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Bergström, Tomas
Alternative names
Publications (8 of 8) Show all publications
von Salomé, J., Gyllensten, U. & Bergström, T. F. (2007). Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles. Immunogenetics, 59(4), 261-271
Open this publication in new window or tab >>Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles
2007 (English)In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 59, no 4, p. 261-271Article in journal (Refereed) Published
Abstract [en]

The HLA region harbors some of the most polymorphic loci in the human genome. Among them is the class II locus HLA-DRB1, with more than 400 known alleles. The age of the polymorphism and the rate at which new alleles are generated at HLA loci has caused much controversy over the years. Previous studies have mostly been restricted to the 270 base pairs that constitute the second exon and represent the most variable part of the gene. Here, we investigate the evolutionary history of the HLA-DRB1 locus on the basis of an analysis of 15 genomic full-length alleles (10–15 kb). In addition, the variation in 49 complete coding sequences and 322 exon 2 sequences were analyzed. When excluding exon 2 from the analysis, the diversity at the synonymous sites was found to be similar to the intron diversity. The overall diversity in noncoding region was also similar to the genome average. The DRB1*03 lineage has been found in human, chimpanzee, bonobo, gorilla, and orangutan. An ancestral “proto HLA-DRB1*03 lineage” appeared to have diverged in the last 5 million years into the human-specific lineages *08, *11, *13, and *14. With exception to exon 2, both the coding- and the noncoding diversity suggests a recent origin (<1 million years ago) for most of the alleles at the HLA-DRB1 locus. Sites encoding for amino acids involved in antigen binding [antigen recognizing sites (ARS)] appear to have a more ancient origin. Taken together, the recent origin of most alleles, the high diversity between allelic lineages, and the ancient origin of sequence motifs in exon 2, is consistent with a relatively rapid generation of novel alleles by gene conversion like events.

Keywords
HLA, MHC, DRB1, Intron, Evolution, Polymorphisms
National Category
Medical and Health Sciences Biological Sciences
Identifiers
urn:nbn:se:uu:diva-10257 (URN)10.1007/s00251-007-0196-8 (DOI)000244786700002 ()
Note
Published on-line (doi:10.1007/s00251-007-0196-8) on Friday, February 16, 2007.Available from: 2007-03-07 Created: 2007-03-07 Last updated: 2017-12-11Bibliographically approved
Wetterbom, A., Sevov, M., Cavelier, L. & Bergström, T. (2006). Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution. Journal of Molecular Evolution, 63(5), 682-690
Open this publication in new window or tab >>Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution
2006 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 63, no 5, p. 682-690Article in journal (Refereed) Published
Abstract [en]

Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

Keywords
indels, comparative genomics, chimpanzee, primate evolution
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-10256 (URN)10.1007/s00239-006-0045-7 (DOI)000242014800010 ()17075697 (PubMedID)
Available from: 2007-04-20 Created: 2007-04-20 Last updated: 2017-12-11Bibliographically approved
Näslund, K., Saetre, P., von Salomé, J., Bergström, T., Jareborg, N. & Jazin, E. (2005). Genome-wide prediction of human VNTRs. Genomics, 85(1), 24-35
Open this publication in new window or tab >>Genome-wide prediction of human VNTRs
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2005 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 85, no 1, p. 24-35Article in journal (Refereed) Published
Abstract [en]

Polymorphic minisatellites, also known as variable number of tandem repeats (VNTRs), are tandem repeat regions that show variation in the number of repeat units among chromosomes in a population. Currently, there are no general methods for predicting which minisatellites have a high probability of being polymorphic, given their sequence characteristics. An earlier approach has focused on potentially highly polymorphic and hypervariable minisatellites, which make up only a small fraction of all minisatellites in the human genome. We have developed a model, based on available minisatellite and VNTR sequence data, that predicts the probability that a minisatellite (unit size > or = 6 bp) identified by the computer program Tandem Repeats Finder is polymorphic (VNTR). According to the model, minisatellites with high copy number and high degree of sequence similarity are most likely to be VNTRs. This approach was used to scan the draft sequence of the human genome for VNTRs. A total of 157,549 minisatellite repeats were found, of which 29,224 are predicted to be VNTRs. Contrary to previous results, VNTRs appear to be widespread and abundant throughout the human genome, with an estimated density of 9.1 VNTRs/Mb.

