1
|
Youssef SS, Abbas EAER, Elfiky AM, Seif S, Nabeel MM, Shousha HI, Abdelaziz AO. The impact of polymorphism in PNPLA3 and TM6SF2 genes on the susceptibility and survival of hepatitis C-related hepatocellular carcinoma. EGYPTIAN LIVER JOURNAL 2022. [DOI: 10.1186/s43066-022-00212-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Abstract
Background
Genetic variants of Patatin-like phospholipase domain-containing protein 3 (PNPLA3) and transmembrane 6 superfamily member 2 (TM6SF2) genes have been reported with the development of hepatocellular carcinoma (HCC). This study aims to explore the role of The PNPLA3 rs738409 and TM6SF2 rs58542926 single-nucleotide polymorphisms (SNPs) on the incidence and survival of HCV-induced HCC in Egyptians.
Methods and results
This case-control study included (120) HCC and (144) hepatitis C virus (HCV) patients. Baseline clinical, laboratory, tumor characteristics data, HCC recurrence, and overall survival were collected. PNPLA3 rs738409 and TM6SF2 rs58542926 polymorphism were detected by TaqMan allelic discrimination assay. We found that HCC patients were significantly older with male predominance. A significant difference between the TT genotypes of TM6SF2 frequency was observed in HCC compared with HCV patients. Moreover, the T allele of TM6SF2 distributions revealed a significant contribution to the different stages of HCC (p=0.03). Both PNPLA3 rs738409 and TM6SF2 rs58542926 variants showed a significant relation with treatment response according to the modified RECIST criteria. Age and diabetes mellitus were the independent factors associated with the development of HCC by multivariate regression analysis.
Conclusions
TM6SF2 rs58542926 polymorphism, not PNPLA3 rs738409, could be implicated in the development of HCV-induced HCC and its progression.
Collapse
|
2
|
Murray JK, Long J, Liu L, Singh S, Pruitt D, Ollmann M, Swearingen E, Hardy M, Homann O, Wu B, Holder JR, Sham K, Herberich B, Lo MC, Dou H, Shkumatov A, Florio M, Rulifson IC. Identification and Optimization of a Minor Allele-Specific Small Interfering RNA to Prevent PNPLA3 I148M-Driven Nonalcoholic Fatty Liver Disease. Nucleic Acid Ther 2021; 31:324-340. [PMID: 34297902 DOI: 10.1089/nat.2021.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human genome wide association studies confirm the association of the rs738409 single nucleotide polymorphism (SNP) in the gene encoding protein patatin like phospholipase domain containing 3 (PNPLA3) with nonalcoholic fatty liver disease (NAFLD); the presence of the resulting mutant PNPLA3 I148M protein is a driver of nonalcoholic steatohepatitis (NASH). While Pnpla3-deficient mice do not display an adverse phenotype, the safety of knocking down endogenous wild type PNPLA3 in humans remains unknown. To expand the scope of a potential targeted NAFLD therapeutic to both homozygous and heterozygous PNPLA3 rs738409 populations, we sought to identify a minor allele-specific small interfering RNA (siRNA). Limiting our search to SNP-spanning triggers, a series of chemically modified siRNA were tested in vitro for activity and selectivity toward PNPLA3 rs738409 mRNA. Conjugation of the siRNA to a triantennary N-acetylgalactosamine (GalNAc) ligand enabled in vivo screening using adeno-associated virus to overexpress human PNPLA3I148M versus human PNPLA3I148I in mouse livers. Structure-activity relationship optimization yielded potent and minor allele-specific compounds that achieved high levels of mRNA and protein knockdown of human PNPLA3I148M but not PNPLA3I148I. Testing of the minor allele-specific siRNA in PNPLA3I148M-expressing mice fed a NASH-inducing diet prevented PNPLA3I148M-driven disease phenotypes, thus demonstrating the potential of a precision medicine approach to treating NAFLD.
Collapse
Affiliation(s)
- Justin K Murray
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jason Long
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Lei Liu
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Shivani Singh
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Danielle Pruitt
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| | - Michael Ollmann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Elissa Swearingen
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, South San Francisco, California, USA
| | - Bin Wu
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Jerry Ryan Holder
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Kelvin Sham
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Brad Herberich
- Therapeutic Discovery, Amgen Research, Thousand Oaks, California, USA
| | - Mei-Chu Lo
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Hui Dou
- Therapeutic Discovery, Amgen Research, South San Francisco, California, USA
| | - Artem Shkumatov
- Translational Safety and Bioanalytical Sciences, Amgen Research, South San Francisco, California, USA
| | - Monica Florio
- Cardiometabolic Disorders, Amgen Research, Thousand Oaks, California, USA
| | - Ingrid C Rulifson
- Cardiometabolic Disorders, Amgen Research, South San Francisco, California, USA
| |
Collapse
|
3
|
Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
Collapse
Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| |
Collapse
|
4
|
Huang Z, Guo X, Zhang G, Liang L, Nong B. Correlation between PNPLA3 rs738409 polymorphism and hepatocellular carcinoma: a meta-analysis of 10,330 subjects. Int J Biol Markers 2019; 34:117-122. [PMID: 30852978 DOI: 10.1177/1724600818812471] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE The correlation between patatin-like phospholipase domain-containing protein 3 (PNPLA3) rs738409 polymorphism and hepatocellular carcinoma was investigated by several pilot studies, but the results of these studies were controversial. Therefore, we performed this study to better assess the relationship between PNPLA3 rs738409 polymorphism and the likelihood of hepatocellular carcinoma. METHODS Eligible studies were searched in PubMed, Medline, EMBASE, and Web of Science. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the relationship between PNPLA3 rs738409 polymorphism and hepatocellular carcinoma. RESULTS A total of 17 studies with 10,330 participants were analyzed. A significant association with the likelihood of hepatocellular carcinoma was detected for the PNPLA3 rs738409 polymorphism in dominant (P = 0.0001; OR 0.66; 95% CI 0.53, 0.82), recessive (P < 0.0001; OR 2.32; 95% CI 1.76, 3.06) and allele (P < 0.0001; OR 0.64; 95% CI 0.53, 0.77) comparisons. Further subgroup analyses revealed that the PNPLA3 rs738409 polymorphism was significantly associated with the likelihood of hepatocellular carcinoma in Caucasians (dominant model: P < 0.0001, OR 0.57, 95% CI 0.45, 0.71; recessive model: P < 0.0001, OR 2.74, 95% CI 2.02, 3.71; allele model: P < 0.0001, OR 0.56, 95% CI 0.46, 0.67). However, no positive results were detected in Asians. CONCLUSIONS Our findings indicated that the PNPLA3 rs738409 polymorphism may serve as a potential biological marker of hepatocellular carcinoma in Caucasians.
