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During the last two decades, comparative cytogenetics and genomics has evolved from a specialized discipline to a highly dynamic field of research. This development was driven by major technological advancements as well as emergence of the deeper insight that many aspects of human genome function can be better understood when information about its evolutionary changes is taken into account. Whole-genome sequencing projects of biomedical model species and domesticated animals provided important clues to the molecular mechanisms that shaped the human genome. These strategies were complemented by the launch of the chimpanzee genome project, leading to the recent publication of the first chimpanzee draft sequence and its alignment with the human reference sequence. [ABSTRACT FROM AUTHOR]

The centromere repositioning phenomenon consists in the move of the centromere along the chromosome during evolution. This phenomenon is relatively frequent, and has been documented in primates, nonprimate mammals, and birds. It implies the inactivation of the old centromere and the rapid progression of the newly seeded centromere toward the complex organization that probably stabilizes its activity. Both events have a huge impact on chromosomal architecture. The segmental duplicon clusters at 6p22.1 and 15q24-26 are clear examples of remains of inactivated ancestral centromeres. These duplicons are dispersed in a relatively large area (approx 10 Mb), and contribute to the bulk of nonpericentromeric segmental duplications that constitute approx 5% of the human genome. [ABSTRACT FROM AUTHOR]

Rapid, high-resolution analysis of genomic rearrangements has become possible using array-comparative genomic hybridization (aCGH), a combination of CGH with DNA microarray technology. Using aCGH, genome copy number changes and rearrangement breakpoints can now be mapped and analyzed at resolutions down to a few kilobases or even less in a single hybridization. This technology is enabling us to identify previously hidden rearrangements in patients with suspected genomic disorders for which no karyotype aberrations could be identified using conventional cytogenetic analysis. Furthermore, the development of array painting has revealed a surprising level of rearrangement complexity in patients with apparently balanced translocations. [ABSTRACT FROM AUTHOR]

Chromosome rearrangements cause genomic disorders and cancer in human. Region-specific low-copy repeats (LCRs) can mediate nonallelic homologous recombination (NAHR) that results in chromosome rearrangements. Using the Cre-loxP site-specific recombination system, chromosome rearrangements that cause genomic disorders and cancer can be recapitulated in the mouse. Technology advancements in mouse genetics, such as recombineering, will undoubtedly facilitate modeling genetic changes associated with genomic disorders in the mouse. [ABSTRACT FROM AUTHOR]

Position effects describe the observed alteration in protein-coding gene expression that may accompany a change in genomic position of a given gene. A position effect may result from chromosomal translocation or other genomic rearrangements. Recent advances in chromatin studies in several different species including yeast, Drosophila, and mouse have contributed significantly to better understanding of human diseases resulting from abnormal epigenetic effects. Molecular models attempting to explain position effects in humans have been proposed; however, none of them adequately addresses a variety of mechanisms. According to the noncontact models, the cis- or trans-regulatory elements, or locus control regions, are physically separated from the target gene and act either at the RNA level, by protein interactions, or by mediation of boundary elements, termed insulators. On the contrary, the contact models invoke spatial-temporal modifications of chromatin structure (e.g., active chromatin hub). In both models, the conserved nongenic sequences (CNGs) may play an important role in genomic regulation of gene expression. The recent introduction of new techniques including tagging and recovery of associated proteins (RNA-TRAP) and capturing chromatin conformation (CCC or 3C), has provided powerful tools to investigate position effects in humans. [ABSTRACT FROM AUTHOR]

Rearrangement breakpoints resulting from nonallelic homologous recombination (NAHR) are typically clustered within small, well-defined portions of the segmental duplications that promote the rearrangement. These NAHR "hotspots" have been identified in every NAHR-promoted rearrangement in which breakpoint junctions have been sequenced in sufficient numbers. Enhancement of recombinatorial activity in NAHR hotspots varies from 3 to 237 times more than in the surrounding "cold" duplicated sequence. NAHR hotspots share many features in common with allelic homologous recombination (AHR) hotspots. Both AHR and NAHR hotspots appear to be relatively small (<2 kb) and are initiated by double-strand breaks. Gene conversion events as well as crossovers are enhanced at NAHR hotspots. Recent work has improved our understanding of the origins of NAHR and AHR hotspots, with both appearing to be relatively short-lived phenomena. Our present understanding of NAHR hotspots comes from a limited number of locus-specific studies. In the future, we can expect genome-wide analyses to provide many further insights. [ABSTRACT FROM AUTHOR]

