2
|
Brody T, Yavatkar AS, Kuzin A, Kundu M, Tyson LJ, Ross J, Lin TY, Lee CH, Awasaki T, Lee T, Odenwald WF. Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers. Dev Dyn 2011; 241:169-89. [PMID: 22174086 PMCID: PMC3243966 DOI: 10.1002/dvdy.22728] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2011] [Indexed: 12/05/2022] Open
Abstract
Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions:cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Thomas Brody
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, Maryland 20892, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Xie T, Rowen L, Aguado B, Ahearn ME, Madan A, Qin S, Campbell RD, Hood L. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res 2004; 13:2621-36. [PMID: 14656967 PMCID: PMC403804 DOI: 10.1101/gr.1736803] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In mammals, the Major Histocompatibility Complex class I and II gene clusters are separated by an approximately 700-kb stretch of sequence called the MHC class III region, which has been associated with susceptibility to numerous diseases. To facilitate understanding of this medically important and architecturally interesting portion of the genome, we have sequenced and analyzed both the human and mouse class III regions. The cross-species comparison has facilitated the identification of 60 genes in human and 61 in mouse, including a potential RNA gene for which the introns are more conserved across species than the exons. Delineation of global organization, gene structure, alternative splice forms, protein similarities, and potential cis-regulatory elements leads to several conclusions: (1) The human MHC class III region is the most gene-dense region of the human genome: >14% of the sequence is coding, approximately 72% of the region is transcribed, and there is an average of 8.5 genes per 100 kb. (2) Gene sizes, number of exons, and intergenic distances are for the most part similar in both species, implying that interspersed repeats have had little impact in disrupting the tight organization of this densely packed set of genes. (3) The region contains a heterogeneous mixture of genes, only a few of which have a clearly defined and proven function. Although many of the genes are of ancient origin, some appear to exist only in mammals and fish, implying they might be specific to vertebrates. (4) Conserved noncoding sequences are found primarily in or near the 5'-UTR or the first intron of genes, and seldom in the intergenic regions. Many of these conserved blocks are likely to be cis-regulatory elements.
Collapse
Affiliation(s)
- Tao Xie
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Davodeau F, Difilippantonio M, Roldan E, Malissen M, Casanova JL, Couedel C, Morcet JF, Merkenschlager M, Nussenzweig A, Bonneville M, Malissen B. The tight interallelic positional coincidence that distinguishes T-cell receptor Jalpha usage does not result from homologous chromosomal pairing during ValphaJalpha rearrangement. EMBO J 2001; 20:4717-29. [PMID: 11532936 PMCID: PMC125590 DOI: 10.1093/emboj/20.17.4717] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The T-cell receptor (TCR) alpha locus is thought to undergo multiple cycles of secondary rearrangements that maximize the generation of alphabeta T cells. Taking advantage of the nucleotide sequence of the human Valpha and Jalpha segments, we undertook a locus-wide analysis of TCRalpha gene rearrangements in human alphabeta T-cell clones. In most clones, ValphaJalpha rearrangements occurred on both homologous chromosomes and, remarkably, resulted in the use of two neighboring Jalpha segments. No such interallelic coincidence was found for the position of the two rearranged Valpha segments, and there was only a loose correlation between the 5' or 3' chromosomal position of the Valpha and Jalpha segments used in a given rearrangement. These observations question the occurrence of extensive rounds of secondary Valpha-->Jalpha rearrangements and of a coordinated and polarized usage of the Valpha and Jalpha libraries. Fluorescence in situ hybridization analysis of developing T cells in which TCRalpha rearrangements are taking place showed that the interallelic positional coincidence in Jalpha usage cannot be explained by the stable juxtaposition of homologous Jalpha clusters.
Collapse
Affiliation(s)
| | - Michael Difilippantonio
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - Esther Roldan
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - Marie Malissen
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - Jean-Laurent Casanova
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | | | | | - Matthias Merkenschlager
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - André Nussenzweig
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - Marc Bonneville
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| | - Bernard Malissen
- INSERM U.463, Institut de Biologie, 9 quai Moncousu, 44035 Nantes Cedex 01,
Centre d’Immunologie de Marseille-Luminy, INSERM-CNRS-Univ. Med., Campus de Luminy, Case 906, 13288 Marseille Cedex 9, Laboratoire de Génétique Humaine des Maladies Infectieuses, Faculté de Médecine Necker, 156 rue de Vaugirard, 75015 Paris, France, Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK and Genetics Branch and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1360, USA Corresponding author e-mail:
| |
Collapse
|