Collapse
Affiliation(s)
- Zongsheng Huang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xianwen Guo
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guo Zhang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Liexin Liang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Bing Nong
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| |
Collapse
|
5
|
Li HG, Liu FF, Zhu HQ, Zhou X, Lu J, Chang H, Hu JH. Significant Association Between Adiponutrin and Hepatocellular Carcinoma Risk. Medicine (Baltimore) 2015; 94:e2019. [PMID: 26632699 PMCID: PMC5058968 DOI: 10.1097/md.0000000000002019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
ADPN I148M polymorphism has been consistently reported to play a role in liver-associated diseases, such as alcoholic liver disease, chronic hepatitis C, and liver fat and fibrosis in nonalcoholic fatty liver disease. This significant association was also indicated in a series of hepatocellular carcinoma (HCC) studies, where the significance may be affected due to the small sample sizes. The aim of this study was to reexamine the ADPN-HCC association by use of meta-analysis. Biweekly computer-based literature searches plus manual screening were undertaken in an effort to identify all studies that met the predefined inclusion criteria. The Mantel-Haenszel method was selected to estimate risk effects (odds ratio [OR] and 95% confidence interval [CI]). To examine reliability of the pooled risk effects, we additionally performed sensitivity analysis and publication bias tests. Ten studies (1335 HCC patients and 2927 HCC-free controls) were identified for the meta-analysis. We found significantly increased risk of HCC attributable to presence of ADPN I148M polymorphism, with the highest risk associated with the M/M genotype under the recessive model of inheritance (OR = 2.23, 95% CI = 1.87-2.67, between-study heterogeneity: P = 0.468). The significant increase persisted in Caucasian and African when data were stratified by ethnicity. Subgroup analysis according to source of controls revealed similar risk effects. Our meta-analysis indicates that I148M polymorphism in the ADPN gene may independently contribute to the progression of HCC irrespective of the etiologies.
Collapse
Affiliation(s)
- Hong-Guang Li
- From the Department of Hepatobiliary Surgery (H-GL, F-FL, H-QZ, XZ, JL, HC) and Department of Gastroenterology Surgery (J-HH), Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | | | | | | | | | | | | |
Collapse
|
6
|
Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD. Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet 2014; 23:4528-42. [PMID: 24781209 DOI: 10.1093/hmg/ddu167] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To globally survey the changes in transcriptional landscape during terminal erythroid differentiation, we performed RNA sequencing (RNA-seq) on primary human CD34(+) cells after ex vivo differentiation from the earliest into the most mature erythroid cell stages. This analysis identified thousands of novel intergenic and intronic transcripts as well as novel alternative transcript isoforms. After rigorous data filtering, 51 (presumptive) novel protein-coding transcripts, 5326 long and 679 small non-coding RNA candidates remained. The analysis also revealed two clear transcriptional trends during terminal erythroid differentiation: first, the complexity of transcript diversity was predominantly achieved by alternative splicing, and second, splicing junctional diversity diminished during erythroid differentiation. Finally, 404 genes that were not known previously to be differentially expressed in erythroid cells were annotated. Analysis of the most extremely differentially expressed transcripts revealed that these gene products were all closely associated with hematopoietic lineage differentiation. Taken together, this study will serve as a comprehensive platform for future in-depth investigation of human erythroid development that, in turn, may reveal new insights into multiple layers of the transcriptional regulatory hierarchy that controls erythropoiesis.
Collapse
Affiliation(s)
- Lihong Shi
- Department of Cell and Developmental Biology and
| | - Yu-Hsuan Lin
- Department of Cell and Developmental Biology and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - M C Sierant
- Department of Cell and Developmental Biology and
| | - Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Osamu Tanabe
- Department of Cell and Developmental Biology and Department of Integrative Genomics, Tohoku Medical Megabank, Tohoku University, 2-1 Seiryo-machi, Sendai 980-8573, Japan
| | - Kim-Chew Lim
- Department of Cell and Developmental Biology and
| | | |
Collapse
|
7
|
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One 2012; 7:e28213. [PMID: 22238572 PMCID: PMC3251577 DOI: 10.1371/journal.pone.0028213] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/03/2011] [Indexed: 12/03/2022] Open
Abstract
The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.
Collapse
Affiliation(s)
- Sarah Djebali
- Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Höglund PJ, Nordström KJV, Schiöth HB, Fredriksson R. The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. Mol Biol Evol 2010; 28:1531-41. [PMID: 21186191 PMCID: PMC3058773 DOI: 10.1093/molbev/msq350] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Solute Carriers (SLCs) are membrane proteins that regulate transport of many types of substances over the cell membrane. The SLCs are found in at least 46 gene families in the human genome. Here, we performed the first evolutionary analysis of the entire SLC family based on whole genome sequences. We systematically mined and analyzed the genomes of 17 species to identify SLC genes. In all, we identified 4,813 SLC sequences in these genomes, and we delineated the evolutionary history of each of the subgroups. Moreover, we also identified ten new human sequences not previously classified as SLCs, which most likely belong to the SLC family. We found that 43 of the 46 SLC families found in Homo sapiens were also found in Caenorhabditis elegans, whereas 42 of them were also found in insects. Mammals have a higher number of SLC genes in most families, perhaps reflecting important roles for these in central nervous system functions. This study provides a systematic analysis of the evolutionary history of the SLC families in Eukaryotes showing that the SLC superfamily is ancient with multiple branches that were present before early divergence of Bilateria. The results provide foundation for overall classification of SLC genes and are valuable for annotation and prediction of substrates for the many SLCs that have not been tested in experimental transport assays.
Collapse
Affiliation(s)
- Pär J Höglund
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | | | | | | |
Collapse
|
9
|
Dunham I, Beare DM, Collins JE. The characteristics of human genes: analysis of human chromosome 22. Comp Funct Genomics 2010; 4:635-46. [PMID: 18629020 PMCID: PMC2447302 DOI: 10.1002/cfg.335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 09/04/2003] [Accepted: 09/08/2003] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ian Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | | | | |
Collapse
|
10
|
Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, Dunham I. Finishing the finished human chromosome 22 sequence. Genome Biol 2008; 9:R78. [PMID: 18477386 PMCID: PMC2441464 DOI: 10.1186/gb-2008-9-5-r78] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 04/10/2008] [Accepted: 05/13/2008] [Indexed: 11/25/2022] Open
Abstract
A combination of approaches was used to close 8 of the 11 gaps in the original sequence of human chromosome 22, and to generate a total 1.018 Mb of new sequence. Background Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences. Results We have used a combination of conventional chromosome walking (aided by the availability of end sequences) in fosmid and bacterial artificial chromosome (BAC) libraries, whole chromosome shotgun sequencing, comparative genome analysis and long PCR to finish 8 of the 11 gaps in the initial chromosome 22 sequence. In addition, we have patched four regions of the initial sequence where the original clones were found to be deleted, or contained a deletion allele of a known gene, with a further 126 kb of new sequence. Over 1.018 Mb of new sequence has been generated to extend into and close the gaps, and we have annotated 16 new or extended gene structures and one pseudogene. Conclusion Thus, we have made significant progress to completing the sequence of the euchromatic regions of human chromosome 22 using a combination of detailed approaches. Our experience suggests that substantial work remains to close the outstanding gaps in the human genome sequence.
