Gene arrangement at the Rhesus blood group locus of chimpanzees detected by fiber-FISH

Abstract

The Rhesus (Rh) blood group system in humans is encoded by two genes with high sequence homology. These two genes, namely, RHCE and RHD, have been implied to be duplicated during evolution. However, the genomic organization of Rh genes in chimpanzees and other nonhuman primates has not been precisely studied. We analyzed the arrangement of the Rh genes of chimpanzees (Pan troglodytes) by two-color fluorescence in situ hybridization on chromatin DNA fibers (fiber-FISH) using two genomic DNA probes that respectively contain introns 3 and 7 of human RH genes. Among the five chimpanzees studied, three were found to be homozygous for the two-Rh-gene type, in an arrangement of Rh (5′→3′) – Rh (3′←5′). Although a similar gene arrangement can be detected in the RH gene locus of typical Rh-positive humans, the distance between the two genes in chimpanzees was about 50 kb longer than that in humans. The remaining two chimpanzees were homozygous for a four-Rh-gene type, in an arrangement of Rh (5′→3′) – Rh (3′←5′) – Rh (3′←5′) – Rh (3′←5′) within a region spanning about 300 kb. This four-Rh-gene type has not been detected in humans. Further analysis of other great apes showed different gene arrangements: a bonobo was homozygous for the three-Rh-gene type; a gorilla was heterozygous for the one-Rh- and two-Rh-gene types; an orangutan was homozygous for the one-Rh-gene type. Our findings on the intra- and interspecific genomic variations in the Rh gene locus in Hominoids would shed further light on reconstructing the genomic pathways of Rh gene duplication during evolution.

Hotspots for copy number variation in chimpanzees and humans

“…This chimpanzee individual was used for the chimpanzee genome project. Other studies have investigated copy number variation at a limited number of individual loci among the genomes of several chimpanzees to gain insight into the dynamics of corresponding human CNVs (15,18). However, a genome-wide analysis of CNVs in a chimpanzee sample population is still lacking.…”

No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group Genes

“…As mentioned before, Suto et al (2003) reported the existence of two-Rh-gene and four-Rh-gene types in chimpanzees. It is likely that PTB-1 ( fig.…”

“…We sequenced the region surrounding exon 7 (∼860 bp) from 12 chimpanzees ( P. troglodytes verus ), 3 bonobos ( P. paniscus ), 3 gorillas ( Gorilla gorilla ), 1 orangutan ( Pongo pygmaeus ), and 2 siamangs ( Symphalangus syndactylus ). Five (“Akina,” “Aluku,” “Chiko,” “Kanao,” and “Mikota”) of the 12 chimpanzees were the same individuals used in the Suto et al (2003) fiber-FISH analysis. Two primers on intron 6 (forward: 5′-TTT GCA TAT GTG TCC ACA TCT G-3′) and on intron 7 (reverse: 5′-GCC AAC AAA TAT TCA CCG AAG C-3′) were used for each PCR experiment and sequencing.…”

“… Wagner and Flegel (2000) went on to report that the 3′ ends of these genes face each other and are separated by an ∼30-kb segment that contains the TMEM50A (transmembrane protein 50A) gene. In addition, Suto et al (2003) later discovered the existence of two-Rh-gene and four-Rh-gene types in chimpanzees, again using fiber-FISH analysis. The two-Rh-gene type is arranged as Rh (5′→3′) – Rh (3′←5′), with the distance between the two genes about 50-kb longer than that in humans, while the arrangement of the four-Rh-gene type is Rh (5′→3′) – Rh (3′←5′) – Rh (3′←5′) – Rh (3′←5′) within a region spanning about 300 kb.…”

Rh and RHAG Blood Group Systems

“…RH gene homologues have been detected in all mammals studied [687] . Like most humans, chimpanzees and gorillas have at least two RH genes, although some chimpanzees have three or four genes; other primates, including orangutans and gibbons, old world and new world monkeys, and prosimians, have only one RH gene per haploid genome [689,690] . The cDNA sequences demonstrated a high degree of homology to the human sequence and predicted proteins of 417 amino acids.…”