Neoplastic disorders are characterized by recurrent somatically acquired chromosomal aberrations that alter the structure and/or expression of a large number of genes. Most "cancer genes" discovered to date in human neoplasms have been identified through isolation of genes at the breakpoints of balanced chromosomal translocations. Although functional studies of such cancer-causing genes have demonstrated their causal role in tumorigenesis, the mechanisms underlying the formation of recurrent chromosomal changes in cancer remain enigmatic. Low-copy repeats (LCRs) are important mediators of erroneous meiotic recombination, resulting in constitutional chromosomal rearrangements. Recently, LCRs have been implicated in the formation of the frequent and characteristic neoplasia-associated chromosomal aberrations t(9;22)(q34;q1 1) and i(17q), suggesting that similar genome architecture features may play an important role in generating also other somatic chromosomal rearrangements. [ABSTRACT FROM AUTHOR]

The presence of a small supernumerary marker chromosome (SMC) in a karyotype creates a diagnostic dilemma, because the resulting duplications/triplications may cause abnormal development, depending on the location and size of the extra material. The most common SMC is the inv dup(15), the effect of which varies with size of triplication as well as the parent of origin. inv dup(22) is associated with the highly variable cat eye syndrome. Both are thought to be caused by U-type recombination between neighboring low-copy repeats (LCRs), resulting in both symmetric and asymmetric bisatellited dicentric supernumerary chromosomes. Studies are underway to associate the abnormal features of each syndrome with specific genes in the duplicated regions. [ABSTRACT FROM AUTHOR]

Deletion of the most distal, telomeric band of human chromosomes can result in a variety of mental retardation and multiple congenital anomaly syndromes. These terminal deletions are some of the most commonly observed structural chromosome abnormalities detected by routine cytogenetic analysis. Terminal deletions of 1p36 occur in approx 1 in 5000 live births, making it the most frequently observed terminal deletion and one of the most commonly observed mental retardation syndromes in humans. Molecular characterization of subjects with monosomy 1p36 indicates that, like other terminal deletions, 1p36 deletions have breakpoints occurring in multiple locations over several megabases and are comprised of terminal truncations, interstitial deletions, complex rearrangements, and derivative chromosomes. In addition, cryptic interrupted inverted duplications have been observed at the end of terminally deleted chromosomes, suggesting premeiotic breakage-fusion-bridge (BFB) cycles can be intermediate steps in the process of generating and stabilizing terminal deletions of 1p36. Overall, these observations are identical to those made in yeast and other model systems in which a double-strand break (DSB) near a telomere can be repaired by a variety of mechanisms to stabilize the end of a broken chromosome. Furthermore, sequence analysis and fluorescent in situ hybridization (FISH) mapping of the terminal 10.5 Mb of 1p36 including a variety of terminal deletion breakpoint junctions indicate that segmental duplications, low-copy repeats (LCRs), and short repetitive DNA sequence elements may mediate the generation and stabilization of terminal deletions of 1p36. We hypothesize that nonallelic homologous recombination (NAHR) between palindromic or inverted LCRs in the subtelomeric region of 1p36 could generate a dicentric chromosome that is broken at a random location during the subsequent anaphase as the centromeres move to opposite poles. This model suggests that the molecular basis of terminal deletions may be directly linked to genomic architectural features in the subtelomeric regions that generate the initial, variable-sized terminally deleted chromo-some, and that stabilization of the broken chromosome occurs by one of a variety of competing DSB repair pathways. [ABSTRACT FROM AUTHOR]

A number of findings revealed that chromosome inversions are more frequent than deduced from classical cytogenetic studies. Indeed, some paracentric cryptic inversions have been found to be flanked by segmental duplications, either causing a Mendelian disease owing to the interruption of specific genes at inversion breakpoints or being present in the normal population as a polymorphism. In the latter case, in the heterozygous state they predispose to further unbalanced rearrangements such as inv dup rearrangements or simple deletions and duplications. The importance of this susceptibility factor has been well clarified with respect to some genomic disorders involving chromosome 8p and it is now emerging as a possible model that may explain the genetic basis of other recurrent chromosome rearrangements. [ABSTRACT FROM AUTHOR]

