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Lim CA, Yao F, Wong JJY, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y, Chin KC. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell 2007; 27:622-35. [PMID: 17707233 DOI: 10.1016/j.molcel.2007.06.038] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 05/04/2007] [Accepted: 06/25/2007] [Indexed: 12/18/2022]
Abstract
NF-kappaB is a key mediator of inflammation. Here, we mapped the genome-wide loci bound by the RELA subunit of NF-kappaB in lipopolysaccharide (LPS)-stimulated human monocytic cells, and together with global gene expression profiling, found an overrepresentation of the E2F1-binding motif among RELA-bound loci associated with NF-kappaB target genes. Knockdown of endogenous E2F1 impaired the LPS inducibility of the proinflammatory cytokines CCL3(MIP-1alpha), IL23A(p19), TNF-alpha, and IL1-beta. Upon LPS stimulation, E2F1 is rapidly recruited to the promoters of these genes along with p50/RELA heterodimer via a mechanism that is dependent on NF-kappaB activation. Together with the observation that E2F1 physically interacts with p50/RELA in LPS-stimulated cells, our findings suggest that NF-kappaB recruits E2F1 to fully activate the transcription of NF-kappaB target genes. Global gene expression profiling subsequently revealed a spectrum of NF-kappaB target genes that are positively regulated by E2F1, further demonstrating the critical role of E2F1 in the Toll-like receptor 4 pathway.
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Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 2007; 17:898-909. [PMID: 17568005 PMCID: PMC1891348 DOI: 10.1101/gr.5583007] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides >/=50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%-86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies.
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Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan K, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res 2007; 17:828-38. [PMID: 17568001 PMCID: PMC1891342 DOI: 10.1101/gr.6018607] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5' and 3' transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.
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Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 2007; 17:839-51. [PMID: 17568002 PMCID: PMC1891343 DOI: 10.1101/gr.5586307] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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Ablikim M, Bai JZ, Ban Y, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chu YP, Dai YS, Diao LY, Deng ZY, Dong QF, Du SX, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo ZJ, Harris FA, He KL, He M, Heng YK, Hou J, Hu HM, Hu JH, Hu T, Huang GS, Huang XT, Ji XB, Jiang XS, Jiang XY, Jiao JB, Jin DP, Jin S, Lai YF, Li G, Li HB, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XN, Li XQ, Liang YF, Liao HB, Liu BJ, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu JLQ, Liu RG, Liu ZA, Lou YC, Lu F, Lu GR, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Mao ZP, Mo XH, Nie J, Olsen SL, Ping RG, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Ruan XD, Shan LY, Shang L, Shen CP, Shen DL, Shen XY, Sheng HY, Sun HS, Sun SS, Sun YZ, Sun ZJ, Tang X, Tong GL, Varner GS, Wang DY, Wang L, Wang LL, Wang LS, Wang M, Wang P, Wang PL, Wang YF, Wang Z, Wang ZY, Wang Z, Wei CL, Wei DH, Weng Y, Wu N, Xia XM, Xie XX, Xu GF, Xu XP, Xu Y, Yan ML, Yang HX, Yang YX, Ye MH, Ye YX, Yu GW, Yuan CZ, Yuan Y, Zang SL, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HQ, Zhang HY, Zhang JW, Zhang JY, Zhang SH, Zhang XY, Zhang Y, Zhang ZX, Zhang ZP, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao ZG, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Measurement of psi2S radiative decays. PHYSICAL REVIEW LETTERS 2007; 99:011802. [PMID: 17678148 DOI: 10.1103/physrevlett.99.011802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Indexed: 05/16/2023]
Abstract
Using 14 x 10(6) psi(2S) events accumulated at the BESII detector, we report first measurements of branching fractions or upper limits for psi(2S) decays into gammapp, gamma2(pi+pi-), gammaKS0K+pi-+c.c., gammaK+K-pi+pi-, gammaK*0K-pi++c.c., gammaK*0K*0, gammapi+pi-pp, gamma2(K+K-), gamma3(pi+pi-), and gamma2(pi+pi-)K+K- with the invariant mass of hadrons below 2.9 GeV/c2. We also report branching fractions of psi(2S) decays into 2(pi+pi-)pi0, omegapi+pi-, omegaf2(1270), b1+/-pi-/+, and pi02(pi+pi-)K+K-.