Keywords
VNTR, Minisatellite
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-73267 (URN)10.1016/j.ygeno.2004.10.009 (DOI)15607419 (PubMedID)
Available from: 2006-07-04 Created: 2006-07-04 Last updated: 2017-12-14Bibliographically approved
Bergström, T. (2005). Raser och Gener. In: Vetenskap eller villfarelse. : Leopard förlag
Open this publication in new window or tab >>Raser och Gener
2005 (Swedish)In: Vetenskap eller villfarelse, Leopard förlag , 2005Chapter in book (Other (popular scientific, debate etc.))
Place, publisher, year, edition, pages
Leopard förlag, 2005
Identifiers
urn:nbn:se:uu:diva-10262 (URN)9789173430852 (ISBN)
Available from: 2007-03-07 Created: 2007-03-07
Bergström, T., Erlandsson, R., Engkvist, H., Josefsson, A., Erlich, H. & Gyllensten, U. (1999). Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences.. Immunol Rev, 167, 351-65
Open this publication in new window or tab >>Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences.
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1999 (English)In: Immunol Rev, ISSN 0105-2896, Vol. 167, p. 351-65Article in journal (Refereed) Published
Abstract [en]

The evolutionary relationships among the MHC class II DRB4, DRB5 and DRB6 loci as well as the allelic lineages and alleles of the DRB1 locus were studied based on intron 1 and intron 2 sequences from humans, chimpanzee (Pan troglodytes), bonobo (Pan paniscus) and gorilla (Gorilla gorilla). The phylogenetic trees for these sequences indicate that most of the DRB1 allelic lineages predate the separation of the hominoid species studied, consistent with previous analysis of the coding sequences of these lineages. However, the intron sequence variation among alleles within DRB1 allelic lineages is very limited, consistent with the notion that the majority of the contemporary alleles have been generated within the last 250,000 years. The clustering of the DRB1 allelic lineages *08 and *12 with *03 supports a common ancestry for the DR8 and DR52 haplotypes. Similarly, the clustering of DRB1 allelic lineages *15 and *01 with the DRB3 locus is consistent with a common ancestry for the DR1 and DR51 haplotypes. Two cases of recombination around the second exon were observed: 1) the HLA-DRB6 locus appears to have been generated through a recombination between a DRB5 allele and an ancestral DRB6 allele, and 2) the gorilla sequence Gogo-DRB1 *03 appears to have been generated through a recombination between the DRB3 locus and an allele from the DRB1 *03 allelic lineage. The nucleotide substitution rate of DRB introns was estimated to 0.85-1.63 x 10(-9) per site per year, based on comparisons between the most closely related sequences from different hominoid species. This estimate is similar to the substitution rate for other intronic regions of the primate genome.

Keywords
Alleles, Animals, Base Sequence, Evolution; Molecular, Gorilla gorilla, HLA-DR Antigens/*genetics, Humans, Introns/*immunology, Molecular Sequence Data, Pan paniscus, Pan troglodytes, Phylogeny, Point Mutation, Recombination; Genetic, Sequence Alignment
Identifiers
urn:nbn:se:uu:diva-10258 (URN)10319273 (PubMedID)
Available from: 2007-03-07 Created: 2007-03-07 Last updated: 2011-01-14
Bergström, T., Engkvist, H., Erlandsson, R., Josefsson, A., Mack, S., Erlich, H. & Gyllensten, U. (1999). Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism.. Am J Hum Genet, 64(6), 1709-18
Open this publication in new window or tab >>Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism.
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1999 (English)In: Am J Hum Genet, ISSN 0002-9297, Vol. 64, no 6, p. 1709-18Article in journal (Refereed) Published
Abstract [en]

