Chromosomal localization of three human poly(A)-binding protein genes and four related pseudogenes

Abstract

In humans, the poly(A)-binding proteins (PABPs) comprise a small nuclear isoform and a conserved gene family that displays at least three functional proteins: PABP1, inducible PABP (iPABP), and PABP3, plus four pseudogenes (1, 2, 3, and PABP4). In situ hybridization of PABP3 cDNA as the probe on metaphasic chromosomes have revealed five possible loci for this gene family at 2q21-q22, 13q11-q12, 12q13.3-q15, 8q22, and 3q24-q25. Amplifications of specific DNA fragments from a human-rodent somatic cell hybrid panel have allowed us to associate PABP1 and PABP3 with 8q22 and 13q11-q12, respectively. The iPABP gene has been assigned to chromosome 1. This result, compared with radiation hybrid database information, strengthens the location of this gene to 1p32-p36. The pseudogenes PABP4, 1, and 2 have been assigned to chromosomes 15, 4, and 14, respectively. Three loci detected on chromosome spreads are not associated with any amplified fragment. They might represent other related PABP genes not yet identified.

Fig. 1

Southern blot of human genomic DNA. Human lymphocyte genomic DNA (20 μg) was digested by using either HindIII (H), PstI (Ps), PvuII (Pv), or EcoR1 (E) restriction enzymes. The blot was hybridized with the PABP3 cDNA as the probe, as described. The size of the lambda DNA/EcoRI + HindIII markers are indicated left (in bp)

Fig. 2

A Sublocalization of human PABP-related sequences. Histogram showing the distribution of 356 grains scored from 150 human metaphase cells following in situ hybridization of the cDNA PABP3 probe. Five significant hybridization peaks were detectable on chromosomes 2, 13, 12, 8, and 3. B Ideograms of the human R-banded chromosomes 2, 13, 12, 8, and 3, illustrating the precise distribution of labeled sites for the cDNA PABP3 probe. The distribution of the total of 356 grains was as follows: 14% chromosome 2, 69% of the grains, 36/52, in the 2q21-q22 region; 12% chromosome 13, 83% of the grains, 35/42, in the 13q11-q12 region; 10% chromosome 12, 77% of the grains, 27/35, in the 12q13.3-q15 region; 9% chromosome 8, 69% of the grains, 22/32, in the 8q22 region; 7% chromosome 3, 64% of the grains, 16/25, in the 3q24-q25 region

Fig. 3

Alignment of the sequence of the PABP3-specific PCR product with the sequence of similar regions in PABP1, iPABP, and PABP4. The underlined sequences correspond to the 5′ and 3′ PCR primers and to the oligonucleotide probe. Asterisks Identical bases between the four PABP sequences. The differences in nucleotides between PABP1, iPABP, and PABP4 sequences as compared with PABP3 primers are boxed

Fig. 4

Selection of the PABP1-specific oligonucleotide sets. The amplified fragment overlaps with the exon 10–11 sequence of the PABP1 gene (accession no. U68101). Lower case Intron sequence. The underlined sequences correspond to the 5′ and 3′ primers and control probe

Fig. 5

Chromosomal assignment of the PABP genes by PCR amplification of specific fragments on human-rodent hybrid cell line genomic DNA samples. Southern blot analysis of products amplified with PABP-specific oligonucleotide primers and revealed with an internal control probe, as described in Table 1. Numbers, X and Y above each lane, indicate the human chromosome contained in the hybrid cell line. Control DNAs were from human (H), mouse (M), and hamster (T) genomes or from PABP-specific plasmid (P). These specific plasmids contain cDNA corresponding to the sequences PABP1 (accession no. U68101), iPABP (accession no. U33818), PABP3 (accession no. AF132026) and PABP4 (accession no. AF132027). No DNA was present in B. The size of the DNA standards (in bp) is indicated left. In addition to the selected chromosomes, some hybrids contain small fragments of other chromosomes as follows: chromosome 1: X; chromosome 6: Xqter-Xq13; chromosome 8: fragment of 22; chromosome 10: Y; chromosome 12: 21 and X; chromosome 13: fragments of 8, 11, and 12; chromosome 14: 16p13.1-q22.1; chromosome 15: 11q and Xp; chromosome 20: X, 22q and fragments of 8 and 4; chromosome 21: X; chromosome 22: fragment of Xp