ABSTRACT
The investigation of the cancer-associated structural and epigenetic changes in cell genome is a major approach for understanding mechanisms of cancerogenesis. To investigate these genome changes, novel technique of microarrays comprising NotI-linking genome clones was developed. Twenty eight samples from patients with cervical cancer were analyzed using NotI microarrays of human chromosome 3. Deletions, amplifications and methylation were detected for 109 out of 182 NotI clones with different frequency. Notably, 17 NotI-linking clones showed genomic changes in more than 35% of tumor samples investigated, which suggests involvement of genes associated with these clones in development of cervical cancer.
Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 3 , DNA, Neoplasm/genetics , Deoxyribonucleases, Type II Site-Specific/metabolism , Gene Expression Regulation, Neoplastic , Uterine Cervical Neoplasms/genetics , Cloning, Molecular , DNA Methylation , Female , Humans , In Situ Hybridization, Fluorescence , Oligonucleotide Array Sequence Analysis , Restriction MappingABSTRACT
The localization of HIV-1 proviruses in compositional DNA fractions from 27 AIDS patients during the chronic phase of the disease with depletion of CD4+ and different levels of viremia showed the following. (1) At low viremia, proviruses are predominantly localized in the GC-richest isochores, which are characterized by an open chromatin structure; this result mimics findings on HIV-1 integration in early infected cells in culture. (2) At higher viremia, an increased distribution of proviruses in GC-poor isochores (which match the GC poorness of HIV-1) was found; this suggests a selection of cells in which the 'isopycnic' localization leads to a higher expression of proviruses and, in turn, to higher viremia. (3) At the highest viremia, integrations in GC-rich isochores are often predominant again, but generally not at the same level as in (1); this may be the consequence of new integrations from the extremely abundant RNA copies.
Subject(s)
Acquired Immunodeficiency Syndrome/genetics , Chromosomes, Human , Genome, Human , HIV-1/genetics , Viremia/genetics , Virus Integration , Base Composition , CD4 Antigens , Chromatin/genetics , DNA, Viral/analysis , DNA, Viral/genetics , GC Rich Sequence , Humans , Isochores , Proviruses/genetics , RNA, Viral/geneticsABSTRACT
New human and mouse cDNAs which are homologous to human intersectin gene (ITSN) mapped on a q22.1-22.2 region of human chromosome 21 have been obtained. ITSN gene structure has been determined using nucleotide sequences of human chromosome 21 presented in nucleotide's data bases. The analysis of human and mouse ITSN gene transcripts revealed that their pre-mRNA splicing could occur in different ways. New form of ITSN gene transcripts with alternatively spliced SH3C domain (exon 25 and 26) was detected in different human and mouse tissues. The other splice form with absence of exons 6-14 that results in reading frame shift and stop-codon formation was identified in the mouse adult lung and kidney. In addition, we showed alternative splicing of exons 20, 25 and part of exon 6.
Subject(s)
Adaptor Proteins, Vesicular Transport , Alternative Splicing/genetics , Carrier Proteins/genetics , Transcription, Genetic , Animals , Base Sequence , Chromosomes, Human, Pair 21/genetics , DNA, Complementary/genetics , Humans , Mice , Molecular Sequence Data , Nucleic Acid Hybridization , RNA, Messenger/genetics , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology, Nucleic AcidABSTRACT
We have reviewed here three sets of data concerning the integration of retroviral sequences in the mammalian genome: (i) our experimental localization of a number of proviruses integrated in isochores characterized by different GC levels; (ii) results from other laboratories on the localization of retroviral sequences in open chromatin regions and/or next to CpG islands; and (iii) our compositional analysis of genes located in the neighborhood of integrated retroviral sequences. The three sets of data have provided a very consistent picture in that a compartmentalized, isopycnic integration of expressed proviruses appears to be the rule ('isopycnic' refers to the compositional match between viral and host sequences around the integration site). The results reviewed here suggest that: (i) integration of proviral sequences is targeted initially towards 'open chromatin regions'; while these exist in both GC-rich and GC-poor isochores, the 'open chromatin regions' of GC-rich isochores are the main targets for integration of retroviral sequences because of their much greater abundance; (ii) isopycnicity is associated with stability of integration; indeed, even non-expressed integrated retroviral sequences tend to show an isopycnic localization in the genome; (iii) transcription of integrated viral sequences (like transcription of host genes) appears to be associated, as a rule, with an isopycnic localization, as indicated by transcribed sequences that show an isopycnic integration and act in trans; (iv) selection plays a role in the choice of specific sites within an isopycnic region; in exceptional cases [such as mouse mammary tumor virus (MMTV) activating GC-rich oncogenes], selection may override isopycnicity.
