1
|
Luan Q, Chen Q, Friedrich M. The Pax6 genes eyeless and twin of eyeless are required for global patterning of the ocular segment in the Tribolium embryo. Dev Biol 2014; 394:367-81. [PMID: 25149513 DOI: 10.1016/j.ydbio.2014.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 06/23/2014] [Accepted: 08/06/2014] [Indexed: 01/08/2023]
Abstract
The transcription factor gene Pax6 is widely considered a master regulator of eye development in bilaterian animals. However, the existence of visual organs that develop without Pax6 input and the considerable pleiotropy of Pax6 outside the visual system dictate further studies into defining ancestral functions of this important regulator. Previous work has shown that the combinatorial knockdown of the insect Pax6 orthologs eyeless (ey) and twin of eyeless (toy) perturbs the development of the visual system but also other areas of the larval head in the red flour beetle Tribolium castaneum. To elucidate the role of Pax6 during Tribolium head development in more detail, we studied head cuticle morphology, brain anatomy, embryonic head morphogenesis, and developmental marker gene expression in combinatorial ey and toy knockdown animals. Our experiments reveal that Pax6 is broadly required for patterning the anterior embryonic head. One of the earliest detectable roles is the formation of the embryonic head lobes, which originate from within the ocular segment and give rise to large parts of the supraesophageal brain including the mushroom body, a part of the posterior head capsule cuticle, and the visual system. We present further evidence that toy continues to be required for the development of the larval eyes after formation of the embryonic head lobes in cooperation with the eye developmental transcription factor dachshund (dac). The sum of our findings suggests that Pax6 functions as a competence factor throughout the development of the insect ocular segment. Comparative evidence identifies this function as an ancestral aspect of bilaterian head development.
Collapse
Affiliation(s)
- Qing Luan
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Qing Chen
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA.
| |
Collapse
|
2
|
Muto R, Yamamori S, Ohashi H, Osawa M. Prediction by FISH analysis of the occurrence of Wilms tumor in aniridia patients. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 108:285-9. [PMID: 11920832 DOI: 10.1002/ajmg.10094] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Aniridia is an autosomal dominant eye anomaly caused by haploinsufficiency of the PAX6 gene, of which abnormalities include base alterations, position effects and deletions. When deletion involves its adjacent genes, i.e., those in the PAX6-WT1 critical region (WTCR), patients are predisposed to Wilms tumor. We studied 18 patients with aniridia, five of whom had chromosome deletion involving 11p13, two a translocation t(10;11)(p13;p13) or a der(14;21)(q10;q10)mat, and 11 had a normal karyotype. Fluorescence in situ hybridization (FISH) using four P1-derived artificial chromosome (PAC) clones located at WTCR was carried out in the 18 patients to identify a deletion extent. Of the 18 patients, eight had a deletion of WTCR: four had microscopic deletion and four a deletion of WTCR. Deleted region in one patient with a microscopic deletion was distal to the critical region. Four of the eight patients with a deletion encompassing WTCR developed Wilms tumor, and the other four did not (two were too young to be evaluated for the tumor development). The data in the present study, together with four similar previous works, indicate that of a total of 102 aniridia patients, 29 had a deletion spanning WTCR. Wilms tumor developed in 13 (45%) of the 29 patients, whereas patients without deletion in this region did not develop the tumor. In other words, aniridia patients with WT1 deletion run a high risk of developing Wilms tumor, and those without the deletion do not.
Collapse
MESH Headings
- Adolescent
- Aniridia/genetics
- Aniridia/pathology
- Child
- Child, Preschool
- Chromosome Deletion
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 21/genetics
- Eye Proteins
- Female
- Homeodomain Proteins/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Infant
- Karyotyping
- Male
- PAX6 Transcription Factor
- Paired Box Transcription Factors
- Repressor Proteins
- Translocation, Genetic
- WT1 Proteins/genetics
- Wilms Tumor/genetics
- Wilms Tumor/pathology
Collapse
Affiliation(s)
- Reiko Muto
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.
| | | | | | | |
Collapse
|
3
|
Soderlund C, Humphray S, Dunham A, French L. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 2000. [PMID: 11076862 DOI: 10.1101/gr.gr‐1375r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.
