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Burdick JT, Comai A, Bruzel A, Sun G, Dedon PC, Cheung VG. Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology. G3 (Bethesda) 2023; 13:jkad200. [PMID: 37655917 PMCID: PMC10627276 DOI: 10.1093/g3journal/jkad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
RNA undergoes complex posttranscriptional processing including chemical modifications of the nucleotides. The resultant-modified nucleotides are an integral part of RNA sequences that must be considered in studying the biology of RNA and in the design of RNA therapeutics. However, the current "RNA-sequencing" methods primarily sequence complementary DNA rather than RNA itself, which means that the modifications present in RNA are not captured in the sequencing results. Emerging direct RNA-sequencing technologies, such as those offered by Oxford Nanopore, aim to address this limitation. In this study, we synthesized and used Nanopore technology to sequence RNA transcripts consisting of canonical nucleotides and 10 different modifications in various concentrations. The results show that direct RNA sequencing still has a baseline error rate of >10%, and although some modifications can be detected, many remain unidentified. Thus, there is a need to develop sequencing technologies and analysis methods that can comprehensively capture the total complexity of RNA. The RNA sequences obtained through this project are made available for benchmarking analysis methods.
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Affiliation(s)
- Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Annelise Comai
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Watts JA, Grunseich C, Rodriguez Y, Liu Y, Li D, Burdick J, Bruzel A, Crouch RJ, Mahley RW, Wilson S, Cheung V. A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE. Nucleic Acids Res 2022; 50:12497-12514. [PMID: 36453989 PMCID: PMC9757052 DOI: 10.1093/nar/gkac1107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
RNA is modified by hundreds of chemical reactions and folds into innumerable shapes. However, the regulatory role of RNA sequence and structure and how dysregulation leads to diseases remain largely unknown. Here, we uncovered a mechanism where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. We found an enhancer RNA, AANCR, that regulates the transcription and expression of apolipoprotein E (APOE). In some human cells such as fibroblasts, AANCR is folded into an R-loop and modified by N-glycosidic cleavage; in this form, AANCR is a partially transcribed nonfunctional enhancer and APOE is not expressed. In contrast, in other cell types including hepatocytes and under stress, AANCR does not form a stable R-loop as its sequence is not modified, so it is transcribed into a full-length enhancer that promotes APOE expression. DNA sequence variants in AANCR are associated significantly with APOE expression and Alzheimer's Disease, thus AANCR is a modifier of Alzheimer's Disease. Besides AANCR, thousands of noncoding RNAs are regulated by abasic sites in R-loops. Together our data reveal the essentiality of the folding and modification of RNA in cellular regulation and demonstrate that dysregulation underlies common complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Jason A Watts
- Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yesenia Rodriguez
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Yaojuan Liu
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dongjun Li
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joshua T Burdick
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan Bruzel
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert W Mahley
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Departments of Pathology and Medicine, University of California, San Francisco, CA, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Vivian G Cheung
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Watts JA, Burdick J, Daigneault J, Zhu Z, Grunseich C, Bruzel A, Cheung VG. cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression. Am J Hum Genet 2019; 105:677-688. [PMID: 31495490 PMCID: PMC6817524 DOI: 10.1016/j.ajhg.2019.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Aberrant gene expression underlies many human diseases. RNA polymerase II (Pol II) pausing is a key regulatory step in transcription. Here, we mapped the locations of RNA Pol II in normal human cells and found that RNA Pol II pauses in a consistent manner across individuals and cell types. At more than 1,000 genes including MYO1E and SESN2, RNA Pol II pauses at precise nucleotide locations. Characterization of these sites shows that RNA Pol II pauses at GC-rich regions that are marked by a sequence motif. Sixty-five percent of the pause sites are cytosines. By differential allelic gene expression analysis, we showed in our samples and a population dataset from the Genotype-Tissue Expression (GTEx) consortium that genes with more paused polymerase have lower expression levels. Furthermore, mutagenesis of the pause sites led to a significant increase in promoter activities. Thus, our data uncover that RNA Pol II pauses precisely at sites with distinct sequence features that in turn regulate gene expression.
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Affiliation(s)
- Jason A Watts
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institute of Health, Bethesda, MD, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Vivian G Cheung
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, Division of Neurology, University of Michigan, Ann Arbor, MI, USA.
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4
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Grunseich C, Wang IX, Watts JA, Burdick JT, Guber RD, Zhu Z, Bruzel A, Lanman T, Chen K, Schindler AB, Edwards N, Ray-Chaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck KH, Cheung VG. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters. Mol Cell 2018; 69:426-437.e7. [PMID: 29395064 PMCID: PMC5815878 DOI: 10.1016/j.molcel.2017.12.030] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 12/11/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022]
Abstract
R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins.
