| Gene Recovery and Analysis Unit |
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Ramaiah Nagaraja, Ph.D., Head
Staff Scientist |
| Overview |
| This Unit is designed to provide state-of-the-art gene materials, along with informatics and related technology for gene analysis. The major elements are: |
- Materials: The goal is to recover and store pooled and arrayed libraries for the mapping and analysis of genomic DNA and gene transcripts (cDNAs). The collection in the Unit includes human X-chromosome yeast artificial chromosomes (YACs), mouse genomic bacterial BACs, and mouse cDNA libraries from various developmental stages and subregions of embryos, created by the Developmental Genomics and Genetics Section.
- Informatics: The goal is to maintain updated suites of programs for the analysis of sequence content of both cDNAs and large-insert genomic clones of up to 300 kb, and to provide computer support for the dissemination of information to collaborating laboratories and public databases. The analysis tools include sequence analysis programs, catalogues of repetitive sequences, and graphical representation programs. An internal WEB site (http://lgsun.grc.nia.nih.gov/cgi-bin/pro6) includes information about clones, maps, sequences, and near homologues of sequences.
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| Two research programs are designed to extend relevant current technology, corresponding to the resource segments of the Unit. |
- Recovery of Genes in Chromatin Form: This program has started with the development of a method to circularize YACs, in order to have the option of studying long-range chromatin-remodeling effects on very large genes and cotranscribed domains. The current goal is to transfer such circular chromosomes (or the smaller circular BACs) into mammalian cells and develop methods to recover them in chromatin form. The achievement of this goal would permit potential direct identification of the proteins that interact with a gene when it is in "open" vs. "closed" chromatin, helping to define those states at a molecular level (see Human Genetics Section above for the choice of genes for study).
- Sequence and Gene Analysis in the Mouse T-complex: The mouse t-complex is defined by a 20 cM region at the centromeric end of mouse chromosome 17. It is of particular interest for the many recessive developmental lethal mutations that map there, and for a phenomenon termed transmission ratio distortion, which may be related to the complicated structure of the region. The structure is characterized by four large inversions as well as many small and large duplications. Thus the mapping and sequence analysis of the t-complex is challenging, requiring special attention, and also provides an entree to candidate genes for "t-lethals".
This program has started with the recovery of BACs to seed contigs across the region. They were identified in high-density gridded BAC libraries with regional gene-specific ESTs identified from preimplantation embryo libraries (see Developmental Genomics and Genetics Section). A minimal tiling path across selected subregions is progressively sequenced and analyzed for gene content. The contigs are extended and integrated into other efforts in the community by reiterated screening with STSs from the ends of the BACs and by comparison to accumulating mouse genomic sequence in public databases.
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