Approximately 0.03% of men carry a Y-chromosomal defect that leads to azoospermia, the absence of sperm cells from semen. Deletion mapping of the Y chromosomes of azoospermic or oligozoospermic men suggested that loss of three nonoverlapping regions, AZFa, AZFb, and AZFc, could be responsible. When the finished Y-chromosomal reference sequence became available, the recurrent deletion of each of these intervals could be explained largely by non-allelic homologous recombination between direct repeats. However, in contrast to the conclusion from deletion mapping, AZFb deletions were found to overlap with AZFc deletions. In addition, a background level of nonhomologous recombination was found to generate a minority of deletions of these intervals. USP9Y appears to be the critical gene underlying the AZFa phenotype, but the critical genes lost in the AZFb and AZFc deletions have not yet been identified. Inspection of the sequence allowed additional duplications, inversions, and partial deletions of the AZF intervals to be anticipated, and many of the predicted structures have subsequently been identified in the population. The phenotypic consequences of these additional rearrangements of the AZFc region are unclear. High levels of gene conversion homogenize duplicated sequences in both direct and inverted orientations on the Y, which could potentiate subsequent rearrangements. The Y chromosome provides an excellent model for understanding genomic disorders; however, more finished sequences and new methodologies are needed. [ABSTRACT FROM AUTHOR]

Pelizaeus-Merzbacher disease (PMD) is a genomic disorder that is caused by altered dosage of a single gene, proteolipid protein 1 (itPLP1). Either duplication or deletion of itPLP1-containing genomic regions on chromosome Xq22.2 results in a severe leukodystrophy characterized by deficits of myelination in the central nervous system (itCNS). In this chapter, the molecular and genomic mechanisms for rearrangements causing PMD are reviewed, emphasizing differences in comparison to Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP) [ABSTRACT FROM AUTHOR]

X chromosome rearrangements usually convey clinical manifestations in the hemizygous males and are, thus, readily ascertained. They are found in all parts of the X chromosome and are associated with more than 20 disorders. Some of the rearrangements are the results of homologous recombination between low-copy repeats (LCRs) on the X chromosome or between large homologous regions on the X and Y chromosome, whereas others are caused by nonhomologous end-joining (NHEJ). For most large deletions associated with contiguous gene syndromes, the deletion breakpoints remain uncharacterized. The deletions, as well as inversions and duplications on the X chromosome, occur mainly in male germ cells, indicating intrachromatid or sister chromatid exchange as the underlying mechanism. [ABSTRACT FROM AUTHOR]

Sotos syndrome (SoS) is a well-known overgrowth syndrome with mental retardation, specific craniofacial features, and advanced bone age. Since NSD1 haploinsufficiency was proven to be the major cause of SoS in 2002, many intragenic mutations and chromosomal microdeletions (MDs) involving the entire NSD1 gene have been described. The sizes of most SoS MDs are identical and a specific genomic architecture around these MDs was found. Recently, precise analyses of the low-copy repeats (LCRs) flanking the SoS common deletion showed that the deletion arises through nonhomologous recombination (NAHR) utilizing the LCRs, and proved that SoS is a genomic disorder. [ABSTRACT FROM AUTHOR]

Williams-Beuren syndrome (WBS; also called Williams syndrome) is a multisystem developmental disorder that is almost always associated with an approx 1.5-Mb deletion of chromosome 7q11.23 (OMIM no. 194050). The deletion was identified in 1993 based on the observation of phenotypic overlap with supravalvular aortic stenosis (SVAS), a distinct autosomal dominant disorder affecting the cardiovascular system (1). It has since been shown that SVAS arises because of the disruption of one copy of the elastin gene, through either deletion, translocation or point mutation (2-4), but the genes contributing to the remaining aspects of WBS have not yet been definitively determined. [ABSTRACT FROM AUTHOR]

Among genomic disorders, submicroscopic deletions underlying neurofibromatosis 1 (NF1) are unusual because they involve the deletion of a tumor suppressor gene (NF1), they show a different preference for low-copy repeats (LCR) as substrates for meiotic vs mitotic recombination events, and they account for only a small fraction of mutations that cause the disorder. The NF1 gene at chromosome 17q1 1.2 is flanked by two sets of LCRs in direct orientation that undergo paralogous recombination. A pair of NF1-REPs mediate the recurrent constitutional 1.4-Mb microdeletion that occurs preferentially during maternal meiosis, whereas a pair of JJAZ1 pseudogene and functional gene mediate the recurrent 1.2-Mb microdeletion that occurs preferentially during postzygotic mitosis in females. Breakpoints have been mapped at the nucleotide level for both deletions and sequence features that may contribute to the choice of discrete sites for strand exchange have been identified. NF1 -REP-mediated NF1 microdeletions involve 13 additional genes, whereas JJAZ1 -mediated microdeletions involve the same genes but one. NF1 microdeletions are of great interest because they predispose to a heavy tumor burden, malignancy, and possibly other severe manifestations. [ABSTRACT FROM AUTHOR]