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81
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Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ETB, Ruan Y, Wei CL, Sung WKK. Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer 2007; 7:109. [PMID: 17594473 PMCID: PMC1929113 DOI: 10.1186/1471-2407-7-109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 06/26/2007] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Melanoma is the major cause of skin cancer deaths and melanoma incidence doubles every 10 to 20 years. However, little is known about melanoma pathway aberrations. Here we applied the robust Gene Identification Signature Paired End diTag (GIS-PET) approach to investigate the melanoma transcriptome and characterize the global pathway aberrations. METHODS GIS-PET technology directly links 5' mRNA signatures with their corresponding 3' signatures to generate, and then concatenate, PETs for efficient sequencing. We annotated PETs to pathways of KEGG database and compared the murine B16F1 melanoma transcriptome with three non-melanoma murine transcriptomes (Melan-a2 melanocytes, E14 embryonic stem cells, and E17.5 embryo). Gene expression levels as represented by PET counts were compared across melanoma and melanocyte libraries to identify the most significantly altered pathways and investigate the expression levels of crucial cancer genes. RESULTS Melanin biosynthesis genes were solely expressed in the cells of melanocytic origin, indicating the feasibility of using the PET approach for transcriptome comparison. The most significantly altered pathways were metabolic pathways, including upregulated pathways: purine metabolism, aminophosphonate metabolism, tyrosine metabolism, selenoamino acid metabolism, galactose utilization, nitrobenzene degradation, and bisphenol A degradation; and downregulated pathways: oxidative phosphorylation, ATPase synthesis, TCA cycle, pyruvate metabolism, and glutathione metabolism. The downregulated pathways concurrently indicated a slowdown of mitochondrial activities. Mitochondrial permeability was also significantly altered, as indicated by transcriptional activation of ATP/ADP, citrate/malate, Mg++, fatty acid and amino acid transporters, and transcriptional repression of zinc and metal ion transporters. Upregulation of cell cycle progression, MAPK, and PI3K/Akt pathways were more limited to certain region(s) of the pathway. Expression levels of c-Myc and Trp53 were also higher in melanoma. Moreover, transcriptional variants resulted from alternative transcription start sites or alternative polyadenylation sites were found in Ras and genes encoding adhesion or cytoskeleton proteins such as integrin, beta-catenin, alpha-catenin, and actin. CONCLUSION The highly correlated results unmistakably point to a systematic downregulation of mitochondrial activities, which we hypothesize aims to downgrade the mitochondria-mediated apoptosis and the dependency of cancer cells on angiogenesis. Our results also demonstrate the advantage of using the PET approach in conjunction with KEGG database for systematic pathway analysis.
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Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SCJ, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816. [PMID: 17571346 PMCID: PMC2212820 DOI: 10.1038/nature05874] [Citation(s) in RCA: 3798] [Impact Index Per Article: 223.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 2007; 3:e87. [PMID: 17542648 PMCID: PMC1885282 DOI: 10.1371/journal.pgen.0030087] [Citation(s) in RCA: 369] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 04/17/2007] [Indexed: 11/19/2022] Open
Abstract
Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor α (ERα) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERα binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5′ and 3′ ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERα binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERα-positive from ERα-negative breast tumors. The expression dynamics of the genes adjacent to ERα binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERα appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERα target genes. Unexpectedly, we found that only 22%–24% of the bona fide human ERα binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERα binding and gene regulation. Estrogen receptors (ERs) play key roles in facilitating the transcriptional effects of hormone functions in target tissues. To obtain a genome-wide view of ERα binding sites, we applied chromatin immunoprecipitation coupled with a cloning and sequencing strategy using chromatin immunoprecipitation pair end-tagging technology to map ERα binding sites in MCF-7 human breast cancer cells. We identified 1,234 high quality ERα binding sites in the human genome and demonstrated that the binding sites are frequently adjacent to genes significantly associated with breast cancer disease status and outcome. The mapping results also revealed that ERα can influence gene expression across distances of up to 100 kilobases or more, that genes that are induced or repressed utilize sites in different regions relative to the transcript (suggesting different mechanisms of action), and that ERα binding sites are only modestly conserved in evolution. Using computational approaches, we identified potential interactions with other transcription factor binding sites adjacent to the ERα binding elements. Taken together, these findings suggest complex but definable rules governing ERα binding and gene regulation and provide a valuable dataset for mapping the precise control nodes for one of the most important nuclear hormone receptors in breast cancer biology.
