRACT The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem– loop (SL) structure. This SL structure interacts with the stem–loop binding protein (SLBP), which is involved in all aspects of RD- histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprecipitate (HITS-CLIP) to analyze the RNA-binding landscape of SLBP. SLBP was not bound to any RNAs other than histone mRNAs. We performed bioinformatic analyses of the HITS-CLIP data that included (i) clustering genes by sequencing read coverage using CVCA, (ii) mapping the bound RNA fragment termini, and (iii) mapping cross-linking induced mutation sites (CIMS) using CLIP-PyL software. These analyses allowed us to identify specific sites of molecular contact between SLBP and its RD-histone mRNA ligands. We performed in vitro crosslinking assays to refine the CIMS mapping and found that uracils one and three in the loop of the histone mRNA SL preferentially crosslink to SLBP, whereas uracil two in the loop preferentially crosslinks to a separate component, likely the 3′hExo.
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Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis
Getting “Under the Skin”: Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis by Kristen Monét Brown A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Epidemiological Science) in the University of Michigan 2017 Doctoral Committee: Professor Ana V. Diez-Roux, Co-Chair, Drexel University Professor Sharon R. Kardia, Co-Chair Professor Bhramar Mukherjee Assistant Professor Belinda Needham Assistant Professor Jennifer A. Smith © Kristen Monét Brown, 2017 [email protected] ORCID iD: 0000-0002-9955-0568 Dedication I dedicate this dissertation to my grandmother, Gertrude Delores Hampton. Nanny, no one wanted to see me become “Dr. Brown” more than you. I know that you are standing over the bannister of heaven smiling and beaming with pride. I love you more than my words could ever fully express. ii Acknowledgements First, I give honor to God, who is the head of my life. Truly, without Him, none of this would be possible. Countless times throughout this doctoral journey I have relied my favorite scripture, “And we know that all things work together for good, to them that love God, to them who are called according to His purpose (Romans 8:28).” Secondly, I acknowledge my parents, James and Marilyn Brown. From an early age, you two instilled in me the value of education and have been my biggest cheerleaders throughout my entire life. I thank you for your unconditional love, encouragement, sacrifices, and support. I would not be here today without you. I truly thank God that out of the all of the people in the world that He could have chosen to be my parents, that He chose the two of you.
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Supplemental Data.Pdf
Supplementary material -Table of content Supplementary Figures (Fig 1- Fig 6) Supplementary Tables (1-13) Lists of genes belonging to distinct biological processes identified by GREAT analyses to be significantly enriched with UBTF1/2-bound genes Supplementary Table 14 List of the common UBTF1/2 bound genes within +/- 2kb of their TSSs in NIH3T3 and HMECs. Supplementary Table 15 List of gene identified by microarray expression analysis to be differentially regulated following UBTF1/2 knockdown by siRNA Supplementary Table 16 List of UBTF1/2 binding regions overlapping with histone genes in NIH3T3 cells Supplementary Table 17 List of UBTF1/2 binding regions overlapping with histone genes in HMEC Supplementary Table 18 Sequences of short interfering RNA oligonucleotides Supplementary Table 19 qPCR primer sequences for qChIP experiments Supplementary Table 20 qPCR primer sequences for reverse transcription-qPCR Supplementary Table 21 Sequences of primers used in CHART-PCR Supplementary Methods Supplementary Fig 1. (A) ChIP-seq analysis of UBTF1/2 and Pol I (POLR1A) binding across mouse rDNA. UBTF1/2 is enriched at the enhancer and promoter regions and along the entire transcribed portions of rDNA with little if any enrichment in the intergenic spacer (IGS), which separates the rDNA repeats. This enrichment coincides with the distribution of the largest subunit of Pol I (POLR1A) across the rDNA. All sequencing reads were mapped to the published complete sequence of the mouse rDNA repeat (Gene bank accession number: BK000964). The graph represents the frequency of ribosomal sequences enriched in UBTF1/2 and Pol I-ChIPed DNA expressed as fold change over those of input genomic DNA.
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HIST1H2BG (H2BC8) (NM 003518) Human Tagged ORF Clone Lentiviral Particle Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC210258L4V HIST1H2BG (H2BC8) (NM_003518) Human Tagged ORF Clone Lentiviral Particle Product data: Product Type: Lentiviral Particles Product Name: HIST1H2BG (H2BC8) (NM_003518) Human Tagged ORF Clone Lentiviral Particle Symbol: H2BC8 Synonyms: dJ221C16.8; H2B.1A; H2B/a; H2BC4; H2BC6; H2BC7; H2BC10; H2BFA; HIST1H2BG Vector: pLenti-C-mGFP-P2A-Puro (PS100093) ACCN: NM_003518 ORF Size: 378 bp ORF Nucleotide The ORF insert of this clone is exactly the same as(RC210258). Sequence: OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_003518.3 RefSeq Size: 445 bp RefSeq ORF: 381 bp Locus ID: 8339 UniProt ID: P62807, B2R4S9 Domains: H2B, histone Protein Pathways: Systemic lupus erythematosus MW: 14.4 kDa This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 HIST1H2BG (H2BC8) (NM_003518) Human Tagged ORF Clone Lentiviral Particle – RC210258L4V Gene Summary: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes.
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Differential Gene Expression by RNA-Seq Analysis of the Primo Vessel in the Rabbit Lymph
J Acupunct Meridian Stud 2019;12(1):11e19 Available online at www.sciencedirect.com Journal of Acupuncture and Meridian Studies journal homepage: www.jams-kpi.com Research Article Differential Gene Expression by RNA-Seq Analysis of the Primo Vessel in the Rabbit Lymph Jun-Young Shin, Sang-Heon Choi, Da-Woon Choi, Ye-Jin An, Jae-Hyuk Seo, Jong-Gu Choi, Min-Suk Rho, Sang-Suk Lee* Department of Oriental Biomedical Engineering, Sangji University, Wonju, Republic of Korea Available online 28 October 2018 Received: May 31, 2018 Abstract Revised: Jul 26, 2018 For the connectome of primo vascular system, some long-type primo vessels dyed with Accepted: Oct 23, 2018 Alcian blue injected into inguinal nodes, abdominal node, and axially nodes were visual- ized, which passed over around the vena cava of the rabbit. The Alcian blue dye revealed KEYWORDS primo vessels and colored blue in the rabbit lymph vessels. The length of long-type primo e m gene expression level; vessels was 18 cm on average, of which diameters were about 20 30 m, and the lymph e m lymph node; vessels had diameters of 100 150 m. Three different tissues of pure primo vessel, mixed primo connectome; primo þ lymph vessel, and only lymph vessel were made to undergo RNA-Seq analysis by RNA-Seq analysis next-generation sequencing. We also analyzed differentially expressed genes (DEGs) from the RNA-Seq data, in which 30 genes of the primo vessels, primo þ lymph vessels, and lymph vessels were selected for primo marker candidates. From the plot of DEG analysis, 10 genes had remarkably different expression pattern on the Group 1 (primo vessel) vs Group 3 (lymph vessel).
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