Collapse
Affiliation(s)
- Charlotte G Cole
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Buckley NJ. Analysis of transcription, chromatin dynamics and epigenetic changes in neural genes. Prog Neurobiol 2007; 83:195-210. [PMID: 17884276 DOI: 10.1016/j.pneurobio.2007.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 06/14/2007] [Accepted: 07/18/2007] [Indexed: 01/08/2023]
Abstract
The ways in which gene transcription is investigated have undergone radical change since the turn of the millennium. Piece-meal approaches focussed upon model genes have increasingly been complemented by genome-wide approaches that allow interrogation of multiple cohorts of genes or even entire genomes. This sea change has been founded upon the increasing availability of whole genome sequences and the attendant evolution of microarray based discovery platforms. Collectively, these approaches are being used to build a global and dynamic perspective of transcription factor occupancy, co-factor recruitment and epigenetic signature. As yet, few of these approaches have been applied to the study of neuronal gene transcription, but this is set to change. Here, I review these key developments and point to their potential application to the study of transcriptional and epigenetic changes in neurons in health and disease.
Collapse
Affiliation(s)
- Noel J Buckley
- King's College London, Department of Neuroscience, Institute of Psychiatry, Centre for the Cellular Basis of Behaviour, CCBB/CCIB, Room 1-045, 125 Coldharbour Lane, London SE5 9NU, UK.
| |
Collapse
|
12
|
Affiliation(s)
- Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenchaftszentrum Weihenstephan, 85350 Freising, Germany
| |
Collapse
|
13
|
Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KTV, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology 2007; 148:1059-79. [PMID: 17170095 DOI: 10.1210/en.2006-0683] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human placentation entails the remarkable integration of fetal and maternal cells into a single functional unit. In the basal plate region (the maternal-fetal interface) of the placenta, fetal cytotrophoblasts from the placenta invade the uterus and remodel the resident vasculature and avoid maternal immune rejection. Knowing the molecular bases for these unique cell-cell interactions is important for understanding how this specialized region functions during normal pregnancy with implications for tumor biology and transplantation immunology. Therefore, we undertook a global analysis of the gene expression profiles at the maternal-fetal interface. Basal plate biopsy specimens were obtained from 36 placentas (14-40 wk) at the conclusion of normal pregnancies. RNA was isolated, processed, and hybridized to HG-U133A&B Affymetrix GeneChips. Surprisingly, there was little change in gene expression during the 14- to 24-wk interval. In contrast, 418 genes were differentially expressed at term (37-40 wk) as compared with midgestation (14-24 wk). Subsequent analyses using quantitative PCR and immunolocalization approaches validated a portion of these results. Many of the differentially expressed genes are known in other contexts to be involved in differentiation, motility, transcription, immunity, angiogenesis, extracellular matrix dissolution, or lipid metabolism. One sixth were nonannotated or encoded hypothetical proteins. Modeling based on structural homology revealed potential functions for 31 of these proteins. These data provide a reference set for understanding the molecular components of the dialogue taking place between maternal and fetal cells in the basal plate as well as for future comparisons of alterations in this region that occur in obstetric complications.
Collapse
Affiliation(s)
- Virginia D Winn
- Reproductive Science, University of Colorado Health Sciences Center, 12800 East 19th Avenue, P.O. Box 6511, Aurora, CO 80045, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Sasaki D, Kondo S, Maeda N, Gingeras TR, Hasegawa Y, Hayashizaki Y. Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals. Genomics 2007; 89:541-51. [PMID: 17292583 DOI: 10.1016/j.ygeno.2006.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 11/14/2006] [Accepted: 12/29/2006] [Indexed: 10/23/2022]
Abstract
An assessment of the hybridization characteristics of oligonucleotide tiling arrays was carried out using 162 full-length sequenced cDNA clones in spike-in experiments. The properties of array probes that influence signal intensity were investigated, and their capability in the detection of the cDNA exons was evaluated. The signal intensities detected in exonic and nonexonic genomic regions were examined by focusing on the features of probe sequences that raise or lower the level of intensity and on the causes of false positive signals found in nonexonic regions. The effectiveness of measures used in published protocols to improve the separation between signal and background intensity distributions, including the use of replicates and threshold parameterization of signal intensity, was assessed. Sensitivity and specificity in the detection of exons were measured using various sets of threshold parameters, and the effects of each parameter on the detection efficiency and the rate of false positives were evaluated. It was also demonstrated that hybridization of full-length cDNA clones is an excellent method to investigate the characteristics of oligonucleotide tiling arrays.
Collapse
Affiliation(s)
- Daisuke Sasaki
- Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
| | | | | | | | | | | |
Collapse
|
15
|
Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 2006; 35:D55-60. [PMID: 17099229 PMCID: PMC1669708 DOI: 10.1093/nar/gkl851] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different approaches to the problem of identification. Consequently, it is difficult to maintain a consistent collection of pseudogenes in detail necessary for their effective use. Our database is designed to address this issue. It integrates a variety of heterogeneous resources and supports a subset structure that highlights specific groups of pseudogenes that are of interest to the research community. Tools are provided for the comparison of sets and the creation of layered set unions, enabling researchers to derive a current ‘consensus’ set of pseudogenes. Additional features include versatile search, the capacity for robust interaction with other databases, the ability to reconstruct older versions of the database (accounting for changing genome builds) and an underlying object-oriented interface designed for researchers with a minimal knowledge of programming. At the present time, the database contains more than 100 000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources.
Collapse
Affiliation(s)
- John E Karro
- Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Damaraju S, Murray D, Dufour J, Carandang D, Myrehaug S, Fallone G, Field C, Greiner R, Hanson J, Cass CE, Parliament M. Association of DNA repair and steroid metabolism gene polymorphisms with clinical late toxicity in patients treated with conformal radiotherapy for prostate cancer. Clin Cancer Res 2006; 12:2545-54. [PMID: 16638864 DOI: 10.1158/1078-0432.ccr-05-2703] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To explore the possible relationship between single nucleotide polymorphisms (SNP) in candidate genes encoding DNA damage recognition/repair/response and steroid metabolism proteins with respect to clinical radiation toxicity in a retrospective cohort of patients previously treated with three-dimensional conformal radiotherapy (3-DCRT) for prostate cancer. EXPERIMENTAL DESIGN One hundred twenty-four patients with prostate cancer underwent 3-DCRT at our institution between September 1996 and December 2000. Of these, 83 consented for follow-up of blood sampling and SNP analysis. Twenty-eight patients were documented as having experienced grade >/=2 late bladder or rectal toxicity (scoring system of Radiation Therapy Oncology Group) on at least one follow-up visit. We analyzed 49 SNPs in BRCA1, BRCA2, ESR1, XRCC1, XRCC2, XRCC3, NBN, RAD51, RAD52, LIG4, ATM, BCL2, TGFB1, MSH6, ERCC2, XPF, NR3C1, CYP1A1, CYP2C9, CYP2C19, CYP3A5, CYP2D6, CYP11B2, and CYP17A1 genes using the Pyrosequencing technique. RESULTS Significant univariate associations with late rectal or bladder toxicity (grade >/=2) were found for XRCC3 (A>G 5' untranslated region NT 4541), LIG4 (T>C Asp(568)Asp), MLH1 (C>T, Val(219)Ile), CYP2D6*4 (G>A splicing defect), mean rectal and bladder dose, dose to 30% of rectum or bladder, and age <60 years. On Cox multivariate analysis, significant associations with toxicity were found for LIG4 (T>C, Asp(568)Asp), ERCC2 (G>A, Asp(711)Asp), CYP2D6*4 (G>A, splicing defect), mean bladder dose >60 Gy, and dose to 30% of rectal volume >75 Gy. CONCLUSIONS In this study, we identified SNPs in LIG4, ERCC2, and CYP2D6 genes as putative markers to predict individuals at risk for complications arising from radiation therapy in prostate cancer.