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84
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Deng ZY, Dong LY, Dong QF, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, He KL, He M, Heng YK, Hu HM, Hu T, Huang XP, Huang XT, Ji XB, Jiang XS, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XQ, Li YL, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu RG, Liu ZA, Lu F, Lu GR, Lu HJ, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Peng HP, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tian YR, Tong GL, Wang DY, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xin B, Xu GF, Xu Y, Yan ML, Yang F, Yang HX, Yang J, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang JW, Zhang JY, Zhang QJ, Zhang XM, Zhang XY, Zhang Y, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Measurements of the continuum R(uds) and R values in e(+)e(-) annihilation in the energy region between 3.650 and 3.872 GeV. PHYSICAL REVIEW LETTERS 2006; 97:262001. [PMID: 17280420 DOI: 10.1103/physrevlett.97.262001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Indexed: 05/13/2023]
Abstract
We report measurements of the continuum R(uds) near the center-of-mass energy of 3.70 GeV, the R[uds(c)+psi(3770)](s) and the R(had)(s) values in e(+)e(-) annihilation at 68 energy points in the energy region between 3.650 and 3.872 GeV with the BES-II detector at the BEPC Collider. We obtain the R(uds) for the continuum light hadron (containing u, d, and s quarks) production near the DD threshold to be R(uds)=2.141+/-0.025+/-0.085.
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Diao LY, Deng ZY, Dong QF, Du SX, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, Heng YK, Hu HM, Hu T, Huang GS, Huang XT, Ji XB, Jiang XS, Jiang XY, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XN, Li XQ, Li YL, Liang YF, Liao HB, Liu BJ, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu Q, Liu RG, Liu ZA, Lou YC, Lu F, Lu GR, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Olsen SL, Peng HP, Ping RG, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen CP, Shen DL, Shen XY, Sheng HY, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tong GL, Varner GS, Wang DY, Wang L, Wang LL, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xu GF, Xu XP, Xu Y, Yan ML, Yang HX, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HQ, Zhang HY, Zhang JW, Zhang JY, Zhang SH, Zhang XM, Zhang XY, Zhang Y, Zhang ZP, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao ZG, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Search for invisible decays of eta and eta' in J/psi --> phi eta and phi eta'. PHYSICAL REVIEW LETTERS 2006; 97:202002. [PMID: 17155676 DOI: 10.1103/physrevlett.97.202002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Indexed: 05/12/2023]
Abstract
Using a data sample of 58 x 10(6) J/psi decays collected with the Beijing Spectrometer II detector at the Beijing Electron Positron Collider, searches for invisible decays of eta and eta' in J/psi to phi eta and phi eta' are performed. The phi signals, which are reconstructed in K+K- final states, are used to tag the eta and eta' decays. No signals are found for the invisible decays of either eta or eta', and upper limits at the 90% confidence level are determined to be 1.65 x 10(-3) for the ratio B(eta-->invisible)/B(eta --> gamma gamma) and 6.69 x 10(-2) for B(eta' --> invisible)/B(eta' --> gammagamma). These are the first searches for eta and eta' decays into invisible final states.
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Zeller KI, Zhao X, Lee CWH, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A 2006; 103:17834-9. [PMID: 17093053 PMCID: PMC1635161 DOI: 10.1073/pnas.0604129103] [Citation(s) in RCA: 401] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The protooncogene MYC encodes the c-Myc transcription factor that regulates cell growth, cell proliferation, cell cycle, and apoptosis. Although deregulation of MYC contributes to tumorigenesis, it is still unclear what direct Myc-induced transcriptomes promote cell transformation. Here we provide a snapshot of genome-wide, unbiased characterization of direct Myc binding targets in a model of human B lymphoid tumor using ChIP coupled with pair-end ditag sequencing analysis (ChIP-PET). Myc potentially occupies > 4,000 genomic loci with the majority near proximal promoter regions associated frequently with CpG islands. Using gene expression profiles with ChIP-PET, we identified 668 direct Myc-regulated gene targets, including 48 transcription factors, indicating that Myc is a central transcriptional hub in growth and proliferation control. This first global genomic view of Myc binding sites yields insights of transcriptional circuitries and cis regulatory modules involving Myc and provides a substantial framework for our understanding of mechanisms of Myc-induced tumorigenesis.
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Ablikim M, Bai JZ, Ban Y, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Deng ZY, Dong LY, Dong QF, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, Heng YK, Hu HM, Hu T, Huang GS, Huang XP, Huang XT, Ji XB, Jiang XS, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XQ, Li YL, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu RG, Liu ZA, Lu F, Lu GR, Lu HJ, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Olsen SL, Peng HP, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tian YR, Tong GL, Varner GS, Wang DY, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xin B, Xu GF, Xu Y, Yan ML, Yang F, Yang HX, Yang J, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang JW, Zhang JY, Zhang QJ, Zhang XM, Zhang XY, Zhang YY, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao ZG, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu Y, Zhu YS, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Observation of a broad 1-- resonant structure around 1.5 GeV/c2 in the K+K- mass spectrum in J/psi-->K+K-pi0. PHYSICAL REVIEW LETTERS 2006; 97:142002. [PMID: 17155241 DOI: 10.1103/physrevlett.97.142002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Indexed: 05/12/2023]
Abstract
A broad peak is observed at low K+K- invariant mass in J/psi-->K+K-pi(0) decays found in a sample of 5.8x10(7) J/psi events collected with the BESII detector. The statistical significance of the broad resonance is much larger than 5sigma. A partial wave analysis shows that the J;{PC} of this structure is 1--. Its pole position is determined to be [1576(-55)(+49)(stat)-91+98(syst)] MeV/c(2)-i/2[818(-23)(+22)(stat)-133+64(syst)] MeV/c(2). These parameters are not compatible with any known meson resonances.