Meiotic unequal crossover events between blocks of low-copy repeats (LCRs) may lead to gene dosage imbalance resulting in genomic disorders. Genomic disorders are frequently associated with mental retardation or learning disabilities and mild to severe congenital anomalies. Chromosome 22q11.2 is particularly susceptible to chromosome rearrangements leading to several genomic disorders including velocardiofacial syndrome/DiGeorge syndrome (VCFS/DGS), der(22) syndrome, and cat-eye syndrome (CES), associated with a monosomy, trisomy, and tetrasomy of 22q11.2, respectively. Most VCFS/DGS patients have a similar hemizygous 3-Mb deletion mediated by meiotic interchromosomal homologous recombination events between LCRs termed LCR22s. The reciprocal duplication of the same interval, predicted on expected products of unequal crossover events, results in a more mild condition termed dup(22)(q11.2; q11.2) syndrome. In contrast to VCFS/DGS, dup(22)(q11.2; q11.2) and CES, der(22) syndrome is caused by a different molecular mechanism. Der(22) disorder arises in offspring of normal carriers of the constitutional t(1 1 ;22) (q23.3; q1 1.2) translocation by recombination between AT-rich (high AT sequence composition) palindromic sequences on 1 1q23.3 and 22q1 1.2. The palindromic sequence on 22q1 1.2 is within one of the LCR22s. Interestingly, both recurrent and novel breakpoints occur most often in LCR22s, making them an important architectural feature associated with susceptibility to genome rearrangements. To gain further insight into the mechanisms of how the LCR22s are involved in chromosome rearrangements, efforts are underway to determine the molecular evolution, structure, size, orientation, and their level of variability in humans. [ABSTRACT FROM AUTHOR]

The Charcot-Marie-Toothtype 1A (CMT1 A) duplication was the first recurrent, large (>1 Mb), submicroscopic DNA duplication rearrangement found to be associated with a common auto-somal dominant trait. Mechanistic studies of the CMT1A duplication have set the paradigm for genomic disorders. The CMT1A-REP low-copy repeats (LCRs) were among the first identified nongenic genomic architectural features that could act as substrates for nonallelic homologous recombination (NAHR). Identification of the predicted reciprocal recombination product, the hereditary neuropathy with liability to pressure palsies (HNPP) deletion, resulted in a model for reciprocal duplication/deletion genomic disorders. [ABSTRACT FROM AUTHOR]

Long interspersed element-1 (LINE-1 or L1) is an abundant retrotransposon that comprises approx 17% of human DNA. L1 retrotransposition events can lead to genome diversification and individual genetic variation by serving as insertional mutagens and by providing recombination substrates either during or long after their insertion. L1 retrotransposition also generates genomic variation by mobilizing DNA derived from its flanks, non-autonomous retrotransposons (e.g., Alu elements), and cellular mRNAs to new genomic locations. Together, these sequences comprise approx 15% of human genomic DNA. Thus, L1-mediated retrotransposition events are responsible for at least one-third of our genome. In this chapter, we discuss how innovative assays developed in recent years have increased our understanding of L1 biology and the impact of L1 on the human genome. [ABSTRACT FROM AUTHOR]

Centromeres are required for normal chromosome segregation in mitosis and meiosis, and a substantial proportion of human pathology stems from abnormalities of chromosome segregation, the underlying genomic basis and mechanism(s) of which are largely unknown. Human centromeres consist of megabases ofα-satelliteDNA, atandemlyrepeatedDNA family whose genomic organization, evolution, and function is increasingly well understood. The study of normal, abnormal, and engineered human chromosomes is providing insights into the nature of human centromeres and their mechanism of action, as well as enabling comparison with centromeres of other eukaryotic organisms and the identification of genomic elements required for normal centromere function. [ABSTRACT FROM AUTHOR]

