Sergei Kvasha - Academia.edu (original) (raw)

Papers by Sergei Kvasha

Research paper thumbnail of Human HRK gene maps to position 12q13.1

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2000

The recently identi¢ed HARAKIRI (HRK, Ac. No. NM003806) human gene encodes a protein that contain... more The recently identi¢ed HARAKIRI (HRK, Ac. No. NM003806) human gene encodes a protein that contains only a BH3 domain and activates apoptosis. HRK is a member of the Bcl-2 family but lacks sig-ni¢cantly homology to other Bcl-2 family members except for an 8-amino acid region that is similar to the Bcl-2 homology domain-3 (BH3) motif of BIK [1]. This novel regulator of cell death, also called neuronal death protein DP5 [2], regulates apoptosis through selective interaction via the BH3 domain with survival-promoting proteins, Bcl-2 and Bcl-X(L) . The induction of HRK is blocked by expression of these death-repressor proteins . HRK localizes to membranes of intracellular organelles in a pattern similar to that previously reported for Bcl-2 and Bcl-X(L) and is mainly expressed in haematopoietic tissues and cultured neurons .

Research paper thumbnail of Cloning and Initial Functional Characterization of Mlk4α and Mlk4ß

We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, ML... more We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, MLK4α (580 aa) and MLK4β (1036 aa), have been identified and mapped to chromosomal band 1q42. MLK4 shows high amino acid homology to the kinase catalytic domain of MLK3 (72%), MLK1 (71%) and MLK2 (69%). Strong expression of MLK4 was detected in the human pancreas and kidneys. pCMV-MLK4β c-myc-tagged protein (human) was expressed in the cytoplasm and nucleus of transiently transfected COS-1 cells, while pCMV-MLK4α c-myc-tagged protein (human) was expressed in cytoplasm only. Both MLK4 isoforms reduced the colony formation ability of MCF7 cells by 85%-95% and almost totally suppressed cell proliferation in the CyQUANT cell proliferation assay. Human pCMV-MLK4β transgenic mice expressed the MLK4β in all tissues examined but no phenotypic abnormalities were observed. Thus, in this work, we present the cloning and sequencing of MLK4α and MLK4β for the first time; the data obtained suggest that MLK4 may function as a MAP kinase.

Research paper thumbnail of Initial isolation and analysis of the human Kv1.7 (KCNA7) gene, a member of the voltage-gated potassium channel gene family

Gene, 2001

A novel human potassium channel gene was identi®ed and isolated. The maximal open reading frame e... more A novel human potassium channel gene was identi®ed and isolated. The maximal open reading frame encodes a protein of 456 amino acids. The predicted product exhibits 91% amino acid identity to the murine voltage-gated potassium channel protein Kv1.7 (Kcna7), which plays an important role in the repolarization of cell membranes. Based on the high similarity, the human gene has been classi®ed as the ortholog of the mouse Kcna7 and given the name Kv1.7 (KCNA7). A structural prediction identi®ed a pore region characteristic of potassium channels and six membrane-spanning domains. Northern expression analysis revealed the gene is expressed preferentially in skeletal muscle, heart and kidney. However, it is expressed at lower level in other tissues, including liver. A single mRNA isoform was observed, with a size of approximately 4.5 kb. Using¯uorescence in situ hybridization, the gene was mapped to chromosomal band 19q13.4 (269.13 cR 3000 ). A genomic sequence was identi®ed in the database from this region, and the KCNA7 gene structure determined. Computational analysis of the genomic sequence reveals the location of a putative promoter and a likely muscle-speci®c regulatory region. Initial comparison to the published murine Kcna7 cDNA suggested a different N-terminal sequence for the human protein, however, further analysis suggests that the original mouse sequence contained an error or an unusual polymorphism. q

Research paper thumbnail of hUNC93B1: a novel human gene representing a new gene family and encoding an unc-93-like protein