We analyzed the origin of allelic diversity at the class II HLA-DRB1 locus, using a complex microsatellite located in intron 2, close to the polymorphic second exon. A phylogenetic analysis of human, gorilla, and chimpanzee DRB1 sequences indicated that the structure of the microsatellite has evolved, primarily by point mutations, from a putative ancestral (GT)x(GA)y-complex-dinucleotide repeat. In all contemporary DRB1 allelic lineages, with the exception of the human *04 and the gorilla *08 lineages, the (GA)y repeat is interrupted, often by a G-->C substitution. In general, the length of the 3' (GA)y repeat correlates with the allelic lineage and thus evolves more slowly than a middle (GA)z repeat, whose length correlates with specific alleles within the lineage. Comparison of the microsatellite sequence from 30 human DRB1 alleles showed the longer 5' (GT)x to be more variable than the shorter middle (GA)z and 3' (GA)y repeats. Analysis of multiple samples with the same exon sequence, derived from different continents, showed that the 5' (GT)x repeat evolves more rapidly than the middle (GA)z and the 3' (GA)y repeats, which is consistent with findings of a higher mutation rate for longer tracts. The microsatellite-repeat-length variation was used to trace the origin of new DRB1 alleles, such as the new *08 alleles found in the Cayapa people of Ecuador and the Ticuna people of Brazil.

Keywords
Alleles, Base Sequence, DNA Primers, HLA-DR Antigens/*genetics, Humans, Microsatellite Repeats/*genetics, Polymorphism; Genetic
Identifiers
urn:nbn:se:uu:diva-10259 (URN)10330359 (PubMedID)
Available from: 2007-03-07 Created: 2007-03-07 Last updated: 2011-01-14
Bergström, T., Josefsson, A., Erlich, H. & Gyllensten, U. (1998). Recent origin of HLA-DRB1 alleles and implications for human evolution.. Nat Genet, 18(3), 237-42
Open this publication in new window or tab >>Recent origin of HLA-DRB1 alleles and implications for human evolution.
1998 (English)In: Nat Genet, ISSN 1061-4036, Vol. 18, no 3, p. 237-42Article in journal (Refereed) Published
Abstract [en]

The HLA class I and class II loci are the most highly polymorphic coding regions in the human genome. Based on the similarity of the coding sequences of alleles between species, it has been claimed that the HLA polymorphism is ancient and predates the separation of human (Homo) and chimpanzee (Pan), 4-7.4 Myr ago. Analysis of intron sequences, however, provides support for a more recent origin and for rapid generation of alleles at the HLA class II DRB1 locus. The human DRB1 alleles can be divided into groups (allelic lineages); most of these lineages have diverged from each other before the separation of Homo and Pan. Alleles within such a lineage, however, appear to be, on average, 250,000 years old, implying that the vast majority (greater than 90%) of the more than 135 contemporary human DRB1 alleles have been generated after the separation of Homo and Pan. The coalescence time of alleles within allelic lineages indicates that the effective population size (Ne) for early hominids (over the last 1 Myr) was approximately 10(4) individuals, similar to estimates based on other nuclear loci and mitochondrial DNA. With a single exception, the genetic mechanisms (gene conversion and point mutation) that have diversified the exon-2 sequences do not appear to extend into the adjacent intron sequences. The part of exon 2 encoding the beta-sheet evolves in concert with the surrounding introns, while the alpha-helix appears to have been subjected to gene conversion-like events, suggesting that such exchange events are highly localised and occur over extremely short sequence tracts.

Keywords
Alleles, Animals, Base Sequence, Evolution, Genetics; Population, HLA-DR Antigens/*genetics, Humans, Introns, Models; Genetic, Molecular Sequence Data, Phylogeny, Polymorphism; Genetic, Primates/genetics, Sequence Homology; Nucleic Acid, Time Factors, Variation (Genetics)
Identifiers
urn:nbn:se:uu:diva-10260 (URN)9500545 (PubMedID)
Available from: 2007-03-07 Created: 2007-03-07 Last updated: 2011-01-14
Erlich, H., Bergström, T., Stoneking, M. & Gyllensten, U. (1996). HLA sequence polymorphism and the origin of humans.. Science, 274(5292), 1552-4
Open this publication in new window or tab >>HLA sequence polymorphism and the origin of humans.
1996 (English)In: Science, ISSN 0036-8075, Vol. 274, no 5292, p. 1552-4Article in journal (Refereed) Published
Keywords
Africa, Animals, DNA; Mitochondrial/*genetics, Evolution; Molecular, Female, Genes; MHC Class II, HLA-DR Antigens/*genetics, Hominidae/*genetics, Humans, Male, Mutation, Polymorphism; Genetic
Identifiers
urn:nbn:se:uu:diva-10261 (URN)8966622 (PubMedID)
Available from: 2007-03-07 Created: 2007-03-07 Last updated: 2011-01-15
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