Collapse
Affiliation(s)
- Sambasivarao Damaraju
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
We introduce a new system, called shortHMM, for predicting exons, which predicts individual exons using two related genomes. In this system, we build a hidden semi-Markov model to identify exons. In the hidden Markov model, we propose joint probability models of nucleotides in introns, splice sites, 5'UTR, 3'UTR, and intergenic regions by exploiting the homology between related genomes. In order to reduce the false positive rate of the hidden Markov model, we develop a screening process which is able to identify intergenic regions. We then build a classifier by combining the statistics from the hidden Markov model and the screening process. We implement shortHMM on human-mouse sequence alignments. The source codes are available at < www.stat.purdue.edu/ jingwu/hmm >. Compared to TWINSCAN and SLAM, shortHMM is substantially more powerful in identifying AT-rich RefSeq exons (8% more AT-rich RefSeq exons were predicted), as well as slightly more powerful in identifying RefSeq exons (3-10% more RefSeq exons were predicted), at a similar or lower false positive rate, with less computing time and with less memory usage. Last, shortHMM is also capable of finding new potential exons.
Collapse
Affiliation(s)
- Jing Wu
- Department of Statistics, Purdue University, West Lafayette, Indiana 47906, USA.
| | | |
Collapse
|
18
|
Flicek P, Brent MR. Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biol 2006; 7 Suppl 1:S8.1-9. [PMID: 16925842 PMCID: PMC1810557 DOI: 10.1186/gb-2006-7-s1-s8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is designed to find human alternatively spliced transcripts that are conserved in only one or a limited number of extant species. MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus. Results MARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS) region overlap. Based on the EGASP assessment, MARS is one of the more accurate dual-genome prediction programs. Compared to the GENCODE annotation, we find that predictive sensitivity increases, while specificity decreases, as more informant species are used. MARS correctly predicts alternatively spliced transcripts for 11 of the 236 multi-exon GENCODE genes that are alternatively spliced in the coding region of their transcripts. For these genes a total of 24 correct transcripts are predicted. Conclusion The MARS algorithm is able to predict alternatively spliced transcripts without the use of expressed sequence information, although the number of loci in which multiple predicted transcripts match multiple alternatively spliced transcripts in the GENCODE annotation is relatively small.
Collapse
Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | | |
Collapse
|
19
|
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 2006; 7 Suppl 1:S2.1-31. [PMID: 16925836 PMCID: PMC1810551 DOI: 10.1186/gb-2006-7-s1-s2] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.
Collapse
Affiliation(s)
- Roderic Guigó
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
- Member of the EGASP Organizing Committee
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josep F Abril
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Julien Lagarde
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - France Denoeud
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - Stylianos Antonarakis
- University of Geneva Medical School and University Hospitals of Geneva, 1211 Geneva, Switzerland
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge CB3 2EH, UK
- Member of the EGASP Advisory Board
| | - Vladimir B Bajic
- South African National Bioinformatics Institute (SANBI), University of Western Cape, Bellville 7535, South Africa
- Member of the EGASP Advisory Board
| | - Ewan Birney
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Member of the EGASP Organizing Committee
| | - Robert Castelo
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - Eduardo Eyras
- Centre de Regulació Genòmica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - Catherine Ucla
- University of Geneva Medical School and University Hospitals of Geneva, 1211 Geneva, Switzerland
| | - Thomas R Gingeras
- Affymetrix Inc., Santa Clara, California 95051, USA
- Member of the EGASP Advisory Board
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Member of the EGASP Organizing Committee
| | - Tim Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Member of the EGASP Organizing Committee
| | - Suzanna E Lewis
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94792, USA
- Member of the EGASP Advisory Board
| | - Martin G Reese
- Omicia Inc., Christie Ave., Emeryville, California 94608, USA
- Member of the EGASP Advisory Board
| |
Collapse
|
20
|
Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006; 7:62. [PMID: 16469098 PMCID: PMC1409804 DOI: 10.1186/1471-2105-7-62] [Citation(s) in RCA: 766] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Accepted: 02/09/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence. RESULTS We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. Our method is only moderately effected by the length of a database match. Further, it exploits the information that can be derived from the absence of such matches. As a special case, AUGUSTUS+ can predict genes under user-defined constraints, e.g. if the positions of certain exons are known. With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly. CONCLUSION Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. When a match of a sequence interval to an EST or protein sequence is used it should be treated as compound information rather than as information about individual positions.
Collapse
Affiliation(s)
- Mario Stanke
- lnstitut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
| | - Oliver Schöffmann
- lnstitut für Numerische und Angewandte Mathematik, Universität Göttingen, Göttingen, Germany
| | - Burkhard Morgenstern
- lnstitut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
| | - Stephan Waack
- lnstitut für Numerische und Angewandte Mathematik, Universität Göttingen, Göttingen, Germany
| |
Collapse
|
21
|
Narang V, Sung WK, Mittal A. Computational modeling of oligonucleotide positional densities for human promoter prediction. Artif Intell Med 2005; 35:107-19. [PMID: 16076553 DOI: 10.1016/j.artmed.2005.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2004] [Revised: 01/31/2005] [Accepted: 02/22/2005] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The gene promoter region controls transcriptional initiation of a gene, which is the most important step in gene regulation. In-silico detection of promoter region in genomic sequences has a number of applications in gene discovery and understanding gene expression regulation. However, computational prediction of eukaryotic poly-II promoters has remained a difficult task. This paper introduces a novel statistical technique for detecting promoter regions in long genomic sequences. METHOD A number of existing techniques analyze the occurrence frequencies of oligonucleotides in promoter sequences as compared to other genomic regions. In contrast, the present work studies the positional densities of oligonucleotides in promoter sequences. The analysis does not require any non-promoter sequence dataset or any model of the background oligonucleotide content of the genome. The statistical model learnt from a dataset of promoter sequences automatically recognizes a number of transcription factor binding sites simultaneously with their occurrence positions relative to the transcription start site. Based on this model, a continuous naïve Bayes classifier is developed for the detection of human promoters and transcription start sites in genomic sequences. RESULTS The present study extends the scope of statistical models in general promoter modeling and prediction. Promoter sequence features learnt by the model correlate well with known biological facts. Results of human transcription start site prediction compare favorably with existing 2nd generation promoter prediction tools.