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Deng ZY, Dong LY, Dong QF, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, He KL, He M, Heng YK, Hu HM, Hu T, Huang XP, Huang XT, Ji XB, Jiang XS, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XQ, Li YL, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu RG, Liu ZA, Lu F, Lu GR, Lu HJ, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Peng HP, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tian YR, Tong GL, Wang DY, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xin B, Xu GF, Xu Y, Yan ML, Yang F, Yang HX, Yang J, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang JW, Zhang JY, Zhang QJ, Zhang XM, Zhang XY, Zhang Y, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Measurements of the branching fractions for psi(3770)-->D(0)D[over ](0), D+D-, DD[over ], and the resonance parameters of psi(3770) and psi(2S). PHYSICAL REVIEW LETTERS 2006; 97:121801. [PMID: 17025950 DOI: 10.1103/physrevlett.97.121801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Indexed: 05/12/2023]
Abstract
We measure the branching fractions for psi(3770)-->D(0)D[over ](0), D+D-, DD[over ], and non-DD[over ] to be (46.7+/-4.7+/-2.3)%, (36.9+/-3.7+/-2.8)%, (83.6+/-7.3+/-4.2)%, and (16.4+/-7.3+/-4.2)%, respectively. The resonance parameters of psi(3770) and psi(2S) are measured to be M_(psi(3770))=3772.2+/-0.7+/-0.3 MeV, Gamma_(psi(3770))(tot)=26.9+/-2.4+/-0.3 MeV, and Gamma_(psi(3770))(ee)=251+/-26+/-11 eV; M_(psi(2S))=3685.5+/-0.0+/-0.3 MeV, Gamma_(psi(2S))(tot)=331+/-58+/-2 keV, and Gamma_(psi(2S))(ee)=2.330+/-0.036+/-0.110 keV. We also measure the light hadron R value to be R(uds)=2.262+/-0.054+/-0.109 in the energy region from 3.660 to 3.872 GeV.
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Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WKK, Ruan Y. PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics 2006; 7:390. [PMID: 16934139 PMCID: PMC1564156 DOI: 10.1186/1471-2105-7-390] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 08/25/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. RESULTS We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the Project Manager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. CONCLUSION The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.
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90
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chang JF, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen J, Chen ML, Chen YB, Chi SP, Chu YP, Cui XZ, Dai HL, Dai YS, Deng ZY, Dong LY, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Fu HY, Gao CS, Gao YN, Gong MY, Gong WX, Gu SD, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, He X, Heng YK, Hu HM, Hu T, Huang GS, Huang L, Huang XP, Ji XB, Jia QY, Jiang CH, Jiang XS, Jin DP, Jin S, Jin Y, Lai YF, Li F, Li G, Li HB, Li HH, Li J, Li JC, Li QJ, Li RB, Li RY, Li SM, Li WG, Li XL, Li XQ, Li XS, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HM, Liu JB, Liu JP, Liu RG, Liu ZA, Liu ZX, Lu F, Lu GR, Lu JG, Luo CL, Luo XL, Ma FC, Ma JM, Ma LL, Ma QM, Ma XY, Mao ZP, Mo XH, Nie J, Nie ZD, Olsen SL, Peng HP, Qi ND, Qian CD, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun SS, Sun YZ, Sun ZJ, Tang X, Tao N, Tian YR, Tong GL, Varner GS, Wang DY, Wang JX, Wang JZ, Wang K, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang SZ, Wang WF, Wang YF, Wang Z, Wang Z, Wang Z, Wang ZY, Wei CL, Wei DH, Wu N, Wu YM, Xia XM, Xie XX, Xin B, Xu GF, Xu H, Xu Y, Xue ST, Yan ML, Yang F, Yang HX, Yang J, Yang SD, Yang YX, Ye M, Ye MH, Ye YX, Yi LH, Yi ZY, Yu CS, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Yue Q, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang J, Zhang JY, Zhang JW, Zhang LS, Zhang QJ, Zhang SQ, Zhang XM, Zhang XY, Zhang YJ, Zhang YY, Zhang Y, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JB, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao XJ, Zhao YB, Zhao ZG, Zheng HQ, Zheng JP, Zheng LS, Zheng ZP, Zhong XC, Zhou BQ, Zhou GM, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zou BS. Observation of two new N* peaks in J/psi-->ppi-n and ppi+n decays. PHYSICAL REVIEW LETTERS 2006; 97:062001. [PMID: 17026161 DOI: 10.1103/physrevlett.97.062001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Indexed: 05/12/2023]
Abstract
The decay J/psi-->NNpi provides an effective isospin 1/2 filter for the piN system due to isospin conservation. Using 58x10(6) J/psi decays collected with the Beijing Electromagnetic Spectrometer at the Beijing Electron Positron Collider, more than 100 thousand J/psi-->ppi-n+c.c. events are obtained. Besides the two well-known N* peaks at around 1500 MeV/c2 and 1670 MeV/c2, there are two new, clear N* peaks in the ppi invariant mass spectrum around 1360 MeV/c2 and 2030 MeV/c2 with statistical significance of 11sigma and 13sigma, respectively. We identify these as the first direct observation of the N*(1440) peak and a long-sought missing N* peak above 2 GeV/c2 in the piN invariant mass spectrum.
