Human chromosome 3: integration of 60 <i>Not</i>I clones into a physical and gene map

Abstract

Sequence tagged sites generated for 60 NotI clones (NotI-STSs) from human chromosome 3-specific NotI-jumping and NotI-linking libraries were physically located using PCR screening of a radiation hybrid (RH) GeneBridge4 panel. The NotI map of chromosome 3 was generated using these RH-mapping data and those obtained earlier by FISH and sequencing of the corresponding NotI clones. The sequences of the NotI clones showed significant homologies with known genes and/or ESTs for 58 NotI-STSs (97%). These 58 NotI clones displayed 91–100% identity to 54 genes and 23 cDNA/EST clones. One known and two hypothetical protein-coding genes were localized for the first time and nine cDNA clones (unknown genes) were also carefully mapped only in this work. Three newly mapped genes are histone gene H1X (NR1-BK20C) and genes for hypothetical proteins THC1032178 and THC1024604 (NL1-243).

Chromosomal localization of seven HSA3q13→q23 <i>Not</i>I linking clones on chicken microchromosomes: orthology of GGA14 and GGA15 to a gene-rich region of HSA3

“…Alternatively, presence of putative WDR1 pseudogenes and a Vrk2 homolog could be supposed on HSA3q21 → q23. A similar observation was reported for three NotI clones from HSA3p21, which were shown to have homology to three different genes located on HSA12 (Sulimova et al, 2002).…”

“…It was experimentally confirmed that there is a certain statistical connection between CpG islands, NotI sites and expressed sequences in the human genome (Zabarovsky et al, 2000). The contigs of NotI clones were created for HSA3p21 → p14 and HSA3q13 → q23 by means of FISH and RH mapping (Kashuba et al, 1999;Sulimova et al, 2002). Maximal densities of NotI clones within the contigs were shown in T-bands on HSA3p15, HSA3p21.3, HSA3q21 and HSA3q29 (Protopopov et al, 1996).…”

“…In two other cases, NL1-097 and NLM-118 did not produce any hits to HSA3. As discussed by Sulimova et al (2002), non-coincidence of locations of original genes (ESTs) and corresponding NotI clones could be explained by various factors such as the large size of some genes and the occurrence of related genes from the same gene family, pseudogenes, or gene duplications. Interestingly, the sequences of HSA3q21 → q23 NotI linking clone NL1-097 are homologous to the HSA4p16.1 WDR1 gene and those of NLM-118 to the mouse Vrk2 gene, the human homolog of which is located on HSA2p16 → p15 (http://www.ncbi.nlm.nih.gov; Table 1).…”

“…The NotI linking clones were used in several investigations on human chromosomes to characterize functional features of genomic regions (Kashuba et al, 1999;Zabarovsky et al, 2000;Sulimova et al, 2002). In the present study, we applied seven NotI linking clones from HSA3q13 → q21 for heterologous in situ hybridization on chicken chromosomes to detect (1) regions of orthology to HSA3q13 → q21 and (2) chromosomal regions with high density of CpG islands and coding genes.…”

Analysis of a new homozygous deletion in the tumor suppressor region at 3p12.3 reveals two novel intronic noncoding RNA genes

“…By means of RT-PCR experiments using primers located within genomic sequence or across splice sites (AP43R, Sulimova et al, 2002; and pyruvate dehydrogenase beta PDHB, primer sequence in Table 1), all cDNA samples were tested and found to be free of genomic DNA (data not shown).…”