Collapse
Affiliation(s)
- Vipin Narang
- Department of Computer Science, S16 #06-02, 3 Science Drive 2, National University of Singapore, Singapore 117543, Singapore.
| | | | | |
Collapse
|
22
|
Lipovich L, King MC. Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res 2005; 16:45-54. [PMID: 16344557 PMCID: PMC1356128 DOI: 10.1101/gr.3883606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel transcriptional units (TUs) are EST-supported transcribed features not corresponding to known genes. Unconventional gene pairs (UGPs) are pairs of genes and/or TUs sharing exon-to-exon cis-antisense overlaps or putative bidirectional promoters. Computational TU and UGP discovery followed by manual curation was performed in the entire published 34.9-Mb human chromosome 22 euchromatic sequence. Novel TUs (n = 517) were as abundant as known genes (n = 492) and typically did not have nonprimate DNA and protein homologies. One hundred seventy-one (33%) of TUs, but only 13 (3%) of genes, both lacked nonprimate conservation and localized to gaps in the human-mouse BLASTZ alignment. Novel TUs were richer in exonic primate-specific interspersed repetitive elements (P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes: 19% of spliced TUs, versus 5% of spliced genes, had a splice site within a primate-specific repeat. Hence, novel TUs and known genes may represent different portions of the transcriptome. Two hundred nine (21%) of chromosome 22 transcripts participated in 77 cis-antisense and 42 promoter-sharing UGPs. Transcripts involved simultaneously in both UGP types were more common than was expected (P = 0.01). UGPs were nonrandomly distributed along the sequence: 89 (75%) clustered in distinct regions, the sum of which equaled 4.4 Mb (<13% of the chromosome). Eighty (67%) of the UGPs possessed significant locus structure differences between primates and rodents. Since some TUs may be functional noncoding transcripts and since the cis-regulatory potential of UGPs is well recognized, TUs and UGPs specific to the primate lineage may contribute to the genomic basis for primate-specific phenotypes.
Collapse
Affiliation(s)
- Leonard Lipovich
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA.
| | | |
Collapse
|
23
|
Seng TJ, Ichimura K, Liu L, Tingby O, Pearson DM, Collins VP. Complex chromosome 22 rearrangements in astrocytic tumors identified using microsatellite and chromosome 22 tile path array analysis. Genes Chromosomes Cancer 2005; 43:181-93. [PMID: 15770670 DOI: 10.1002/gcc.20181] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Many studies have reported chromosome 22 as being abnormal in astrocytic tumors. In an attempt to map precisely the abnormal region or regions that potentially harbor tumor-suppressor genes or oncogenes, we constructed a chromosome 22 tile path array covering 82% of 22q with the use of 441 chromosome 22 clones. A 10-Mb whole-genome array consisting of 270 clones from all autosomes was included in the array. A total of 126 astrocytic tumors-5 diffuse astrocytomas (A), 29 anaplastic astrocytomas (AA), and 92 glioblastomas (GB)-were examined for chromosome 22 alterations both by microsatellite analysis (using 28 markers to identify allelic imbalance) and with the tile path array. The results showed that chromosome 22 alterations in astrocytic tumors could be complex. A number of tumors had a combination of deletions with and without reduplication of the retained chromosome, as well as copy number gains and amplifications. In two glioblastomas, overlapping homozygous deletions were identified that involved three genes (DEPDC5/KIAA0645, YWHAH, C22ORF24/HSN44A4A). The terminal region telomeric to the clone RP3-398C22 appeared to be the most frequently deleted region. The estimated incidence of any chromosome 22 alteration was 5% in A, 33% in AA, and 38% in GB. This study demonstrated the advantages of combining array comparative genomic hybridization and microsatellite analysis in elucidating complex genomic rearrangements in primary human tumor tissue. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html.
Collapse
Affiliation(s)
- Tzer Jing Seng
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | | | | | | | | |
Collapse
|
24
|
Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol 2005; 349:27-45. [PMID: 15876366 DOI: 10.1016/j.jmb.2005.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 02/16/2005] [Accepted: 02/23/2005] [Indexed: 02/06/2023]
Abstract
Pseudogenes are inheritable genetic elements formally defined by two properties: their similarity to functioning genes and their presumed lack of activity. However, their precise characterization, particularly with respect to the latter quality, has proven elusive. An opportunity to explore this issue arises from the recent emergence of tiling-microarray data showing that intergenic regions (containing pseudogenes) are transcribed to a great degree. Here we focus on the transcriptional activity of pseudogenes on human chromosome 22. First, we integrated several sets of annotation to define a unified list of 525 pseudogenes on the chromosome. To characterize these further, we developed a comprehensive list of genomic features based on conservation in related organisms, expression evidence, and the presence of upstream regulatory sites. Of the 525 unified pseudogenes we could confidently classify 154 as processed and 49 as duplicated. Using data from tiling microarrays, especially from recent high-resolution oligonucleotide arrays, we found some evidence that up to a fifth of the 525 pseudogenes are potentially transcribed. Expressed sequence tags (EST) comparison further validated a number of these, and overall we found 17 pseudogenes with strong support for transcription. In particular, one of the pseudogenes with both EST and microarray evidence for transcription turned out to be a duplicated pseudogene in the cat eye syndrome critical region. Although we could not identify a meaningful number of transcription factor-binding sites (based on chromatin immunoprecipitation-chip data) near pseudogenes, we did find that approximately 12% of the pseudogenes had upstream CpG islands. Finally, analysis of corresponding syntenic regions in the mouse, rat and chimp genomes indicates, as previously suggested, that pseudogenes are less conserved than genes, but more preserved than the intergenic background (all notation is available from http://www.pseudogene.org).
Collapse
Affiliation(s)
- Deyou Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
Genome comparisons are behind the powerful new annotation methods being developed to find all human genes, as well as genes from other genomes. Genomes are now frequently being studied in pairs to provide cross-comparison datasets. This 'Noah's Ark' approach often reveals unsuspected genes and may support the deletion of false-positive predictions. Joining mouse and human as the cross-comparison dataset for the first two mammals are: two Drosophila species, D. melanogaster and D. pseudoobscura; two sea squirts, Ciona intestinalis and Ciona savignyi; four yeast (Saccharomyces) species; two nematodes, Caenorhabditis elegans and Caenorhabditis briggsae; and two pufferfish (Takefugu rubripes and Tetraodon nigroviridis). Even genomes like yeast and C. elegans, which have been known for more than five years, are now being significantly improved. Methods developed for yeast or nematodes will now be applied to mouse and human, and soon to additional mammals such as rat and dog, to identify all the mammalian protein-coding genes. Current large disparities between human Unigene predictions (127,835 genes) and gene-scanning methods (45,000 genes) still need to be resolved. This will be the challenge during the next few years.