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91
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Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res 2006; 34:e84. [PMID: 16840528 PMCID: PMC1524903 DOI: 10.1093/nar/gkl444] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The paired-end ditagging (PET) technique has been shown to be efficient and accurate for large-scale transcriptome and genome analysis. However, as with other DNA tag-based sequencing strategies, it is constrained by the current efficiency of Sanger technology. A recently developed multiplex sequencing method (454-sequencing™) using picolitre-scale reactions has achieved a remarkable advance in efficiency, but suffers from short-read lengths, and a lack of paired-end information. To further enhance the efficiency of PET analysis and at the same time overcome the drawbacks of the new sequencing method, we coupled multiplex sequencing with paired-end ditagging (MS-PET) using modified PET procedures to simultaneously sequence 200 000 to 300 000 dimerized PET (diPET) templates, with an output of nearly half-a-million PET sequences in a single 4 h machine run. We demonstrate the utility and robustness of MS-PET by analyzing the transcriptome of human breast carcinoma cells, and by mapping p53 binding sites in the genome of human colorectal carcinoma cells. This combined sequencing strategy achieved an approximate 100-fold efficiency increase over the current standard for PET analysis, and furthermore enables the short-read-length multiplex sequencing procedure to acquire paired-end information from large DNA fragments.
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92
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Diao LY, Deng ZY, Dong QF, Du SX, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, Heng YK, Hu HM, Hu T, Huang GS, Huang XT, Ji XB, Jiang XS, Jiang XY, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XN, Li XQ, Li YL, Liang YF, Liao HB, Liu BJ, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu Q, Liu RG, Liu ZA, Lou YC, Lu F, Lu GR, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Olsen SL, Peng HP, Ping RG, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen CP, Shen DL, Shen XY, Sheng HY, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tong GL, Varner GS, Wang DY, Wang L, Wang LL, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xu GF, Xu XP, Xu Y, Yan ML, Yang HX, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HQ, Zhang HY, Zhang JW, Zhang JY, Zhang SH, Zhang XM, Zhang XY, Zhang Y, Zhang ZP, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao ZG, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Observation of a near-threshold enhancement in the omega(phi) mass spectrum from the doubly OZI-suppressed decay J/psi-->gamma(omega)phi. PHYSICAL REVIEW LETTERS 2006; 96:162002. [PMID: 16712215 DOI: 10.1103/physrevlett.96.162002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Indexed: 05/09/2023]
Abstract
An enhancement near threshold is observed in the omega(phi) invariant mass spectrum from the doubly Okubo-Zweig-Iizuka-suppressed decays of J/psi-->gamma(omega)phi, based on a sample of 5.8 x 10(7) J/psi events collected with the BESII detector. A partial wave analysis shows that this enhancement favors JP=0+, and its mass and width are M=1812(+19)(-26)(stat)+/-18(syst) MeV/c2 and Gamma=105+/-20(stat)+/-28(syst) MeV/c2. The product branching fraction is determined to be B(J/psi-->gammaX)B(X-->omega(phi))=[2.61+/-0.27(stat)+/-0.65(syst)]x10(-4).
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Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CWH, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006; 38:431-40. [PMID: 16518401 DOI: 10.1038/ng1760] [Citation(s) in RCA: 1797] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 02/06/2006] [Indexed: 02/06/2023]
Abstract
Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Using de novo motif discovery algorithms, we defined the cis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference-mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.