Gene, 2002

We have identified a novel human gene UNC93B1 encoding a protein related to unc-93 of Caenorhabdi... more We have identified a novel human gene UNC93B1 encoding a protein related to unc-93 of Caenorhabditis elegans. The combined sequence derived from several cDNA clones is 2282 bp and comparison with genomic sequence shows that the gene contains 11 exons. The longest open reading frame encodes a deduced sequence of 597 amino acids. Homology analysis shows that the hUNC93B1 gene is highly conserved and related to sequences in Arabidopsis thaliana, C. elegans, Drosophila melanogaster, chicken and mouse. Structural analysis of the deduced amino acid sequence of hUNC93B1 points to possible existence of multiple membrane-spanning domains. hUNC93B1 protein also displays some similarities to the bacterial ABC-2 type transporter signature and to ion transporters of Deinococcus radiodurans and Helicobacter pylori. As revealed by Northern analysis, the level of expression varies significantly between tissues, with the highest level detected in the heart. The gene was mapped to chromosomal band 11q13 by fluorescence in situ hybridization. We suggest that this gene is a member of a novel hUNC93B-related gene family.

Research paper thumbnail of NotI flanking sequences: a tool for gene discovery and verification of the human genome

Nucleic Acids Research, 2002

A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of th... more A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of the set had regions with significant similarity to known proteins and expressed sequences. The data demonstrate that regions flanking NotI sites are less likely to form nucleosomes efficiently and resemble promoter regions. The draft human genome sequence contained 55.7% of the NotI flanking sequences, Celera's database contained matches to 57.2% of the clones and all public databases (including non-human and previously sequenced NotI flanks) matched 89.2% of the NotI flanking sequences (identity > or =90% over at least 50 bp, data from December 2001). The data suggest that the shotgun sequencing approach used to generate the draft human genome sequence resulted in a bias against cloning and sequencing of NotI flanks. A rough estimation (based primarily on chromosomes 21 and 22) is that the human genome contains 15 000-20 000 NotI sites, of which 6000-9000 are unmethylated in any particular cell. The results of the study suggest that the existing tools for computational determination of CpG islands fail to identify a significant fraction of functional CpG islands, and unmethylated DNA stretches with a high frequency of CpG dinucleotides can be found even in regions with low CG content.

Research paper thumbnail of Human HRK gene maps to position 12q13.1

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2000

The recently identi¢ed HARAKIRI (HRK, Ac. No. NM003806) human gene encodes a protein that contain... more The recently identi¢ed HARAKIRI (HRK, Ac. No. NM003806) human gene encodes a protein that contains only a BH3 domain and activates apoptosis. HRK is a member of the Bcl-2 family but lacks sig-ni¢cantly homology to other Bcl-2 family members except for an 8-amino acid region that is similar to the Bcl-2 homology domain-3 (BH3) motif of BIK [1]. This novel regulator of cell death, also called neuronal death protein DP5 [2], regulates apoptosis through selective interaction via the BH3 domain with survival-promoting proteins, Bcl-2 and Bcl-X(L) . The induction of HRK is blocked by expression of these death-repressor proteins . HRK localizes to membranes of intracellular organelles in a pattern similar to that previously reported for Bcl-2 and Bcl-X(L) and is mainly expressed in haematopoietic tissues and cultured neurons .

Research paper thumbnail of Cloning and Initial Functional Characterization of Mlk4α and Mlk4ß

We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, ML... more We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, MLK4α (580 aa) and MLK4β (1036 aa), have been identified and mapped to chromosomal band 1q42. MLK4 shows high amino acid homology to the kinase catalytic domain of MLK3 (72%), MLK1 (71%) and MLK2 (69%). Strong expression of MLK4 was detected in the human pancreas and kidneys. pCMV-MLK4β c-myc-tagged protein (human) was expressed in the cytoplasm and nucleus of transiently transfected COS-1 cells, while pCMV-MLK4α c-myc-tagged protein (human) was expressed in cytoplasm only. Both MLK4 isoforms reduced the colony formation ability of MCF7 cells by 85%-95% and almost totally suppressed cell proliferation in the CyQUANT cell proliferation assay. Human pCMV-MLK4β transgenic mice expressed the MLK4β in all tissues examined but no phenotypic abnormalities were observed. Thus, in this work, we present the cloning and sequencing of MLK4α and MLK4β for the first time; the data obtained suggest that MLK4 may function as a MAP kinase.