The completion of the human genome sequencing has opened new opportunities to better understand complex biological systems. In this realm, the human sense of smell is an excellent example of how genome analysis provides new information on genome organization and on deficits. Before the advent of genomic tools, the understanding of this highly sophisticated sensory neuronal pathway has been rather sketchy. In this chapter we summarize the relevant progress made in the last decade, and highlight the initial elucidation of two classes of olfactory deficits and their possible underlying genetic mechanisms. [ABSTRACT FROM AUTHOR]

Certain DNA sequences in the genome may exist either in the canonical right-handed B-duplex or in alternative non-B conformations, depending on conditions such as transcription, supercoil stress, protein binding, and so on. Analyses of breakpoint junctions at deletions, translocations, and inversions, where the sites of DNA breakage could be determined at the nucleotide level, revealed that most, if not all, of the breaks occurred within, or adjacent to, the predicted non-B conformations. These findings support a model whereby rearrangements are caused by recombination/repair processes between two distinct non-B conformations, which may reside either on the same chromosome or on two distinct chromosomes. This model was applicable to both Escherichia coli and humans, suggesting that the mechanisms involved are highly conserved. [ABSTRACT FROM AUTHOR]

Until recent times, the identification and characterization of segmental duplications has often been based purely on anecdotal reports. However, the completion of the Human Genome Project has now made possible the systematic analysis of the extent and distribution of duplicated sequences in humans. Both in situ hybridization and in silico approaches have shown that approx 5% of our genome is composed of highly homologous duplicated sequence (1,2), with enrichments of six- to sevenfold in pericentromeric (3), and two- to threefold in subtelomeric regions (4), respectively. Not only does the presence of these paralogous segments represent a significant challenge to the correct assembly of the human genome, but there is also an increasing awareness of their role in human evolution, variation, and disease. We present a review of segmental duplications in the mammalian genome. We describe their basic characteristics, distribution, and dynamic nature during recent evolutionary history. Based on these features, we discuss models to account for the proliferation of these sequences in the mammalian lineage, and also their contribution towards karyotypic evolution and phe-notypic differences between primates. Finally, we highlight the role of segmental duplications as mediators of human variation at the genomic level. [ABSTRACT FROM AUTHOR]

The human genome contains a large number of repetitive elements derived from transposable elements (TEs). In addition to active Alu and long interspersed element (LINE or L1) interspersed repeats, the human genome comprises a large number of ancient TEs. These include fossil germ-line insertions of DNA transposons, fossil short interspersed elements (SINEs), L2, and L3 LINEs. Processed pseudogenes and human endogenous retroviruses (HERVs) have amplified more recently in evolutionary history and some of them are still well preserved. Copies of some of the recently extinct TEs continue to contribute to genomic rearrangements by homologous recombination. In this chapter, we review ancient SINE and LINE repeats, processed pseudogenes, HERVs, and DNA transposons. We briefly introduce the genomic structure and replication strategy of these elements, their expression competence, and focus on the contribution of these repeats to human diseases. We also discuss some of the TE-derived genes and regulatory elements. [ABSTRACT FROM AUTHOR]

Alu elements represent one of the most successful mobile elements found in any genome. They have reached a copy number in excess of one million copies, making up more than 10% of the human genome. The level of amplification required to reach this high copy number has created an enormous number of insertion mutations resulting in human disease and genome evolution. They also add extensive diversity to the genome by introducing alternative splicing and editing to a wide range of RNA transcripts. In addition, after insertion Alu elements contribute to a high level of genetic instability through recombination. This instability contributes to a significant number of germ-line mutations and may be an even bigger factor in cancer and/or aging. [ABSTRACT FROM AUTHOR]

I came to Houston, Texas in 1986 with one goal being to identify "the gene" for Charcot-Marie-Tooth (CMT) disease. I was peripherally aware of the paper by Botstein and colleagues (1) proposing the genetic mapping of human "disease genes" using linked restriction fragment length polymorphisms (RFLPs) to position the gene within the human genome and indeed became very excited as a graduate student when Gusella' s paper (2) appeared in Nature linking the Huntington disease locus to markers on chromosome 4. It was a natural extension to think this "positional cloning" approach might be applied to a host of other human traits. There was apersonal, one might say egocentric, reason to choose CMT because I have the disease (3) and, in fact, the first blood samples collected for DNA linkage studies were from my own family wherein CMT segregated as an apparent autosomal recessive trait. [ABSTRACT FROM AUTHOR]