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Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y. A global map of p53 transcription-factor binding sites in the human genome. Cell 2006; 124:207-19. [PMID: 16413492 DOI: 10.1016/j.cell.2005.10.043] [Citation(s) in RCA: 780] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 09/13/2005] [Accepted: 10/25/2005] [Indexed: 01/29/2023]
Abstract
The ability to derive a whole-genome map of transcription-factor binding sites (TFBS) is crucial for elucidating gene regulatory networks. Herein, we describe a robust approach that couples chromatin immunoprecipitation (ChIP) with the paired-end ditag (PET) sequencing strategy for unbiased and precise global localization of TFBS. We have applied this strategy to map p53 targets in the human genome. From a saturated sampling of over half a million PET sequences, we characterized 65,572 unique p53 ChIP DNA fragments and established overlapping PET clusters as a readout to define p53 binding loci with remarkable specificity. Based on this information, we refined the consensus p53 binding motif, identified at least 542 binding loci with high confidence, discovered 98 previously unidentified p53 target genes that were implicated in novel aspects of p53 functions, and showed their clinical relevance to p53-dependent tumorigenesis in primary cancer samples.
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95
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen YB, Chi SP, Chu YP, Cui XZ, Dai YS, Deng ZY, Dong LY, Dong QF, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Gao CS, Gao YN, Gu SD, Gu YT, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, Heng YK, Hu HM, Hu T, Huang GS, Huang XP, Huang XT, Ji XB, Jiang XS, Jiao JB, Jin DP, Jin S, Jin Y, Lai YF, Li G, Li HB, Li HH, Li J, Li RY, Li SM, Li WD, Li WG, Li XL, Li XQ, Li YL, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HH, Liu HM, Liu J, Liu JB, Liu JP, Liu RG, Liu ZA, Lu F, Lu GR, Lu HJ, Lu JG, Luo CL, Ma FC, Ma HL, Ma LL, Ma QM, Ma XB, Mao ZP, Mo XH, Nie J, Olsen SL, Peng HP, Qi ND, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun JF, Sun SS, Sun YZ, Sun ZJ, Tan ZQ, Tang X, Tian YR, Tong GL, Varner GS, Wang DY, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang WF, Wang YF, Wang Z, Wang ZY, Wang Z, Wang Z, Wei CL, Wei DH, Wu N, Xia XM, Xie XX, Xin B, Xu GF, Xu Y, Yan ML, Yang F, Yang HX, Yang J, Yang YX, Ye MH, Ye YX, Yi ZY, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang JW, Zhang JY, Zhang QJ, Zhang XM, Zhang XY, Zhang YY, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao ZG, Zheng HQ, Zheng JP, Zheng ZP, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu Y, Zhu YS, Zhu ZA, Zhuang BA, Zhuang XA, Zou BS. Observation of a resonance in Chi(1835) in J/psi --> gammapi+ pi- eta-. PHYSICAL REVIEW LETTERS 2005; 95:262001. [PMID: 16486345 DOI: 10.1103/physrevlett.95.262001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Indexed: 05/06/2023]
Abstract
The decay channel J/psi --> gamma(pi)(+)pi(-)eta is analyzed using a sample of 5.8 x 10(7) J/psi events collected with the BESII detector. A resonance, the Chi(1835), is observed in the pi(+)pi(-)eta invariant-mass spectrum with a statistical significance of 7.7 sigma. A fit with a Breit-Wigner function yields a mass M = 1833.7 +/- 6.1(stat) +/- 2.7(syst) MeV/c(2), a width Tau = 67.7 +/- 20.3(stat) +/- 7.7(syst) MeV/c(2), and a product branching fraction B(J/psi --> gammaChi) . B(Chi --> pi(+)pi(-)eta) = [2.2 +/- 0.4(stat) +/- 0.4(syst)] x 10(-4). The mass and width of the Chi(1835) are not compatible with any known meson resonance. Its properties are consistent with expectations for the state that produces the strong pp mass threshold enhancement observed in the J/psi --> gammapp process at BESII.
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Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest ARR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SPT, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CAM, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science 2005; 309:1559-63. [PMID: 16141072 DOI: 10.1126/science.1112014] [Citation(s) in RCA: 2607] [Impact Index Per Article: 137.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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97
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Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2005; 2:105-11. [PMID: 15782207 DOI: 10.1038/nmeth733] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 12/15/2004] [Indexed: 11/09/2022]
Abstract
We have developed a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. We demonstrated this approach with 116,252 PET sequences derived from mouse embryonic stem cells. Initial analysis of this dataset identified hundreds of previously uncharacterized transcripts, including alternative transcripts of known genes. We also uncovered several intergenically spliced and unusual fusion transcripts, one of which was confirmed as a trans-splicing event and was differentially expressed. The concept of paired-end ditagging described here for transcriptome analysis can also be applied to whole-genome analysis of cis-regulatory and other DNA elements and represents an important technological advance for genome annotation.