Collapse
Affiliation(s)
- David R Nelson
- Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA
| | - Daniel W Nebert
- Department of Environmental Health and Center for Environmental Genetics (CEG), University of Cincinnati Medical Center, Cincinnati, Ohio 45267-0056, USA
| |
Collapse
|
26
|
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigó R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quétier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004; 431:946-57. [PMID: 15496914 DOI: 10.1038/nature03025] [Citation(s) in RCA: 1406] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 09/08/2004] [Indexed: 12/16/2022]
Abstract
Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
Collapse
Affiliation(s)
- Olivier Jaillon
- UMR 8030 Genoscope, CNRS and Université d'Evry, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Finishing the euchromatic sequence of the human genome. Nature 2004; 431:931-45. [PMID: 15496913 DOI: 10.1038/nature03001] [Citation(s) in RCA: 2806] [Impact Index Per Article: 140.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 09/07/2004] [Indexed: 12/13/2022]
Abstract
The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
Collapse
|
28
|
Arcand SL, Mes-Masson AM, Provencher D, Hudson TJ, Tonin PN. Gene expression microarray analysis and genome databases facilitate the characterization of a chromosome 22 derived homogeneously staining region. Mol Carcinog 2004; 41:17-38. [PMID: 15352123 DOI: 10.1002/mc.20038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Karyotype and fluorescence in situ hybridization (FISH) analyses previously identified a homogeneously staining region (HSR) derived from chromosome 22 in OV90, an epithelial ovarian cancer (EOC) cell line. Affymetrix expression microarrays in combination with the UniGene and Human Genome Browser databases were used to identify the candidate genes comprising the amplicon of the HSR, based on comparison of expression profiles of OV90, EOC cell lines lacking HSRs and primary cultures of normal ovarian surface epithelial (NOSE) cells. A group of probe sets displaying a minimum 3-fold overexpression with a high reliability score (P-call) in OV90 were identified which represented genes that mapped within a 1-2 Mb interval on chromosome 22. A large number of probe sets, some of which represent the same genes, displayed no evidence of overexpression and/or low reliability scores (A-call). An investigation of the probe set sequences with the Affymetrix and Sanger Institute Chromosome 22 Group databases revealed that some of the probe sets displaying discordant results for the same gene were complementary to intronic sequences and/or the antisense strand. Microarray results were validated by RT-PCR. Genomic analysis suggests that the HSR was derived from the amplification of a 1.1 Mb interval defined by the chromosomal map positions of ZNF74 and Hs.372662, at 22q11.21. The deduced amplicon is derived from a complex region of chromosome 22 that harbors low-copy repeats (LCRs). The amplicon contains 18 genes as likely targets for gene amplification. This study illustrates that large-scale expression microarray analysis in combination with genome databases is sufficient for deducing target genes associated with amplicons and stresses the importance of investigating probe set design before engaging in validation studies.
Collapse
Affiliation(s)
- Suzanna L Arcand
- Department of Human Genetics, McGill University, Montreal, Canada
| | | | | | | | | |
Collapse
|
29
|
Lipovich L, King MC. Novel transcriptional units and unconventional gene pairs in the human genome: toward a sequence-level basis for primate-specific phenotypes? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:461-70. [PMID: 15338649 DOI: 10.1101/sqb.2003.68.461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- L Lipovich
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA
| | | |
Collapse
|
30
|
Collins JE, Wright CL, Edwards CA, Davis MP, Grinham JA, Cole CG, Goward ME, Aguado B, Mallya M, Mokrab Y, Huckle EJ, Beare DM, Dunham I. A genome annotation-driven approach to cloning the human ORFeome. Genome Biol 2004; 5:R84. [PMID: 15461802 PMCID: PMC545604 DOI: 10.1186/gb-2004-5-10-r84] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Revised: 07/16/2004] [Accepted: 08/11/2004] [Indexed: 11/10/2022] Open
Abstract
We have developed a systematic approach to generating cDNA clones containing full-length open reading frames (ORFs), exploiting knowledge of gene structure from genomic sequence. Each ORF was amplified by PCR from a pool of primary cDNAs, cloned and confirmed by sequencing. We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined.
Collapse
Affiliation(s)
- John E Collins
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Charmain L Wright
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Carol A Edwards
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Current address: Department of Anatomy, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Matthew P Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James A Grinham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Charlotte G Cole
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Melanie E Goward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Begoña Aguado
- MRC Rosalind Franklin Centre for Genomics Research (formerly MRC UK Human Genome Mapping Resource Centre), Hinxton, Cambridge, CB10 1SB, UK
- Current address: Centro Nacional de Biotecnología (CNB), Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Meera Mallya
- MRC Rosalind Franklin Centre for Genomics Research (formerly MRC UK Human Genome Mapping Resource Centre), Hinxton, Cambridge, CB10 1SB, UK
- Current address: Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2XY, UK
| | - Younes Mokrab
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Current address: Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Elizabeth J Huckle
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David M Beare
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ian Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
31
|
Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004; 5:R73. [PMID: 15461792 PMCID: PMC545593 DOI: 10.1186/gb-2004-5-10-r73] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 07/07/2004] [Accepted: 08/16/2004] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. RESULTS The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. CONCLUSIONS These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized.
Collapse
Affiliation(s)
- Eric E Schadt
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Stephen W Edwards
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | - Dan Holder
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Lisa Ying
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Vladimir Svetnik
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Amy Leonardson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Kyle W Hart
- Rally Scientific, 41 Fayette Street, Suite 1, Watertown, MA 02472, USA
| | - Archie Russell
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guoya Li
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guy Cavet
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - John Castle
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Paul McDonagh
- Amgen Inc, 1201 Amgen Court W, Seattle, WA 98119, USA
| | - Zhengyan Kan
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ronghua Chen
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Andrew Kasarskis
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Mihai Margarint
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ramon M Caceres
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Jason M Johnson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | | | | | - Daniel D Shoemaker
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| |
Collapse
|
32
|
Down TA, Hubbard TJP. What can we learn from noncoding regions of similarity between genomes? BMC Bioinformatics 2004; 5:131. [PMID: 15369604 PMCID: PMC523850 DOI: 10.1186/1471-2105-5-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 09/15/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to known protein-coding genes, large amounts of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome. METHODS Here we used a motif-oriented machine learning method based on the Relevance Vector Machine algorithm to extract the strongest signal from a set of non-coding conserved sequences. RESULTS We successfully fitted models to reflect the non-coding sequences, and showed that the results were quite consistent for repeated training runs. Using the learned models to scan genomic sequence, we found that they often made predictions close to the start of annotated genes. We compared this method with other published promoter-prediction systems, and showed that the set of promoters which are detected by this method is substantially similar to that detected by existing methods. CONCLUSIONS The results presented here indicate that the promoter signal is the strongest single motif-based signal in the non-coding functional fraction of the genome. They also lend support to the belief that there exists a substantial subset of promoter regions which share several common features including, but not restricted to, a relative abundance of CpG dinucleotides. This subset is detectable by a variety of distinct computational methods.
Collapse
Affiliation(s)
- Thomas A Down
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tim JP Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
33
|
Taylor TD. After 'completion': the changing face of human chromosomes 21 and 22. Genome Biol 2004; 5:111. [PMID: 15239819 PMCID: PMC463270 DOI: 10.1186/gb-2004-5-7-111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the four years since the publication of the first two 'complete' human chromosome sequences the type of research being done on each has shifted subtly, reflecting the impact of genomic data on biological science in general. In the four years since the publication of the first two 'complete' human chromosome sequences the type of research being done on each has shifted subtly, reflecting the impact of genomic data on biological science in general. There is now considerably more gene-expression evidence to support predicted genes, and the annotation of functions for previously unknown genes, including those implicated in disease, is gradually improving.
Collapse
Affiliation(s)
- Todd Duane Taylor
- RIKEN Genomic Sciences Center, Human Genome Research Group, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
34
|
Abstract
We have the human genome sequence. It is freely available, accurate and nearly complete. But is the genome ready for medicine? The new resource is already changing genetic research strategies to find information of medical value. Now we need high-quality annotation of all the functionally important sequences and the variations within them that contribute to health and disease. To achieve this, we need more genome sequences, systematic experimental analyses, and extensive information on human phenotypes. Flexible and user-friendly access to well-annotated genomes will create an environment for innovation, and the potential for unlimited use of sequencing in biomedical research and practice.
