Duplication of a Genomic Region Containing the Cdc2L1-2 and MMP21-22 Genes on Human Chromosome 1p36.3 and their Linkage to D1Z2

Abstract

Cdc2L1 and Cdc2L2 span ∼140 kb on human chromosome 1p36.3. The products of the Cdc2L genes encode almost identical protein kinases, the PITSLRE kinases, which have functions that may be relevant to the regulation of transcription/splicing and apoptotic signaling. These genes are deleted/translocated in neuroblastomas with MYCN gene amplification, a subset of malignant melanomas, and in a newly delineated deletion syndrome. Here we report that the p36.3 region of human chromosome 1 consists of two identical genomic regions, each of which contain a Cdc2L gene linked to a metalloprotease (MMP) gene in a tail-to-tail configuration. This duplicated genomic region is also linked tightly to D1Z2, a genetic marker containing a highly polymorphic VNTR (variable number tandem repeat) consisting of an unusual 40-bp reiterated sequence. Thus, these genes and the polymorphic marker D1Z2 are organized as follows: telomere-D1Z2-5Ј-MMP22-3Ј-3Ј-Cdc2L2-5Ј-5Ј-Cdc2L1-3Ј-3Ј-MMP21-5Ј-centromere. Remarkably, the introns and exons of Cdc2L1 and Cdc2L2, as well as their flanking regions, are essentially identical. A total of 15 amino acid differences, 12 nonconservative and 3 conservative, can be found in the 773-786 amino acids specified by the various products of the Cdc2L genes. Two separate promoter/5Ј untranslated (UT) regions, CpG1 and CpG2, are identical to a reported previously methylated genomic CpG sequence and are used to express >20 different Cdc2L transcripts from the two genes. The expression of CpG2 transcripts from Cdc2L1 and Cdc2L2 is tissue/cell-line specific. CpG1 transcripts are expressed ubiquitously from both genes, with perhaps some bias towards the expression of CpG1 Cdc2L1 mRNAs in certain hematopoietic cells.[The sequence data described in this paper have been submitted to the GenBank data library under the following accession nos.: (cDNAs) AF067511-AF067529; (genomic) AF080678-AF080697.]The human Cdc2L1 and Cdc2L2 genes were localized previously to chromosome band 1p36.3, and they are deleted/altered frequently in neuroblastomas with amplified MYCN genes, a subset of malignant melanoma, and a 1p36 deletion disorder Shapira et al. 1997;Nelson et al. 1998). In fact, these genes are in close proximity to p73, which like Cdc2L1/2 is located proximally to D1Z2 (Kaghad et al. 1997). The Cdc2L1/2 genes express >20 distinct PITSLRE protein kinase isoforms, many arising by alternative splicing ; this study). Indirect immunofluorescence has demonstrated that the larger p110 PITSLRE isoforms expressed by Cdc2L1 and Cdc2L2 are localized in the nucleus, with a high concentration in nuclear speckles (Loyer et al. 1998). The cell cycle-regulated RNA-binding protein RNPS1 was isolated with the PITSLRE p110 isoforms by two-hybrid cloning (Loyer et al. 1998). Overexpression of RNPS1 in mammalian cells results in the redistribution of this kinase, RNPS1, and certain splicing components into fewer, and much larger, nuclear speckles. Treatment of the same mammalian cells with transcriptional inhibitors (e.g., H8, DRB) results in a...

Characterization of Cyclin L1 and L2 Interactions with CDK11 and Splicing Factors

“…8A) that encodes unspliced and five alternatively spliced variant transcripts (13,12,11,10, and 9S) was employed to investigate whether ectopic expression of wild-type (WT) and kinase-dead (DN) forms of CDK11 p110 and cyclins L1␣, L2␣, and L2␤ (those isoforms that interact with CDK11 p110 ) affects alternative splicing activity in HuH7 hepatoma cells. In these experiments, total RNA was extracted from HuH7 cells following transient transfection with the E1A minigene and CDK11 p110 and cyclin L expression vectors.…”

Analysis of mutations and identification of several polymorphisms in the putative promoter region of the P34CDC2‐related CDC2L1 gene located at 1P36 in melanoma cell lines and melanoma families

“…31 For the CDC2L1 gene, it has been reported that 2 distinct promoters, containing CpG-rich sequences corresponding to a previously isolated CpG genomic sequence characterized by Bird and colleagues, are responsible for the expression of transcripts from CDC2L1 gene. 10 However, our study on the methylation status of melanoma cell lines showed that there was no aberrant methylation of CpG islands in the CDC2L1 promoter and thus the decreased PITSLRE expression in these melanoma cell lines was not caused by hypermethylation of the CpG island.…”

“…Two CpG-rich sequences upstream of the gene are responsible for the expression of transcripts from CDC2L1 and CDC2L2. 10 In our previous study, we found that 1 allele of the CDC2L1 gene complex on chromosome 1 was either deleted or translocated in 8 of 14 different melanoma cell lines using fluorescence in situ hybridization 11 and that the alterations in these alleles correlate with differences in sensitivity of melanoma cells to apoptotic stimuli. Decreased expression of PITSLRE proteins from the remaining allele was observed in several cell lines and surgical malignant melanoma specimens.…”

“…The CDC2L locus encoding PITSLRE protein kinases maps to chromosome 1p36.3 9 and consists of 2 duplicated and tandemly linked genes CDC2L1 and CDC2L2. 10 The 2 genes are almost identical, yet transcripts are expressed ubiquitously from these genes in most human cell lines and tissues examined. Two CpG-rich sequences upstream of the gene are responsible for the expression of transcripts from CDC2L1 and CDC2L2.…”

The Annotation of Both Human and Mouse Kinomes in UniProtKB/Swiss-Prot

“…One sequence described by Manning et al (2), SgK424, may have been an erroneous prediction in that we can find no firm evidence for its existence, although part of the sequence is identifiable within the current genome build, and a further three proteins were recognized subsequent to the Manning et al (2) publication. Two gene products have now been identified within a duplicated genomic region that gives rise to two proteins, CDC2L1 (P21127) and CDC2L2 (Q9UQ88), that differ by only 15 amino acids (4). The second of these, CDC2L2, was not on the original list.…”