Formation of de novo centromeres and construction of first-generation human artificial microchromosomes.

We have combined long synthetic arrays of alpha satellite DNA with telomeric DNA and genomic DNA to generate artificial chromosomes in human HT1080 cells. The resulting linear microchromosomes contain exogenous alpha satellite DNA, are mitotically and cytogenetically stable in the absence of selection for up to six months in culture, bind centromere proteins specific for active centromeres, and are estimated to be 6-10 megabases in size, approximately one-fifth to one-tenth the size of endogenous human chromosomes. We conclude that this strategy results in the formation of de novo centromere activity and that the microchromosomes so generated contain all of the sequence elements required for stable mitotic chromosome segregation and maintenance. This first-generation system for the construction of human artificial chromosomes should be suitable for dissecting the sequence requirements of human centromeres, as well as developing constructs useful for therapeutic applications.

A promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation.

X-chromosome inactivation is the process by which a cell recognizes the presence of two copies of an X chromosome early in the development of XX embryos and chooses one to be active and one to be inactive. Although it is commonly believed that the initiation of X inactivation is random, with an equal probability (50:50) that either X chromosome will be the inactive X in a given cell, significant variation in the proportion of cells with either X inactive is observed both in mice heterozygous for alleles at the Xce locus and among normal human females in the population. Families in which multiple females demonstrate extremely skewed inactivation patterns that are otherwise quite rare in the general population are thought to reflect possible genetic influences on the X-inactivation process. Here we report a rare cytosine to guanine mutation in the XIST minimal promoter that underlies both epigenetic and functional differences between the two X chromosomes in nine females from two unrelated families. All females demonstrate preferential inactivation of the X chromosome carrying the mutation, suggesting that there is an association between alterations in the regulation of XIST expression and X-chromosome inactivation.

A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome.

Chromatin on the mammalian inactive X chromosome differs in a number of ways from that on the active X. One protein, macroH2A, whose amino terminus is closely related to histone H2A, is enriched on the heterochromatic inactive X chromosome in female cells. Here, we report the identification and localization of a novel and more distant histone variant, designated H2A-Bbd, that is only 48% identical to histone H2A. In both interphase and metaphase female cells, using either a myc epitope-tagged or green fluorescent protein-tagged H2A-Bbd construct, the inactive X chromosome is markedly deficient in H2A-Bbd staining, while the active X and the autosomes stain throughout. In double-labeling experiments, antibodies to acetylated histone H4 show a pattern of staining indistinguishable from H2A-Bbd in interphase nuclei and on metaphase chromosomes. Chromatin fractionation demonstrates association of H2A-Bbd with the histone proteins. Separation of micrococcal nuclease-digested chromatin by sucrose gradient ultracentrifugation shows cofractionation of H2A-Bbd with nucleosomes, supporting the idea that H2A-Bbd is incorporated into nucleosomes as a substitute for the core histone H2A. This finding, in combination with the overlap with acetylated forms of H4, raises the possibility that H2A-Bbd is enriched in nucleosomes associated with transcriptionally active regions of the genome. The distribution of H2A-Bbd thus distinguishes chromatin on the active and inactive X chromosomes.

XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure.

The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.

Genomics and gene therapy. Artificial chromosomes coming to life.

One of the biggest obstacles to gene therapy is the delivery of the therapeutic gene to the target tissue so that it is appropriately expressed. In his Perspective, Willard looks at the potential advantages of using a human artificial chromosome to maintain expression of a therapeutic gene and discusses some of the hurdles yet to be overcome before this gene delivery system can be tried out in the clinic.

Assignment of the gene for myelin proteolipid protein to the X chromosome: implications for X-linked myelin disorders.

Several inherited disorders in humans and in rodents result in myelin dysgenesis and a deficiency of the molecular constituents of myelin. A complementary DNA to one of the two major myelin proteins, myelin proteolipid protein (also known as lipophilin), has been used with Southern blot analysis of somatic cell hybrid DNA to map the human proteolipid protein gene to the middle of the long arm of the human X chromosome (bands Xq13-Xq22) and to assign the murine proteolipid protein gene to the mouse X chromosome. Comparison of the gene maps of the human and mouse X chromosomes suggests that myelin proteolipid protein may be involved in X-linked mutations at the mouse jimpy locus and has implications for Pelizaeus-Merzbacher disease, a human inherited X-linked myelin disorder.

Duchenne muscular dystrophy involving translocation of the dmd gene next to ribosomal RNA genes.