Collapse
Affiliation(s)
- David R Bentley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| |
Collapse
|
35
|
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol 2004; 24:3804-14. [PMID: 15082775 PMCID: PMC387762 DOI: 10.1128/mcb.24.9.3804-3814.2004] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An unbiased, global analysis of where CREB binds has not been performed. We have mapped for the first time the binding distribution of CREB along an entire human chromosome. Chromatin immunoprecipitation of CREB-associated DNA and subsequent hybridization of the associated DNA to a genomic DNA microarray containing all of the nonrepetitive DNA of human chromosome 22 revealed 215 binding sites corresponding to 192 different loci and 100 annotated potential gene targets. We found binding near or within many genes involved in signal transduction and neuronal function. We also found that only a small fraction of CREB binding sites lay near well-defined 5' ends of genes; the majority of sites were found elsewhere, including introns and unannotated regions. Several of the latter lay near novel unannotated transcriptionally active regions. Few CREB targets were found near full-length cyclic AMP response element sites; the majority contained shorter versions or close matches to this sequence. Several of the CREB targets were altered in their expression by treatment with forskolin; interestingly, both induced and repressed genes were found. Our results provide novel molecular insights into how CREB mediates its functions in humans.
Collapse
Affiliation(s)
- Ghia Euskirchen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8005, USA>
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Eichler EE, Clark RA, She X. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 2004; 5:345-54. [PMID: 15143317 DOI: 10.1038/nrg1322] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Evan E Eichler
- Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, BRB720, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
| | | | | |
Collapse
|
37
|
Searle SMJ, Gilbert J, Iyer V, Clamp M. The otter annotation system. Genome Res 2004; 14:963-70. [PMID: 15123593 PMCID: PMC479127 DOI: 10.1101/gr.1864804] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Accepted: 03/04/2004] [Indexed: 11/25/2022]
Abstract
With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly even more important, is the requirement to curate and improve this annotation in the light of future data. For this to be possible, there is a need for tools to access and manage the annotation. Ensembl provides an excellent means for storing gene structures, genome features, and sequence, but it does not support the extra textual data necessary for manual annotation. We have extended Ensembl to create the Otter manual annotation system. This comprises a relational database schema for storing the manual annotation data, an application-programming interface (API) to access it, an extensible markup language (XML) format to allow transfer of the data, and a server to allow multiuser/multimachine access to the data. We have also written a data-adaptor plugin for the Apollo Browser/Editor to enable it to utilize an Otter server. The otter database is currently used by the Vertebrate Genome Annotation (VEGA) site (http://vega.sanger.ac.uk), which provides access to manually curated human chromosomes. Support is also being developed for using the AceDB annotation editor, FMap, via a perl wrapper called Lace. The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20.
Collapse
Affiliation(s)
- Stephen M J Searle
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | | | | |
Collapse
|
38
|
Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RIS, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SCM, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JGR, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJF, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, Ross MT. The DNA sequence and analysis of human chromosome 13. Nature 2004; 428:522-8. [PMID: 15057823 PMCID: PMC2665288 DOI: 10.1038/nature02379] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 01/27/2004] [Indexed: 12/14/2022]
Abstract
Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.
Collapse
Affiliation(s)
- A Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004; 14:331-42. [PMID: 14993201 PMCID: PMC353210 DOI: 10.1101/gr.2094104] [Citation(s) in RCA: 417] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density oligonucleotide arrays on cytosolic poly(A)(+) RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas an additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and up to 21% of known genes have only a single isoform based on exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with an identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of any known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation in expression than the well-characterized genes. Novel transcripts were further characterized based on their distance to annotations, transcript size, coding capacity, and identification as antisense to intronic sequences. By RT-PCR, 126 novel transcripts were independently verified, resulting in a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome.
Collapse
Affiliation(s)
- Dione Kampa
- Affymetrix, Santa Clara, California 95051, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Porcel BM, Delfour O, Castelli V, De Berardinis V, Friedlander L, Cruaud C, Ureta-Vidal A, Scarpelli C, Wincker P, Schächter V, Saurin W, Gyapay G, Salanoubat M, Weissenbach J. Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. Genome Res 2004; 14:463-71. [PMID: 14962985 PMCID: PMC353234 DOI: 10.1101/gr.1481104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A collection of 90,000 human cDNA clones generated to increase the fraction of "full-length" cDNAs available was analyzed by sequence alignment on the human genome assembly. Five hundred fifty-two gene models not found in LocusLink, with coding regions of at least 300 bp, were defined by using this collection. Exon composition proposed for novel genes showed an average of 4.7 exons per gene. In 20% of the cases, at least half of the exons predicted for new genes coincided with evolutionary conserved regions defined by sequence comparisons with the pufferfish Tetraodon nigroviridis. Among this subset, CpG islands were observed at the 5' end of 75%. In-frame stop codons upstream of the initiator ATG were present in 49% of the new genes, and 16% contained a coding region comprising at least 50% of the cDNA sequence. This cDNA resource also provided candidate small protein-coding genes, usually not included in genome annotations. In addition, analysis of a sample from this cDNA collection indicates that approximately 380 gene models described in LocusLink could be extended at their 5' end by at least one new exon. Finally, this cDNA resource provided an experimental support for annotations based exclusively on predictions, thus representing a resource substantially improving the human genome annotation.
Collapse
Affiliation(s)
- Betina M Porcel
- Genoscope-Centre National de Séquençage and CNRS UMR-8030, 91000 Evry, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE. Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res 2004; 13:2519-32. [PMID: 14656960 PMCID: PMC403794 DOI: 10.1101/gr.1549503] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, der(22) syndrome, and cat-eye syndrome. The ability to trace the substrates and products of recombination events provides a unique opportunity to identify the mechanisms responsible for shaping LCR22s. We examined the genomic sequence of known LCR22 genes and their duplicated derivatives. We found Alu (SINE) elements at the breakpoints in the substrates and at the junctions in the truncated products of recombination for USP18, GGT, and GGTLA, consistent with Alu-mediated unequal crossing-over events. In addition, we were able to trace a likely interchromosomal Alu-mediated fusion between IGSF3 on 1p13.1 and GGT on 22q11.2. Breakpoints occurred inside Alu elements as well as in the 5' or 3' ends of them. A possible stimulus for the 5' or 3' terminal rearrangements may be the high sequence similarities between different Alu elements, combined with a potential recombinogenic role of retrotransposon target-site duplications flanking the Alu element, containing potentially kinkable DNA sites. Such sites may represent focal points for recombination. Thus, genome shuffling by Alu-mediated rearrangements has contributed to genome architecture during primate evolution.
Collapse
Affiliation(s)
- Melanie Babcock
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 2004; 13:2559-67. [PMID: 14656963 PMCID: PMC403797 DOI: 10.1101/gr.1455503] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide substitutions (KA/KS). We identified 19,724 regions of which 95% +/- 3% are estimated to evolve neutrally and thus are likely to encode pseudogenes. Half of these have no detectable truncation in their pseudocoding regions and therefore are not identifiable by methods that require the presence of truncations to prove nonfunctionality. A comparative analysis with the mouse genome showed that 70% of these pseudogenes have a retrotranspositional origin (processed), and the rest arose by segmental duplication (nonprocessed). Although the spread of both types of pseudogenes correlates with chromosome size, nonprocessed pseudogenes appear to be enriched in regions with high gene density. It is likely that the human pseudogenes identified here represent only a small fraction of the total, which probably exceeds the number of genes.