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98
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Ablikim M, Bai JZ, Ban Y, Bian JG, Cai X, Chang JF, Chen HF, Chen HS, Chen HX, Chen JC, Chen J, Chen J, Chen ML, Chen YB, Chi SP, Chu YP, Cui XZ, Dai HL, Dai YS, Deng ZY, Dong LY, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Fu HY, Gao CS, Gao YN, Gong MY, Gong WX, Gu SD, Guo YN, Guo YQ, Guo ZJ, Harris FA, He KL, He M, He X, Heng YK, Hu HM, Hu T, Huang GS, Huang L, Huang XP, Ji XB, Jia QY, Jiang CH, Jiang XS, Jin DP, Jin S, Jin Y, Lai YF, Li F, Li G, Li HH, Li J, Li JC, Li QJ, Li RB, Li RY, Li SM, Li WG, Li XL, Li XQ, Li XS, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HM, Liu JB, Liu JP, Liu RG, Liu ZA, Liu ZX, Lu F, Lu GR, Lu JG, Luo CL, Luo XL, Ma FC, Ma JM, Ma LL, Ma QM, Ma XY, Mao ZP, Mo XH, Nie J, Nie ZD, Olsen SL, Peng HP, Qi ND, Qian CD, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Sun HS, Sun SS, Sun YZ, Sun ZJ, Tang X, Tao N, Tian YR, Tong GL, Varner GS, Wang DY, Wang JX, Wang JZ, Wang K, Wang L, Wang LS, Wang M, Wang P, Wang PL, Wang SZ, Wang WF, Wang YF, Wang Z, Wang Z, Wang Z, Wang ZY, Wei CL, Wei DH, Wu N, Wu YM, Xia XM, Xie XX, Xin B, Xu GF, Xu H, Xu Y, Xue ST, Yan ML, Yang F, Yang HX, Yang J, Yang SD, Yang YX, Ye M, Ye MH, Ye YX, Yi LH, Yi ZY, Yu CS, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Yue Q, Zang SL, Zeng Y, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang J, Zhang JY, Zhang JW, Zhang LS, Zhang QJ, Zhang SQ, Zhang XM, Zhang XY, Zhang YJ, Zhang YY, Zhang Y, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JB, Zhao JW, Zhao MG, Zhao PP, Zhao WR, Zhao XJ, Zhao YB, Zhao ZG, Zheng HQ, Zheng JP, Zheng LS, Zheng ZP, Zhong XC, Zhou BQ, Zhou GM, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu YC, Zhu YS, Zhu Y, Zhu ZA, Zhuang BA, Zou BS. Observation of a threshold enhancement in the plambda invariant-mass spectrum. PHYSICAL REVIEW LETTERS 2004; 93:112002. [PMID: 15447331 DOI: 10.1103/physrevlett.93.112002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Indexed: 05/24/2023]
Abstract
An enhancement near the m(p)+M(Lambda) mass threshold is observed in the combined pLambda and pLambda invariant-mass spectrum from J/psi-->pK(-)Lambda;+c.c. decays. It can be fit with an S-wave Breit-Wigner resonance with a mass m=2075+/-12(stat)+/-5(syst) MeV and a width of Gamma=90+/-35(stat)+/-9(syst) MeV; it can also be fit with a P-wave Breit-Wigner resonance. Evidence for a similar enhancement is also observed in psi(')-->pK(-)Lambda;+c.c. decays. The analysis is based on samples of 5.8x10(7)J/psi and 1.4x10(7)psi(') decays accumulated in the BES II detector at the Beijing Electron-Positron Collider.
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Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y. 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 2004; 101:11701-6. [PMID: 15272081 PMCID: PMC511040 DOI: 10.1073/pnas.0403514101] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Indexed: 11/18/2022] Open
Abstract
Complete genome annotation relies on precise identification of transcription units bounded by a transcription initiation site (TIS) and a polyadenylation site (PAS). To facilitate this process, we developed a set of two complementary methods, 5' Long serial analysis of gene expression (LS) and 3'LS. These analyses are based on the original SAGE and LS methods coupled with full-length cDNA cloning, and enable the high-throughput extraction of the first and the last 20 bp of each transcript. We demonstrate that the mapping of 5'LS and 3'LS tags to the genome allows the localization of TIS and PAS. By using 537 tag pairs mapping to the region of known genes, we confirmed that >90% of the tag pairs appropriately assigned to the first and last exons. Moreover, by using tag sequences as primers for RT-PCRs, we were able to recover putative full-length transcripts in 81% of the attempts. This large-scale generation of transcript terminal tags is at least 20-40 times more efficient than full-length cDNA cloning and sequencing in the identification of complete transcription units. The apparent precision and deep coverage makes 5'LS and 3'LS an advanced approach for genome annotation through whole-transcriptome characterization.
