ABSTRACT
Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.
Subject(s)
RNA Precursors/genetics , RNA Processing, Post-Transcriptional , RNA/genetics , Trans-Splicing , Base Sequence , Cell Nucleus/genetics , DNA, Mitochondrial/genetics , Expressed Sequence Tags/chemistry , Gene Expression , HEK293 Cells , HeLa Cells , Humans , Introns/genetics , Models, Genetic , Molecular Sequence Data , RNA, Messenger/genetics , RNA, Mitochondrial , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , Reverse Transcriptase Polymerase Chain ReactionABSTRACT
Transcription of a pre-mRNA in eukaryotic cells elongates from the 5' to the 3' end, but intron removal during a pre-mRNA splicing does not always proceed in this orientation. In this study, we identified eight mouse p53 transcripts that retained one or more of introns 6, 7 and 8. The 5' part of intron 9 was also retained while the 3' part was not studied. These intron-containing transcripts, abbreviated as p53-ICTs, were detected at low abundance in many mouse embryonic fibroblasts (MEF) as well as cancer cell lines and tissues, and the highest ratio of these p53-ICTs to the mature p53 mRNA was seen in the normal pancreas. Serum starvation decreased those p53-ICTs that retained introns 6 and 7 but increased the levels of those lacking these introns while the level of the mature p53 mRNA was unaffected. Treatment of several cancer cell lines with cisplatin increased the mature p53 mRNA level but decreased these p53-ICTs. Transfection of p53(-/-) MEF with the p53 cDNA or several p53-ICT mini-genes slightly increased the cell viability and rendered the cells resistant to cisplatin. These data also suggest that p53 pre-mRNA splicing may have multiple orders of intron removal, some of which may not follow the "first come, first served" principle. It remains possible that these p53-ICTs are splicing intermediates existing as a mechanism for the cell to respond more promptly to a demand for more p53 and that p53 protein may be required for a normal life of MEF.
Subject(s)
Cisplatin/pharmacology , RNA Precursors/genetics , RNA Splicing/drug effects , RNA Splicing/genetics , Tumor Suppressor Protein p53/genetics , Animals , Base Sequence , Cell Line , Culture Media, Serum-Free , Gene Expression Regulation/drug effects , Gene Order , Mice , Molecular Sequence Data , RNA Precursors/chemistry , RNA, Messenger/chemistry , RNA, Messenger/genetics , Transcription, GeneticABSTRACT
A pair of degenerate primers were designed according to the DNA sequences of the C(2)H(2) zinc finger genes conservative domain and then homologious PCR was performed with the human genomic total DNA as template. The zinc finger fragments thus obtained were used as probes to screen cDNA libraries of human fetal kidney, muscle and marrow and 22 C(2)H(2) zinc finger gene fragments were selected. Among these fragments, 17 were confirmed to be novel zinc finger gene fragments by literature searches in the National Center Biotechnology Information (NCBI) database. Expression patterns of the clones K3-4 and K5-12 selected from kidney cDNA library were analyzed. The results showed that the expression level of K3-4 in kidney is obviously higher than in other tissues and K5-12 is expressed at different levels in 8 tissues.