Research paper thumbnail of Initial isolation and analysis of the human Kv1.7 (KCNA7) gene, a member of the voltage-gated potassium channel gene family

Gene, 2001

A novel human potassium channel gene was identi®ed and isolated. The maximal open reading frame e... more A novel human potassium channel gene was identi®ed and isolated. The maximal open reading frame encodes a protein of 456 amino acids. The predicted product exhibits 91% amino acid identity to the murine voltage-gated potassium channel protein Kv1.7 (Kcna7), which plays an important role in the repolarization of cell membranes. Based on the high similarity, the human gene has been classi®ed as the ortholog of the mouse Kcna7 and given the name Kv1.7 (KCNA7). A structural prediction identi®ed a pore region characteristic of potassium channels and six membrane-spanning domains. Northern expression analysis revealed the gene is expressed preferentially in skeletal muscle, heart and kidney. However, it is expressed at lower level in other tissues, including liver. A single mRNA isoform was observed, with a size of approximately 4.5 kb. Using¯uorescence in situ hybridization, the gene was mapped to chromosomal band 19q13.4 (269.13 cR 3000 ). A genomic sequence was identi®ed in the database from this region, and the KCNA7 gene structure determined. Computational analysis of the genomic sequence reveals the location of a putative promoter and a likely muscle-speci®c regulatory region. Initial comparison to the published murine Kcna7 cDNA suggested a different N-terminal sequence for the human protein, however, further analysis suggests that the original mouse sequence contained an error or an unusual polymorphism. q

Research paper thumbnail of hUNC93B1: a novel human gene representing a new gene family and encoding an unc-93-like protein

Gene, 2002

We have identified a novel human gene UNC93B1 encoding a protein related to unc-93 of Caenorhabdi... more We have identified a novel human gene UNC93B1 encoding a protein related to unc-93 of Caenorhabditis elegans. The combined sequence derived from several cDNA clones is 2282 bp and comparison with genomic sequence shows that the gene contains 11 exons. The longest open reading frame encodes a deduced sequence of 597 amino acids. Homology analysis shows that the hUNC93B1 gene is highly conserved and related to sequences in Arabidopsis thaliana, C. elegans, Drosophila melanogaster, chicken and mouse. Structural analysis of the deduced amino acid sequence of hUNC93B1 points to possible existence of multiple membrane-spanning domains. hUNC93B1 protein also displays some similarities to the bacterial ABC-2 type transporter signature and to ion transporters of Deinococcus radiodurans and Helicobacter pylori. As revealed by Northern analysis, the level of expression varies significantly between tissues, with the highest level detected in the heart. The gene was mapped to chromosomal band 11q13 by fluorescence in situ hybridization. We suggest that this gene is a member of a novel hUNC93B-related gene family.

Research paper thumbnail of NotI flanking sequences: a tool for gene discovery and verification of the human genome

Nucleic Acids Research, 2002

A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of th... more A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of the set had regions with significant similarity to known proteins and expressed sequences. The data demonstrate that regions flanking NotI sites are less likely to form nucleosomes efficiently and resemble promoter regions. The draft human genome sequence contained 55.7% of the NotI flanking sequences, Celera's database contained matches to 57.2% of the clones and all public databases (including non-human and previously sequenced NotI flanks) matched 89.2% of the NotI flanking sequences (identity > or =90% over at least 50 bp, data from December 2001). The data suggest that the shotgun sequencing approach used to generate the draft human genome sequence resulted in a bias against cloning and sequencing of NotI flanks. A rough estimation (based primarily on chromosomes 21 and 22) is that the human genome contains 15 000-20 000 NotI sites, of which 6000-9000 are unmethylated in any particular cell. The results of the study suggest that the existing tools for computational determination of CpG islands fail to identify a significant fraction of functional CpG islands, and unmethylated DNA stretches with a high frequency of CpG dinucleotides can be found even in regions with low CG content.