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Affiliation(s)
- Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jason A Watts
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Robert D Guber
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tyler Lanman
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Kelian Chen
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Alice B Schindler
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Nancy Edwards
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Abhik Ray-Chaudhury
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jianhua Yao
- Department of Radiology and Imaging Sciences, Clinical Center, NIH, Bethesda, MD, USA
| | - Tanya Lehky
- Electromyography Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Grzegorz Piszczek
- Biophysics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Barbara Crain
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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5
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Wang IX, Core LJ, Kwak H, Brady L, Bruzel A, McDaniel L, Richards AL, Wu M, Grunseich C, Lis JT, Cheung VG. RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. Cell Rep 2014; 6:906-15. [PMID: 24561252 DOI: 10.1016/j.celrep.2014.01.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/27/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022] Open
Abstract
RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs) in nascent RNA. Our results show that RDDs begin to occur in RNA chains ~55 nt from the RNA polymerase II (Pol II) active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.
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Affiliation(s)
- Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lauren Brady
- Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lee McDaniel
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Allison L Richards
- Human Genetics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming Wu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Abstract
The transmission of information from DNA to RNA is a critical process. We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. All 12 possible categories of discordances were observed. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. Using mass spectrometry, we detected peptides that are translated from the discordant RNA sequences and thus do not correspond exactly to the DNA sequences. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation.
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Affiliation(s)
- Mingyao Li
- Departments of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Isabel X. Wang
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Yun Li
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alan Bruzel
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Allison L. Richards
- Cell and Molecular Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan M. Toung
- Genomics and Computational Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Vivian G. Cheung
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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7
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Abstract
Reassociating double-stranded DNA from single-stranded components is necessary for many molecular genetics experiments. The choice of a DNA reassociation method is dictated by the complexity of the starting material. Reassociation of simple oligomers needs only slow cooling in an aqueous environment, whereas reannealing the many single-stranded DNAs of complex genomic mixtures requires both a phenol emulsion to accelerate DNA reassociation and dedicated equipment to maintain the emulsion. We present a method that is equally suitable for reassociating either simple or complex DNA mixtures. The Oscillating Phenol Emulsion Reassociation Technique (OsPERT) was primarily developed to prepare heteroduplex DNA from alkali-denatured high molecular weight human genomic DNA samples in which hundreds of thousands of fragments need to be reannealed, but the simplicity of the technique makes it practical for less demanding DNA reassociation applications.
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Affiliation(s)
- Alan Bruzel
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Abstract
Direct identical-by-descent (IBD) mapping is a technique, that combines genomic mismatch scanning (GMS) and DNA microarray technology, for mapping regions shared IBD between two individuals without locus-by-locus genotyping or sequencing. The lack of reagents has limited its widespread application. In particular, two key reagents have been limiting, 1). mismatch repair proteins MutS, L and H, and 2). genomic microarrays for identifying the genomic locations of the GMS-selected IBD fragments. Here, we describe steps that optimized the procedure and resources that will facilitate the development of direct IBD mapping.
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Affiliation(s)
- Denis Smirnov
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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BAC Resource Consortium T, Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 2001; 409:953-8. [PMID: 11237021 PMCID: PMC7845515 DOI: 10.1038/35057192] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.