Duchenne muscular dystrophy (DMD) is a severe X-linked disorder leading to early death of affected males. Females with the disease are rare, but seven are known to be affected because of a chromosomal rearrangement involving a site at or near the dmd gene on the X chromosome. One of the seven has a translocation between the X and chromosome 21. The translocation-derived chromosomes from this patient have been isolated, and the translocation is shown to have split the block of genes encoding ribosomal RNA on the short arm of chromosome 21. Thus ribosomal RNA gene probes may be used to identify a junction fragment from the translocation site, allowing access to cloned segments of the X at or near the dmd gene and presenting a new approach to the study of this disease.

Genomic and genetic definition of a functional human centromere.

The definition of centromeres of human chromosomes requires a complete genomic understanding of these regions. Toward this end, we report integration of physical mapping, genetic, and functional approaches, together with sequencing of selected regions, to define the centromere of the human X chromosome and to explore the evolution of sequences responsible for chromosome segregation. The transitional region between expressed sequences on the short arm of the X and the chromosome-specific alpha satellite array DXZ1 spans about 450 kilobases and is satellite-rich. At the junction between this satellite region and canonical DXZ1 repeats, diverged repeat units provide direct evidence of unequal crossover as the homogenizing force of these arrays. Results from deletion analysis of mitotically stable chromosome rearrangements and from a human artificial chromosome assay demonstrate that DXZ1 DNA is sufficient for centromere function. Evolutionary studies indicate that, while alpha satellite DNA present throughout the pericentromeric region of the X chromosome appears to be a descendant of an ancestral primate centromere, the current functional centromere based on DXZ1 sequences is the product of the much more recent concerted evolution of this satellite DNA.

Gene encoding the beta subunit of S100 protein is on chromosome 21: implications for Down syndrome.

S100 protein is a calcium-binding protein found predominantly in the vertebrate nervous system. Genomic and complementary DNA probes were used in conjunction with a panel of rodent-human somatic cell hybrids to assign the gene for the beta subunit of S100 protein to the distal half of the long arm of human chromosome 21. This gene was identified as a candidate sequence which, when expressed in the trisomic state, may underlie the neurologic disturbances in Down syndrome.

Cloning of human androgen receptor complementary DNA and localization to the X chromosome.

The androgen receptor (AR) mediates the actions of male sex steroids. Human AR genomic DNA was cloned from a flow-sorted human X chromosome library by using a consensus nucleotide sequence from the DNA-binding domain of the family of nuclear receptors. The AR gene was localized on the human X chromosome between the centromere and q13. Cloned complementary DNA, selected with an AR-specific oligonucleotide probe, was expressed in monkey kidney (COS) cells and yielded a high-affinity androgen-binding protein with steroid-binding specificity corresponding to that of native AR. A predominant messenger RNA species of 9.6 kilobases was identified in human, rat, and mouse tissues known to contain AR and was undetectable in tissues lacking AR androgen-binding activity, including kidney and liver from androgen-insensitive mice. The deduced amino acid sequence of AR within the DNA-binding domain has highest sequence identity with the progesterone receptor.

Human ribosomal RNA genes: orientation of the tandem array and conservation of the 5' end.

The multiple copies of the human ribosomal RNA genes (rDNA) are arranged as tandem repeat clusters that map to the middle of the short arms of chromosomes 13, 14, 15, 21, and 22. Concerted evolution of the gene family is thought to be mediated by interchromosomal recombination between rDNA repeat units, but such events would also result in conservation of the sequences distal to the rDNA on these five pairs of chromosomes. To test this possibility, a DNA fragment spanning the junction between rDNA and distal flanking sequence has been cloned and characterized. Restriction maps, sequence data, and gene mapping studies demonstrate that (i) the rRNA genes are transcribed in a telomere-to-centromere direction, (ii) the 5' end of the cluster and the adjacent non-rDNA sequences are conserved on the five pairs of chromosomes, and (iii) the 5' end of the cluster is positioned about 3.7 kb upstream from the transcription initiation site of the first repeat unit. The data support a model of concerted evolution by interchromosomal recombination.

Centromeres: the missing link in the development of human artificial chromosomes.

Successful construction of artificial chromosomes is an important step for studies to elucidate the DNA elements necessary for chromosome structure and function. A roadblock to developing a tractable system in multicellular organisms, including humans, is the poorly understood nature of centromeres. Progress, has been made in defining the satellite DNA that appears to contribute to the centromere in both humans and Drosophila and large arrays of alpha satellite DNA have been used to construct first-generation human artificial chromosomes. Non-satellite DNA sequences are also capable of forming 'neo-centromeres' under some circumstances, however, raising questions about the sequence-dependence of centromere and kinetochore assembly. Taken together with new information on the nature of protein components of the kinetochore, these data support a model in which functional kinetochores are assembled on centromeric chromatin, the competence of which is established epigenetically. The development of human artificial chromosome systems should facilitate investigation of the DNA and chromatin requirements for active centromere assembly.

