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Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

Bajaj V, Markandaya M, Krishna L, Kumar A - BMC Genet. (2004)

Bottom Line: Genomic imprinting is an epigenetic chromosomal modification in the gametes or zygotes that results in a non-random monoallelic expression of specific autosomal genes depending upon their parent of origin.This study reports the imprinting status of the SLC22A1LS gene for the first time.The results suggest imprinting of the paternal allele of this gene in five fetal tissues: brain, liver, placenta, kidneys and lungs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India. vineeta@mrdg.iisc.ernet.in

ABSTRACT

Background: Genomic imprinting is an epigenetic chromosomal modification in the gametes or zygotes that results in a non-random monoallelic expression of specific autosomal genes depending upon their parent of origin. Approximately 44 human genes have been reported to be imprinted. A majority of them are clustered, including some on chromosome segment 11p15.5. We report here the imprinting status of the SLC22A1LS gene from the human chromosome segment 11p15.5

Results: In order to test for allele specific expression patterns, PCR primer sets from the SLC22A1LS gene were used to look for heterozygosity in DNA samples from 17 spontaneous abortuses using PCR-SSCP and DNA sequence analyses. cDNA samples from different tissues of spontaneous abortuses showing heterozygosity were subjected to PCR-SSCP analysis to determine the allele specific expression pattern. PCR-SSCP analysis revealed heterozygosity in two of the 17 abortuses examined. DNA sequence analysis showed that the heterozygosity is caused by a G>A change at nucleotide position 473 (c.473G>A) in exon 4 of the SLC22A1LS gene. PCR-SSCP analysis suggested that this gene is paternally imprinted in five fetal tissues examined.

Conclusions: This study reports the imprinting status of the SLC22A1LS gene for the first time. The results suggest imprinting of the paternal allele of this gene in five fetal tissues: brain, liver, placenta, kidneys and lungs.

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Genomic imprinting of the SLC22A1LS gene: A) diagrammatic representation of SLC22A1L and SLC22A1LS genes; positions of the primer set 22F-22R are marked by arrow heads. B) PCR-SSCP analysis of genomic DNA samples from 17 abortuses (no. 2 to no. 18) with the primer set 22F-22R; two abortuses, no. 2 and no. 9 are heterozygous for a nucleotide change. C) Direct sequence analysis of the PCR product with the primer 22F from the abortus no. 2 showing a G>A change at nucleotide position 473 (c.473G>A) marked by an arrow. D) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 2 (2), mother of the abortus no. 2 (M), and cDNA samples from lungs (L), liver (Li), brain (B), kidneys (K) and placenta (P). Note, only one allele 473G is expressed in five tissues analyzed. Since the abortus is heterozygous and the mother is homozygous, the imprinted allele 476A in the abortus should have come from its father. E) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 9 (9), mother of the abortus no. 9 (M), and cDNA samples from lungs (L), liver (Li), brain (B), and kidneys (K). Note, only one allele 473G is expressed in all four tissues analyzed, corroborating the finding from the abortus no. 2. Since both the mother and the abortus are heterozygous, it is not possible to determine the parental origin of the expressed allele.
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Figure 1: Genomic imprinting of the SLC22A1LS gene: A) diagrammatic representation of SLC22A1L and SLC22A1LS genes; positions of the primer set 22F-22R are marked by arrow heads. B) PCR-SSCP analysis of genomic DNA samples from 17 abortuses (no. 2 to no. 18) with the primer set 22F-22R; two abortuses, no. 2 and no. 9 are heterozygous for a nucleotide change. C) Direct sequence analysis of the PCR product with the primer 22F from the abortus no. 2 showing a G>A change at nucleotide position 473 (c.473G>A) marked by an arrow. D) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 2 (2), mother of the abortus no. 2 (M), and cDNA samples from lungs (L), liver (Li), brain (B), kidneys (K) and placenta (P). Note, only one allele 473G is expressed in five tissues analyzed. Since the abortus is heterozygous and the mother is homozygous, the imprinted allele 476A in the abortus should have come from its father. E) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 9 (9), mother of the abortus no. 9 (M), and cDNA samples from lungs (L), liver (Li), brain (B), and kidneys (K). Note, only one allele 473G is expressed in all four tissues analyzed, corroborating the finding from the abortus no. 2. Since both the mother and the abortus are heterozygous, it is not possible to determine the parental origin of the expressed allele.

Mentions: Studies on uniparental disomies (UPDs) have identified five imprinted segments in the human genome including the chromosome segment 11p15.5 [6,7]. The imprinted segment on chromosome 11p15.5 is involved in the pathogenesis of Beckwith-Wiedemann syndrome. It is ~1 Mb in size and harbors a total of 21 genes [8]. Of these, 11 genes are known to be imprinted, seven genes show biallelic expression and the imprinting status of the remaining three genes including the SLC22A1LS is unknown. The SLC22A1LS gene contains four exons and encodes for a transcript of 1,342 bp length [9,10]. It is expressed in the liver, gastrointestinal tract, kidneys and placenta [10]. It codes for a putative protein of 253 amino acids length with unknown function. The SLC22A1LS protein does not show sequence homology to any known proteins [9,10]. The SLC22A1LS gene has no counterpart in the mouse genome [9], perhaps reflecting an example of the rapid evolution of human genomic sequences. The DNA sequence of this gene partially overlaps with that of another gene, SLC22A1L (BWR1A), which has been shown to be paternally imprinted [9,10]. These two genes are transcribed in opposite directions (Fig. 1A). We report here a study on the imprinted status of the SLC22A1LS (BWR1B) gene.


Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

Bajaj V, Markandaya M, Krishna L, Kumar A - BMC Genet. (2004)

Genomic imprinting of the SLC22A1LS gene: A) diagrammatic representation of SLC22A1L and SLC22A1LS genes; positions of the primer set 22F-22R are marked by arrow heads. B) PCR-SSCP analysis of genomic DNA samples from 17 abortuses (no. 2 to no. 18) with the primer set 22F-22R; two abortuses, no. 2 and no. 9 are heterozygous for a nucleotide change. C) Direct sequence analysis of the PCR product with the primer 22F from the abortus no. 2 showing a G>A change at nucleotide position 473 (c.473G>A) marked by an arrow. D) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 2 (2), mother of the abortus no. 2 (M), and cDNA samples from lungs (L), liver (Li), brain (B), kidneys (K) and placenta (P). Note, only one allele 473G is expressed in five tissues analyzed. Since the abortus is heterozygous and the mother is homozygous, the imprinted allele 476A in the abortus should have come from its father. E) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 9 (9), mother of the abortus no. 9 (M), and cDNA samples from lungs (L), liver (Li), brain (B), and kidneys (K). Note, only one allele 473G is expressed in all four tissues analyzed, corroborating the finding from the abortus no. 2. Since both the mother and the abortus are heterozygous, it is not possible to determine the parental origin of the expressed allele.
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Related In: Results  -  Collection

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Figure 1: Genomic imprinting of the SLC22A1LS gene: A) diagrammatic representation of SLC22A1L and SLC22A1LS genes; positions of the primer set 22F-22R are marked by arrow heads. B) PCR-SSCP analysis of genomic DNA samples from 17 abortuses (no. 2 to no. 18) with the primer set 22F-22R; two abortuses, no. 2 and no. 9 are heterozygous for a nucleotide change. C) Direct sequence analysis of the PCR product with the primer 22F from the abortus no. 2 showing a G>A change at nucleotide position 473 (c.473G>A) marked by an arrow. D) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 2 (2), mother of the abortus no. 2 (M), and cDNA samples from lungs (L), liver (Li), brain (B), kidneys (K) and placenta (P). Note, only one allele 473G is expressed in five tissues analyzed. Since the abortus is heterozygous and the mother is homozygous, the imprinted allele 476A in the abortus should have come from its father. E) PCR-SSCP analysis of genomic DNA samples from a control individual (N), abortus no. 9 (9), mother of the abortus no. 9 (M), and cDNA samples from lungs (L), liver (Li), brain (B), and kidneys (K). Note, only one allele 473G is expressed in all four tissues analyzed, corroborating the finding from the abortus no. 2. Since both the mother and the abortus are heterozygous, it is not possible to determine the parental origin of the expressed allele.
Mentions: Studies on uniparental disomies (UPDs) have identified five imprinted segments in the human genome including the chromosome segment 11p15.5 [6,7]. The imprinted segment on chromosome 11p15.5 is involved in the pathogenesis of Beckwith-Wiedemann syndrome. It is ~1 Mb in size and harbors a total of 21 genes [8]. Of these, 11 genes are known to be imprinted, seven genes show biallelic expression and the imprinting status of the remaining three genes including the SLC22A1LS is unknown. The SLC22A1LS gene contains four exons and encodes for a transcript of 1,342 bp length [9,10]. It is expressed in the liver, gastrointestinal tract, kidneys and placenta [10]. It codes for a putative protein of 253 amino acids length with unknown function. The SLC22A1LS protein does not show sequence homology to any known proteins [9,10]. The SLC22A1LS gene has no counterpart in the mouse genome [9], perhaps reflecting an example of the rapid evolution of human genomic sequences. The DNA sequence of this gene partially overlaps with that of another gene, SLC22A1L (BWR1A), which has been shown to be paternally imprinted [9,10]. These two genes are transcribed in opposite directions (Fig. 1A). We report here a study on the imprinted status of the SLC22A1LS (BWR1B) gene.

Bottom Line: Genomic imprinting is an epigenetic chromosomal modification in the gametes or zygotes that results in a non-random monoallelic expression of specific autosomal genes depending upon their parent of origin.This study reports the imprinting status of the SLC22A1LS gene for the first time.The results suggest imprinting of the paternal allele of this gene in five fetal tissues: brain, liver, placenta, kidneys and lungs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India. vineeta@mrdg.iisc.ernet.in

ABSTRACT

Background: Genomic imprinting is an epigenetic chromosomal modification in the gametes or zygotes that results in a non-random monoallelic expression of specific autosomal genes depending upon their parent of origin. Approximately 44 human genes have been reported to be imprinted. A majority of them are clustered, including some on chromosome segment 11p15.5. We report here the imprinting status of the SLC22A1LS gene from the human chromosome segment 11p15.5

Results: In order to test for allele specific expression patterns, PCR primer sets from the SLC22A1LS gene were used to look for heterozygosity in DNA samples from 17 spontaneous abortuses using PCR-SSCP and DNA sequence analyses. cDNA samples from different tissues of spontaneous abortuses showing heterozygosity were subjected to PCR-SSCP analysis to determine the allele specific expression pattern. PCR-SSCP analysis revealed heterozygosity in two of the 17 abortuses examined. DNA sequence analysis showed that the heterozygosity is caused by a G>A change at nucleotide position 473 (c.473G>A) in exon 4 of the SLC22A1LS gene. PCR-SSCP analysis suggested that this gene is paternally imprinted in five fetal tissues examined.

Conclusions: This study reports the imprinting status of the SLC22A1LS gene for the first time. The results suggest imprinting of the paternal allele of this gene in five fetal tissues: brain, liver, placenta, kidneys and lungs.

Show MeSH
Related in: MedlinePlus