Sequence and analysis of approximately 0.5 mega-basepair of the DiGeorge Syndrome Critical Region in human chromosome 22 band q11 and a syntenic mouse BAC.

Abstract

From the data collected, part of the genomic sequence of the human clathrin heavy chain like gene (CLTCL), entire genomic sequence of the human homolog of yeast repressors of histone gene transcription HIR1 and HIR2 (HIRA), the human ubiquitin-fusion degradation protein 1-like gene (UFD1L), the human homolog of mouse T10 gene, and a putative transmembrane gene were revealed. CLTCL may be involved in endocytosis. HIRA may be a negative regulator of core histone gene transcription. UFD1L may be involved in protein degradation. The T10 gene and the putative transmembrane gene have no homolog to any known functional genes in the database. The sequence of this approximate 0.5 mb of human genomic sequence reveals a gene density of slightly more than one gene per 100 kb with numerous ESTs and an extensive amount of repeat sequences. In addition, a ribosomal protein L34 pseudogene and a human Tigger 1-like transposon were reported. Different families of interspersed repetitive elements and their contents also were determined. The total content of these repetitive elements in these region is about 32%. The comparison of two 36 kb fragments of human genomic sequences from two individuals revealed a overall difference of 0.2%. The 90 kb of mouse genomic sequence syntenic to human HIRA gene was compared with human sequence. Although the coding regions of the human and mouse HIRA gene are almost identical and the genomic sequence level similarity between these two genes is low, their genomic organization is similar.

The complete nucleotide sequence of four regions of DiGeorge Sydrome Critical Region in human chromosome 22 band q11, totally 482 kb, and a syntenic mouse BAC, 89 kb, has been determined by sequencing an overlapping set of genomic clones that have been mapped to these regions. The sequencing strategy involved a modified large scale DNA isolation procedure to obtain the genomic clones, physical shearing of the clones by nebulization to generate randomly distributed DNA fragments, subcloning the end-repaired, kinased and size-selected DNA fragments into pUC-based vectors to get chimeric subclones. The subclones then were isolated using a modified alkaline lysis procedure. Cycling Sequencing reactions were performed using dye-labeled primer or terminator chemistry, and loaded on an ABI$\sp\circler$ 377 DNA sequencer for automated sample electrophoresis, detection, data collection and base calling. The ABI-called shotgun sequences were transferred to Sun$\sp\circler$ SPARCstation and then edited, assembled and proofread by using several available editing and assembly programs. The final contiguous sequence in each regain was analyzed for features such as potential promoters, potential coding regions, repeated elements and database homology using XGrail and Powerblast.