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Affiliation(s)
| | - V. G. Cheung
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - N. Nowak
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - W. Jang
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - I. R. Kirsch
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - S. Zhao
- grid.469946.0The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, 20850 Maryland USA
| | - X.-N. Chen
- grid.50956.3f0000 0001 2152 9905Departments of Pediatrics and Human Genetics, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, 90048 California USA
| | - T. S. Furey
- grid.205975.c0000 0001 0740 6917Computer Science Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064-1077 California USA
| | - U.-J. Kim
- grid.20861.3d0000000107068890Department of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, 91125 California USA ,Present Address: PanGenomics, 6401 Foothill Boulevard, Tujunga, California 91024 USA
| | - W.-L. Kuo
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - M. Olivier
- grid.168010.e0000000419368956Stanford University, Genome Lab, Mail Code 5120, Stanford, 94305-5120 California USA
| | - J. Conroy
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - A. Kasprzyk
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - H. Massa
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
| | - R. Yonescu
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - S. Sait
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - C. Thoreen
- grid.34477.330000000122986657Department of Molecular Biotechnology, University of Washington, Box 357730, Seattle, 98195-7730 Washington USA ,grid.38142.3c000000041936754XPresent Address: Harvard Medical School, Cell Biology, 240 Longwood Avenue, Cambridge, Massachusetts 02115 USA
| | - A. Snijders
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - E. Lemyre
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - J. A. Bailey
- grid.67105.350000 0001 2164 3847Department of Human Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, 44106 Ohio USA
| | - A. Bruzel
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - W. D. Burrill
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - S. M. Clegg
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - S. Collins
- grid.34477.330000000122986657Department of Molecular Biotechnology, University of Washington, Box 357730, Seattle, 98195-7730 Washington USA
| | - P. Dhami
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - C. Friedman
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
| | - C. S. Han
- grid.148313.c0000 0004 0428 3079Joint Genome Institute-Los Alamos National Laboratory, MS M888 B-N1, P.O. Box 1663, Los Alamos, 87545 New Mexico USA
| | - S. Herrick
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - J. Lee
- grid.20861.3d0000000107068890Department of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, 91125 California USA
| | - A. H. Ligon
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - S. Lowry
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - M. Morley
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - S. Narasimhan
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - K. Osoegawa
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA ,grid.414016.60000 0004 0433 7727Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, 94609 California USA
| | - Z. Peng
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - I. Plajzer-Frick
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - B. J. Quade
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - D. Scott
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - K. Sirotkin
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - A. A. Thorpe
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - J. W. Gray
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - J. Hudson
- grid.418190.50000 0001 2187 0556Research Genetics, 2130 Memorial Parkway, Huntsville, 35801 Alabama USA
| | - D. Pinkel
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - T. Ried
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - L. Rowen
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, 4225 Roosevelt Way NE, Suite 200, Seattle, 98105-6099 Washington USA
| | - G. L. Shen-Ong
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA ,Present Address: Gene Logic, Inc., 708 Quince Orchard Road, Gaithersburg, Maryland 20878 USA
| | - R. L. Strausberg
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - E. Birney
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - D. F. Callen
- grid.1694.aDepartment of Cytogenetics and Molecular Genetics, Women's and Children's Hospital, 72 King William Road, North Adelaide, 5006 South Australia Australia
| | - J.-F. Cheng
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - D. R. Cox
- grid.168010.e0000000419368956Stanford University, Genome Lab, Mail Code 5120, Stanford, 94305-5120 California USA
| | - N. A. Doggett
- grid.148313.c0000 0004 0428 3079Joint Genome Institute-Los Alamos National Laboratory, MS M888 B-N1, P.O. Box 1663, Los Alamos, 87545 New Mexico USA
| | - N. P. Carter
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - E. E. Eichler
- grid.67105.350000 0001 2164 3847Department of Human Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, 44106 Ohio USA
| | - D. Haussler
- grid.205975.c0000 0001 0740 6917Computer Science Department, Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064–1077 California USA
| | - J. R. Korenberg
- grid.50956.3f0000 0001 2152 9905Departments of Pediatrics and Human Genetics, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, 90048 California USA
| | - C. C. Morton
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - D. Albertson
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - G. Schuler
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - P. J. de Jong
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA ,grid.414016.60000 0004 0433 7727Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, 94609 California USA
| | - B. J. Trask
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
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10
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Cheung VG, Dalrymple HL, Narasimhan S, Watts J, Schuler G, Raap AK, Morley M, Bruzel A. A resource of mapped human bacterial artificial chromosome clones. Genome Res 1999; 9:989-93. [PMID: 10523527 PMCID: PMC310825 DOI: 10.1101/gr.9.10.989] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To date, despite the increasing number of genomic tools, there is no repository of ordered human BAC clones that covers entire chromosomes. This project presents a resource of mapped large DNA fragments that span eight human chromosomes at approximately 1-Mb resolution. These DNA fragments are bacterial artificial chromosome (BAC) clones anchored to sequence tagged site (STS) markers. This clone collection, which currently contains 759 mapped clones, is useful in a wide range of applications from microarray-based gene mapping to identification of chromosomal mutations. In addition to the clones themselves, we describe a database, GenMapDB (http://genomics.med.upenn.edu/genmapdb), that contains information about each clone in our collection.
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Affiliation(s)
- V G Cheung
- Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA.