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100
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Bai JZ, Ban Y, Bian JG, Cai X, Chang JF, Chen HF, Chen HS, Chen HX, Chen J, Chen JC, Chen J, Chen ML, Chen YB, Chi SP, Chu YP, Cui XZ, Dai HL, Dai YS, Deng ZY, Dong LY, Du SX, Du ZZ, Fang J, Fang SS, Fu CD, Fu HY, Fu LP, Gao CS, Gao ML, Gao YN, Gong MY, Gong WX, Gu SD, Guo YN, Guo YQ, Guo ZJ, Han SW, Harris FA, He J, He KL, He M, He X, Heng YK, Hu HM, Hu T, Huang GS, Huang L, Huang XP, Ji XB, Jia QY, Jiang CH, Jiang XS, Jin DP, Jin S, Jin Y, Lai YF, Li F, Li G, Li HH, Li J, Li JC, Li QJ, Li RB, Li RY, Li SM, Li W, Li WG, Li XL, Li XQ, Li XS, Liang YF, Liao HB, Liu CX, Liu F, Liu F, Liu HM, Liu JB, Liu JP, Liu RG, Liu Y, Liu ZA, Liu ZX, Lu GR, Lu F, Lu JG, Luo CL, Luo XL, Ma FC, Ma JM, Ma LL, Ma XY, Mao ZP, Meng XC, Mo XH, Nie J, Nie ZD, Olsen SL, Peng HP, Qi ND, Qian CD, Qin H, Qiu JF, Ren ZY, Rong G, Shan LY, Shang L, Shen DL, Shen XY, Sheng HY, Shi F, Shi X, Song LW, Sun HS, Sun SS, Sun YZ, Sun ZJ, Tang X, Tao N, Tian YR, Tong GL, Varner GS, Wang DY, Wang JZ, Wang L, Wang LS, Wang M, Wang M, Wang P, Wang PL, Wang SZ, Wang WF, Wang YF, Wang Z, Wang Z, Wang Z, Wang ZY, Wei CL, Wu N, Wu YM, Xia XM, Xie XX, Xin B, Xu GF, Xu H, Xu Y, Xue ST, Yan ML, Yan WB, Yang F, Yang HX, Yang J, Yang SD, Yang YX, Yi LH, Yi ZY, Ye M, Ye MH, Ye YX, Yu CS, Yu GW, Yuan CZ, Yuan JM, Yuan Y, Yue Q, Zang SL, Zeng Y, Zhang BX, Zhang BY, Zhang CC, Zhang DH, Zhang HY, Zhang J, Zhang JM, Zhang JY, Zhang JW, Zhang LS, Zhang QJ, Zhang SQ, Zhang XM, Zhang XY, Zhang Y, Zhang YJ, Zhang YY, Zhang ZP, Zhang ZQ, Zhao DX, Zhao JB, Zhao JW, Zhao PP, Zhao WR, Zhao XJ, Zhao YB, Zhao ZG, Zheng HQ, Zheng JP, Zheng LS, Zheng ZP, Zhong XC, Zhou BQ, Zhou GM, Zhou L, Zhou NF, Zhu KJ, Zhu QM, Zhu Y, Zhu YC, Zhu YS, Zhu ZA, Zhuang BA, Zou BS. Observation of the decay psi(2S)-->K0SK0L. PHYSICAL REVIEW LETTERS 2004; 92:052001. [PMID: 14995298 DOI: 10.1103/physrevlett.92.052001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Indexed: 05/24/2023]
Abstract
The decay psi(2S)-->K(0)(S)K(0)(L) is observed using psi(2S) data collected with the Beijing Spectrometer at the Beijing Electron-Positron Collider; the branching fraction is determined to be B(psi(2S)-->K(0)(S)K(0)(L))=(5.24+/-0.47+/-0.48)x10(-5). Compared with J/psi-->K(0)(S)K(0)(L), the psi(2S) branching fraction is enhanced relative to the prediction of the perturbative QCD "12%" rule. The result, together with the branching fractions of psi(2S) decays to other pseudoscalar meson pairs (pi(+)pi(-) and K+K-), is used to investigate the relative phase between the three-gluon and the one-photon annihilation amplitudes of psi(2S) decays.
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