Collapse
Affiliation(s)
- C Soderlund
- Clemson University Genomic Institute, Clemson, South Carolina 29634-5808, USA.
| | | | | | | |
Collapse
|
4
|
MacKenzie A, Payne C, Boyle S, Clarke AR, Quinn JP. The human preprotachykinin-A gene promoter has been highly conserved and can drive human-like marker gene expression in the adult mouse CNS. Mol Cell Neurosci 2000; 16:620-30. [PMID: 11083923 DOI: 10.1006/mcne.2000.0902] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Toward an understanding of the mechanisms controlling Preprotachykinin-A (PPTA) transcription, we introduced a 380-kb human yeast artificial chromosome containing the PPTA gene tagged with the beta-galactosidase gene into transgenic mice. This resulted in a pattern of LacZ expression in the central nervous system (CNS) remarkably similar to that reported for PPTA mRNA in the rat. However, the human gene drove expression in areas of the mouse CNS not associated with strong PPTA expression in rodents but which have been shown to express PPTA in the human. This study clearly demonstrates the high degree of conservation of the mechanisms involved in PPTA transcription that has occurred throughout 100 million of divergent human and rodent evolution. This study also defines the maximum linear extent of the human PPT-A promoter. We believe these findings constitute the removal of a significant obstacle in studying the transcriptional regulation of the human PPTA gene in vivo.
Collapse
Affiliation(s)
- A MacKenzie
- Department of Veterinary Pathology, Royal (Dick) School of Veterinary Studies, Summerhall Square, The University of Edinburgh, Edinburgh EH91QH, Scotland
| | | | | | | | | |
Collapse
|
5
|
Soderlund C, Humphray S, Dunham A, French L. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 2000; 10:1772-87. [PMID: 11076862 PMCID: PMC310962 DOI: 10.1101/gr.gr-1375r] [Citation(s) in RCA: 267] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.
Collapse
Affiliation(s)
- C Soderlund
- Clemson University Genomic Institute, Clemson, South Carolina 29634-5808, USA.
| | | | | | | |
Collapse
|
6
|
Gawin B, Niederführ A, Schumacher N, Hummerich H, Little PF, Gessler M. A 7.5 Mb sequence-ready PAC contig and gene expression map of human chromosome 11p13-p14.1. Genome Res 1999; 9:1074-86. [PMID: 10568747 PMCID: PMC310838 DOI: 10.1101/gr.9.11.1074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The region p13 of the short arm of human chromosome 11 has been studied intensely during the search for genes involved in the etiology of the Wilms' tumor, aniridia, genitourinary abnormalities, mental retardation (WAGR) syndrome, and related conditions. The gene map for this region is far from being complete, however, strengthening the need for additional gene identification efforts. We describe the extension of an existing contig map with P1-derived artificial chromosomes (PACs) to cover 7.5 Mb of 11p13-14.1. The extended sequence-ready contig was established by end probe walking and fingerprinting and consists of 201 PAC clones. Utilizing bins defined by overlapping PACs, we generated a detailed gene map containing 20 genes as well as 22 anonymous ESTs which have been identified by searching the RH databases. RH maps and our established gene map show global correlation, but the limits of resolution of the current RH panels are evident at this scale. Initial expression studies on the novel genes have been performed by Northern blot analyses. To extend these expression profiles, corresponding mouse cDNA clones were identified by database search and employed for Northern blot analyses and RNA in situ hybridizations to mouse embryo sections. Genomic sequencing of clones along a minimal tiling path through the contig is currently under way and will facilitate these expression studies by in silico gene identification approaches.
Collapse
Affiliation(s)
- B Gawin
- Physiologische Chemie I, Biozentrum der Universität Würzburg, Germany
| | | | | | | | | | | |
Collapse
|
7
|
Hildmann T, Kong X, O’Brien J, Riesselman L, Christensen HM, Dagand E, Lehrach H, Yaspo ML. A Contiguous 3-Mb Sequence-Ready Map in the S3–MX Region on 21q22.2 Based on High- Throughput Nonisotopic Library Screenings. Genome Res 1999. [DOI: 10.1101/gr.9.4.360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Progress in complete genomic sequencing of human chromosome 21 relies on the construction of high-quality bacterial clone maps spanning large chromosomal regions. To achieve this goal, we have applied a strategy based on nonradioactive hybridizations to contig building. A contiguous sequence-ready map was constructed in the Down syndrome congenital heart disease (DS-CHD) region in 21q22.2, as a framework for large-scale genomic sequencing and positional candidate gene approach. Contig assembly was performed essentially by high throughput nonisotopic screenings of genomic libraries, prior to clone validation by (1) restriction digest fingerprinting, (2) STS analysis, (3) Southern hybridizations, and (4) FISH analysis. The contig contains a total of 50 STSs, of which 13 were newly isolated. A minimum tiling path (MTP) was subsequently defined that consists of 20 PACs, 2 BACs, and 5 cosmids covering 3 Mb between D21S3 and MX1. Gene distribution in the region includes 9 known genes (c21–LRP, WRB, SH3BGR, HMG14, PCP4, DSCAM, MX2, MX1, and TMPRSS2) and 14 new additional gene signatures consisting of cDNA selection products and ESTs. Forthcoming genomic sequence information will unravel the structural organization of potential candidate genes involved in specific features of Down syndrome pathogenesis.
Collapse
|