Evolution of alpha satellite.

Alpha satellite is one of the most thoroughly studied repetitive DNA families and is a paradigm for understanding other satellite DNA and multigene families. Alpha satellite illustrates both intra- and interchromosomal modes of evolution. Recent advances in understanding the structure and evolution of human and other primate alpha satellites are summarized in this review.

Mammalian X-chromosome inactivation and the XIST gene.

X-chromosome inactivation is a unique developmental event that results in the cis-limited transcriptional inactivation of most genes on one of the two X chromosomes in female mammals. Studies in both human and mouse have demonstrated that X inactivation requires the presence in cis of a locus, the X-inactivation center, that is thought to be involved in the initiation and/or spreading of the inactivation signal in early development. Identification and characterization of a gene, XIST, which is located at or near the X-inactivation center and which is expressed specifically from the inactive X chromosome in both humans and mouse, suggests that it may be involved in X inactivation.

Mammalian chromosome structure.

The DNA sequences that are necessary for the formation of a functional mammalian chromosome are thought to be the origins of replication, the telomeres and the centromere. Telomere structure is now well understood, with the functional element characterized as the motif (TTAGGG)n. The structures of the DNA regions that contain origins of replication and a centromere are known, but the functionally important elements within these regions are still only poorly defined.

Centromeres of mammalian chromosomes.

The centromere is the major cis-acting genetic locus involved in chromosome segregation in mitosis and meiosis. The mammalian centromere is characterized by large amounts of tandemly repeated satellite DNA and by a number of specific centromere proteins, at least one of which has been shown to interact directly with centromeric satellite DNA sequences. Although direct functional assays of chromosome segregation are still lacking, the data are most consistent with a structural and possibly functional role for satellite DNA in the mammalian centromere.

Inherited methylmalonyl CoA mutase apoenzyme deficiency in human fibroblasts: evidence for allelic heterogeneity, genetic compounds, and codominant expression.

We have measured and characterized methylmalonyl coenzyme A (CoA) mutase activity in extracts of cultured human fibroblasts from 23 patients with inherited deficiency of the mutase apoenzyme and from eight obligate heterozygotes for this defect. The mutant cell lines fall into two categories. Those without detectable residual mutase activity in cell extracts (>0.1% of control), and whose ability to utilize propionate in intact cells is refractory to supplementation of the culture medium with hydroxocobalamin, are designated mut degrees mutants. Those with detectable residual activity in cell extracts ( approximately 0.5-50% of control), and whose ability to utilize propionate in intact cells in markedly increased by hydroxocobalamin supplementation, are designated mut(-) mutants. The mutant enzyme in the mut(-) mutants exhibits a 50- to 5,000-fold elevated Michaelis constant (K(m)) for adenosylcobalamin in vitro, a normal K(m) for methylmalonyl CoA, and a strikingly reduced thermal stability at 45 degrees C relative to control. Mutase from one mut(-) mutant turns over at a rate three to four times that of control enzyme when cells are grown in hydroxocobalamin-supplemented medium.To detect heterozygous carriers of mutant mut alleles, we compared mutase activity in fibroblast extracts from four controls with that from eight parents of either mut degrees or mut(-) mutants. After cell growth in either unsupplemented or hydroxocobalamin-supplemented medium, activity in cell lines from heterozygotes was reduced to 47 or 37% of the mean control activities, respectively. We also examined the effect of adenosylcobalamin concentration on reaction kinetics of mutase from heterozygote cell lines. All four cell lines from parents of mut(-) mutants exhibited complex enzyme kinetics; approximately 80% of mutase activity demonstrated a K(m) indistinguishable from control, whereas a smaller component of activity exhibited a K(m) similar to the abnormal K(m) expressed by the mut(-) propositus in each family. In two families with a mut degrees propositus, mutase from three of the four parents exhibited only the normal K(m) for adenosylcobalamin, whereas mutase from one parent displayed complex kinetics, indicating expression of both a normal allele (mut(+)) and a mutant allele with an abnormal K(m). From these studies, we conclude that mut mutants reflect mutations at the autosomal gene locus for the methylmalonyl CoA mutase apoenzyme; that mut degrees , mut(-), and mut(+) alleles at this locus are codominantly expressed; and that some mut mutants may be genetic compounds, inheriting two different mut degrees or mut(-) alleles from their parents.