Collapse
|
43
|
Thomas S, Porteous D, Visscher PM. Power of direct vs. indirect haplotyping in association studies. Genet Epidemiol 2004; 26:116-24. [PMID: 14748011 DOI: 10.1002/gepi.10300] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Haplotype analysis is essential to studies of the genetic factors underlying human disease, but requires a large sample size of phase-known data. Recently, directly haplotyping individuals was suggested as a means of maximizing the phase-known data from a sample. Haplotyping, however, is much more labor-intensive than indirectly inferring haplotypes from genotypes (genotyping). This study uses simulations to compare the power of each methodology to detect associations between a haplotype and a trait or disease locus under conditions of varying linkage disequilibrium. The relative power of haplotyping over genotyping in association studies increases with decreasing sample size, decreasing linkage disequilibrium, increasing [corrected] numbers of marker loci, and decreasing numbers of different haplotypes. In addition, the frequency of the haplotype of interest and the magnitude of its association with the disease affect the power. From a cost-benefit standpoint, genotyping would be favored with large multiplicative risks (relative risk of haplotype >2.5). If case numbers are limiting rather than cost, haplotyping would maximize the information obtained. At small haplotype frequencies (e.g., <0.05), haplotyping is relatively more efficient, but there is little absolute power to detect associations under either methodology. Given the much larger laboratory resources required for direct haplotyping, genotyping would probably be favored under most conditions, but this must be balanced against the unit costs associated with recruitment and phenotyping. In the context of multipurpose, prospective cohort studies (e.g., the UK Biobank study), there may be a general value in establishing a series of directly haplotyped individuals to serve as controls for a number of alternative studies.
Collapse
Affiliation(s)
- Stuart Thomas
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
| | | | | |
Collapse
|
44
|
Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP. Replication timing of the human genome. Hum Mol Genet 2003; 13:191-202. [PMID: 14645202 DOI: 10.1093/hmg/ddh016] [Citation(s) in RCA: 242] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have developed a directly quantitative method utilizing genomic clone DNA microarrays to assess the replication timing of sequences during the S phase of the cell cycle. The genomic resolution of the replication timing measurements is limited only by the genomic clone size and density. We demonstrate the power of this approach by constructing a genome-wide map of replication timing in human lymphoblastoid cells using an array with clones spaced at 1 Mb intervals and a high-resolution replication timing map of 22q with an array utilizing overlapping sequencing tile path clones. We show a positive correlation, both genome-wide and at a high resolution, between replication timing and a range of genome parameters including GC content, gene density and transcriptional activity.
Collapse
Affiliation(s)
- Kathryn Woodfine
- The Welcome Trust Sanger Institute, Welcome Genome Campus, Cambridge, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JGR, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RIS, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJR, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJF, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S. The DNA sequence and analysis of human chromosome 6. Nature 2003; 425:805-11. [PMID: 14574404 DOI: 10.1038/nature02055] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2003] [Accepted: 09/11/2003] [Indexed: 01/17/2023]
Abstract
Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.
Collapse
Affiliation(s)
- A J Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A 2003; 100:12247-52. [PMID: 14527995 PMCID: PMC218744 DOI: 10.1073/pnas.2135255100] [Citation(s) in RCA: 266] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-kappaB family of transcription factors plays an essential role in regulating the induction of genes involved in several physiological processes, including apoptosis, immunity, and inflammation. The binding sites of the NF-kappaB family member p65 were determined by using chromatin immunoprecipitation and a genomic microarray of human chromosome 22 DNA. Sites of binding were observed along the entire chromosome in both coding and noncoding regions, with an enrichment at the 5' end of genes. Strikingly, a significant proportion of binding was seen in intronic regions, demonstrating that transcription factor binding is not restricted to promoter regions. NF-kappaB binding was also found at genes whose expression was regulated by tumor necrosis factor alpha, a known inducer of NF-kappaB-dependent gene expression, as well as adjacent to genes whose expression is not affected by tumor necrosis factor alpha. Many of these latter genes are either known to be activated by NF-kappaB under other conditions or are consistent with NF-kappaB's role in the immune and apoptotic responses. Our results suggest that binding is not restricted to promoter regions and that NF-kappaB binding occurs at a significant number of genes whose expression is not altered, thereby suggesting that binding alone is not sufficient for gene activation.
Collapse
Affiliation(s)
- Rebecca Martone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8005, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003; 100:11484-9. [PMID: 14500911 PMCID: PMC208784 DOI: 10.1073/pnas.1932072100] [Citation(s) in RCA: 603] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2003] [Indexed: 11/18/2022] Open
Abstract
This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a "syntenic" subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that approximately 2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
Collapse
Affiliation(s)
- W James Kent
- Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064, USA.
| | | | | | | | | |
Collapse
|
48
|
Abstract
Fifty years after the publication of DNA structure, the whole human genome sequence will be officially finished. This achievement marks the beginning of the task to catalogue every human gene and identify each of their function expression patterns. Currently, researchers estimate that there are about 30,000 human genes and approximately 70% of these can be automatically predicted using a combination of ab initio and similarity-based programs. However, to experimentally investigate every gene's function, the research community requires a high-quality annotation of alternative splicing, pseudogenes, and promoter regions that can only be provided by manual intervention. Manual curation of the human genome will be a long-term project as experimental data are continually produced to confirm or refine the predictions, and new features such as noncoding RNAs and enhancers have not been fully identified. Such a highly curated human gene-set made publicly available will be a great asset for the experimental community and for future comparative genome projects.
Collapse
Affiliation(s)
- Jennifer L Ashurst
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
| | | |
Collapse
|
49
|
Wang J, Li S, Zhang Y, Zheng H, Xu Z, Ye J, Yu J, Wong GKS. Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 2003; 4:741-9. [PMID: 12951575 DOI: 10.1038/nrg1160] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns)--genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted.
Collapse
Affiliation(s)
- Jun Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Chong A, Zhang G, Bajic VB. FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. Nucleic Acids Res 2003; 31:3546-53. [PMID: 12824363 PMCID: PMC169010 DOI: 10.1093/nar/gkg604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
FIE2 (5' end Information Extraction v2) is a web-based program for easy identification and extraction of nucleotide sequence around the start of genes (promoter region) and their translation initiation site (TIS). Using information provided by the National Center for Biotechnology Information's (NCBI's) LocusLink, FIE2 identifies the 5'-most end of a gene on its respective chromosome based on alignment of a selected set of mRNAs representative of the gene. FIE2 then uses currently available human genome sequence information to extract the desired sequences. The accuracy of the information extracted is therefore limited by the accuracy and completeness of the sequence annotation and sequence alignment provided by LocusLink. In addition, multiple TIS positions are also occasionally presented, for example, as a result of multiple alignments of transcript variants. One of the key criteria of FIE2 is that it should extract only the correct information or attempt no extraction at all. To date, the authors are not aware of any publicly available web-based tool that uses the human genomic sequence to extract pertinent promoter- and TIS-region information in this fashion. FIE2 is freely available at http://sdmc.lit.org.sg/FIE2.0.
Collapse
Affiliation(s)
- Allen Chong
- Molecular Bioinformatics Group, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613.
| | | | | |
Collapse
|