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An assessment of the sequence gaps: Unfinished business in a finished human genome

Nature Reviews Genetics volume 5, pages 345–354 (2004)Cite this article

Key Points

  • The finished human genome sequence contains two types of gap: those that are associated with heterochromatic sequences and those that are embedded in euchromatin.

  • Approximately 50% of the gaps in euchromatin are flanked by duplications with a high degree of sequence identity. Transition regions between euchromatin and heterochromatin are particularly enriched. Not all of these regions are recalcitrant to subcloning.

  • Regions of duplication are sites of genetic instability and large-scale structural polymorphism. These properties have complicated their sequence and assembly.

  • Specialized genomic technologies, including the construction of hydatidiform mole bacterial artificial chromosome (BAC) libraries, optical mapping, half-YAC (yeast-artificial chromosome) mapping and transformation-associated recombination, might resolve a fraction of the euchromatic gaps.

  • Closure of the remaining 1% of the euchromatin will improve gene and SNP annotation in the human reference genome sequence.

Abstract

Biological research increasingly depends on 'finished' genome sequences. Deducing what is absent from these sequences is not trivial. More than 99% of the euchromatic portion of the human genome is now represented as a high-quality finished sequence with each base ordered and oriented. However, two principal types of gap remain: heterochromatic (estimated to be ∼200 Mb) and euchromatic (23.0 Mb) gaps. Here, we use various global sources of data to help understand the nature of the gaps in the finished human genome. Not all gaps are recalcitrant to subcloning, nor are most heterochromatic. The presence of recent segmental duplications is the most important predictor of gap location in euchromatic sequences. The resolution of these regions remains an important challenge for the completion of the human genome, gene annotation and SNP assignment.

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Figure 1: Chromosomal distribution of sequence gaps.
Figure 2: Duplications and sequence gaps.
Figure 3: In silico versus cytogenetic analysis of the human genome.
Figure 4: Gaps, duplications and structural variation.
Figure 5: SNP enrichment in duplicated sequences.

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Acknowledgements

We would like to thank F. Collins, A. Pelsenfeld, B. Waterston and E. Lander for helpful comments in the preparation of this manuscript. This work was supported, in part, by grants from the National Institutes of Health to E.E.E.

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Authors and Affiliations

  1. Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, BRB720, 10900 Euclid Avenue, Cleveland, 44106, Ohio, USA

    Evan E. Eichler, Royden A. Clark & Xinwei She

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  1. Evan E. Eichler
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  2. Royden A. Clark
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  3. Xinwei She
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Correspondence to Evan E. Eichler.

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DATABASES

LocusLink

TPTE

FURTHER INFORMATION

GenBank Database

Human Paralogy Server Segmental Duplication Database

Proposal for Construction of a Human Haploid BAC Library from Hydatidiform Mole Source Material

University of California Santa Cruz Genome Bioinformatics

Glossary

HETEROCHROMATIN

Parts of chromosomes with an unusual degree of contraction and that consequently have different staining properties from the euchromatin at nuclear divisions. Largely composed of repetitive DNA, heterochromatin forms dark bands after Giemsa staining.

EUCHROMATIN

Parts of chromosomes that show the normal cycle of condensation and normal staining properties at nuclear divisions. Euchromatin generally contains active or potentially active genes and falls within light bands after Giemsa staining.

SATELLITE DNA

Various classes of highly repetitive DNA that are tandemly repeated and most often associated with centromeric or pericentromeric regions of the genome. α-Satellite DNA is a class of centromeric satellite in which the monomeric unit is 171 bp. Higher-order structures of this satellite define the DNA component of human centromeres. β-Satellite DNA is a class of pericentromeric satellite in which the basic repeat unit is a 68-bp monomer.

ACROCENTRIC

A chromosome in which the centromere is located subterminally, and concomitantly the chromosome arms are unequal in length.

PARALOGOUS

The quality of having sequence similarity as a result of duplication.

CONTIG

A set of contiguous overlapping clones that span a genomic region.

MULTISITE SIGNALS

Multiple fluorescence in situ hybridization (FISH) signals on metaphase chromosomal preparations.

GIEMSA

A cytogenetic stain that is applied to metaphase chromosomes after limited digestion with trypsin. Individual chromosomes are distinguished on the basis of a characteristic banding pattern of dark and light bands.

MONOCHROMOSOMAL HYBRID

A cell line that carries a single, intact human chromosome in a rodent somatic cell background.

FOSMID

A low-copy vector for the construction of stable genomic libraries that uses the Escherichia coli F-factor origin for replication.

NON-ROBERTSONIAN TRANSLOCATION

A chromosomal rearrangement that is characterized by the fusion of different chromosomes, but does not involve the fusion of whole long arms of two acrocentric chromosomes (chromosomes 13, 14, 15, 21 and 22 in humans).

PALINDROME

DNA sequence in which the 5′–3′ composition is identical on each strand with respect to its midpoint.

ORTHOLOGOUS

The quality of having sequence similarity as a result of speciation.

BALANCING SELECTION

Natural selection in which heterozygotes have increased evolutionary fitness with respect to either homozygous condition.

SPHEROPLAST FUSION

A method for transferring DNA into cells or between cells whereby the host cell wall is removed (spheroplast) before polyethylene glycol fusion.

TRANSFORMATION-ASSOCIATED RECOMBINATION-BASED GENOMIC LIBRARIES

Genomic libraries that are constructed by a transformation-associated recombination (TAR) cloning system (see box 1).

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Eichler, E., Clark, R. & She, X. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 5, 345–354 (2004). https://doi.org/10.1038/nrg1322

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