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11
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Thrash-Bingham CA, Greenberg RE, Howard S, Bruzel A, Bremer M, Goll A, Salazar H, Freed JJ, Tartof KD. Comprehensive allelotyping of human renal cell carcinomas using microsatellite DNA probes. Proc Natl Acad Sci U S A 1995; 92:2854-8. [PMID: 7708737 PMCID: PMC42317 DOI: 10.1073/pnas.92.7.2854] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The von Hippel-Lindau locus on chromosome 3p is a tumor suppressor gene known to be involved in nonpapillary renal cell carcinoma. A previous loss of heterozygosity (LOH) study aimed at determining the allelotype of kidney tumors has indicated that in addition to 3p, chromosome arms 5q, 6q, 10q, 11q, 17p, and 19p may also harbor tumor suppressor genes. However, cytogenetic studies reveal that chromosomes 3p, 6q, 8p, 9pq, and 14q most frequently undergo karyotypic changes in renal tumors. To resolve these differences, a collection of microsatellite DNA probes has been used to scan for LOH so that 90% of individual tumor genomes were rendered informative for allele loss. The assay is capable of detecting quantitative genomic alterations in tumor cells as well. We find that LOH is most frequent for chromosome arm 3p. However, in no tumor is 3p exclusively affected. LOH for 6q, 8p, 9pq, and 14q is also distinctly elevated for both nonpapillary as well as papillary tumors and suggest that many of the tumor suppressor loci involved may be common to the etiology of both forms of kidney cancer.
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MESH Headings
- Alleles
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Chromosome Deletion
- Chromosome Mapping
- Chromosomes, Human
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 3
- DNA Probes
- DNA, Neoplasm/isolation & purification
- DNA, Satellite/genetics
- Genes, Tumor Suppressor
- Genetic Markers
- Humans
- In Situ Hybridization, Fluorescence
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Lymphocytes
- Ploidies
- Polymerase Chain Reaction
- Polymorphism, Genetic
- von Hippel-Lindau Disease/genetics
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Affiliation(s)
- C A Thrash-Bingham
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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12
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Hino O, Testa JR, Buetow KH, Taguchi T, Zhou JY, Bremer M, Bruzel A, Yeung R, Levan G, Levan KK. Universal mapping probes and the origin of human chromosome 3. Proc Natl Acad Sci U S A 1993; 90:730-4. [PMID: 8093645 PMCID: PMC45739 DOI: 10.1073/pnas.90.2.730] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Universal mapping probes (UMPs) are defined as short segments of human DNA that are useful for physical and genetic mapping in a wide variety of mammals. The most useful UMPs contain a conserved DNA sequence immediately adjoined to a highly polymorphic CA repeat. The conserved region determines physical gene location, whereas the CA repeat facilitates genetic mapping. Both the CA repeat and its neighboring sequence are highly conserved in evolution. This permits molecular, cytogenetic, and genetic mapping of UMPs throughout mammalia. UMPs are significant because they make genetic information cumulative among well-studied species and because they transfer such information from "map rich" organisms to those that are "map poor." As a demonstration of the utility of UMPs, comparative maps between human chromosome 3 (HSA3) and the rat genome have been constructed. HSA3 is defined by at least 12 syntenic clusters located on seven different rat chromosomes. These data, together with previous comparative mapping information between human, mouse, and bovine genomes, allow us to propose a distinct evolutionary pathway that connects HSA3 with the chromosomes of rodents, artiodactyls, and primates. The model predicts a parsimonious phylogenetic tree, is readily testable, and will be of considerable use for determining the pathways of mammalian evolution.
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Affiliation(s)
- O Hino
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111
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13
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Yoo-Warren H, Monahan JE, Short J, Short H, Bruzel A, Wynshaw-Boris A, Meisner HM, Samols D, Hanson RW. Isolation and characterization of the gene coding for cytosolic phosphoenolpyruvate carboxykinase (GTP) from the rat. Proc Natl Acad Sci U S A 1983; 80:3656-60. [PMID: 6304730 PMCID: PMC394109 DOI: 10.1073/pnas.80.12.3656] [Citation(s) in RCA: 170] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The gene for cytosolic phosphoenolpyruvate carboxykinase (GTP) [GTP:oxaloacetate carboxy-lyase (transphosphorylating), EC 4.1.1.32] from the rat was isolated from a recombinant library containing the rat genome in phage lambda Charon 4A. The isolated clone, lambda PCK1, contains the complete gene for phosphoenolpyruvate carboxykinase and approximately equal to 7 kilobases (kb) of flanking sequence at the 5' end and 1 kb at the 3' terminus. Restriction endonuclease mapping, R-loop mapping, and partial DNA sequence assay indicate that the gene is approximately equal to 6.0 kb in length (coding for a mRNA of 2.8 kb) and contains eight introns. Southern blotting of rat DNA digested with various restriction enzymes shows a pattern predicted from the restriction map of lambda PCK1. A control region at the 5' end of the gene contained in a 1.2-kb restriction fragment was isolated and subcloned into pBR322. This segment of the gene contains the usual transcription start sequences and a 24-base sequence virtually identical to the sequence found in the 5'-flanking region of the human proopiomelonocortin gene, which is known to be regulated by glucocorticoids. The 1.2-kb fragment of the phosphoenolpyruvate carboxykinase gene can be transcribed into a unique RNA fragment of predicted size by an in vitro transcription assay.
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