Basic genetics concepts: Chromosomes and cell division

INTRODUCTION — The incorporation of genetic information into the practice of medicine is increasing at a rapid pace, and an understanding of the basic principles underlying chromosomal organization and segregation is often useful in patient care.

The basic principles of chromosome organization and segregation are reviewed here, along with the types of genomic disorders that can occur and tools available to evaluate them.

DNA regulation, gene expression, and epigenetic regulation (DNA and histone modifications that alter gene expression) are presented separately. (See "Basic genetics concepts: DNA regulation and gene expression" and "Principles of epigenetics".)

The following subjects are also discussed in separate topic reviews:

●Genetics terminology – (See "Genetics: Glossary of terms".)

●Genetic testing – (See "Genetic testing".)

●Genetic counseling – (See "Genetic counseling: Family history interpretation and risk assessment".)

●Genomic disorders – (See "Genomic disorders: An overview".)

CHROMOSOME ORGANIZATION — Chromosome structure facilitates packaging of a massive amount of DNA (nearly two meters in length if stretched end-to-end) into the cell nucleus, a compaction to nearly one 1-millionth of the original length [1].

The highly regulated organization of this compaction allows selective accessibility of the transcription machinery to certain genes or regulatory regions, without the need to completely decondense and unwind an entire chromosome.

Parts of the chromosome — Genomic DNA is organized into higher-order structures, beginning with nucleosomes, which consist of 147 base-pair stretches of double-stranded DNA wrapped around a core of eight histones [2]. These nucleosomes in turn are further organized into chromatin, which contains additional regulatory proteins that facilitate tighter packaging or unwinding, to allow access to transcription factors and other protein complexes (figure 1).

Chromatin is further packaged as chromosomes, recognizable by their characteristic banded appearance on mitotic chromosome spreads (figure 2). (See "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Chromosomal analysis'.)

Chromosomes have the following features visible on traditional G-banded chromosome spreads:

●Centromere – The centromere is the site of attachment of paired chromosomes to the microtubules of the mitotic spindle. Centromeric DNA is largely comprised of repetitive DNA sequences that bind to histones and other proteins that form the kinetochore, which facilitates chromosome alignment on the metaphase plate and segregation during anaphase. On a chromosome spread, the centromere appears as a constriction, not necessarily at the midpoint of the chromosome arms. During anaphase, chromosomes are pulled apart by microtubules attached to the centromeres. (See 'Mitosis' below.)

●Chromosome arms – The chromosome arms are the regions on either side of the centromere. The short arm is designated as "p" (from the French "petite" – small), and the long arm as "q" (the next letter after p). Gene positions can be described with reference to the chromosome number, arm, region, band, sub-band, and secondary sub-bands. For example, the hemoglobin beta locus (HBB), which encodes the beta globin chain, resides on a chromosome 11q15.4 (read "eleven – Q – one five point four"; not "15 point four").

●Telomeres – Telomeres are regions at the ends of chromosomes that protect the ends from loss of genetic material or fusion to other chromosomes. Telomeres shorten with successive cell division, and enzymes such as telomerase are required to maintain adequate telomere length. Telomere disorders such as dyskeratosis congenita can occur when telomere length is not sufficiently maintained. (See "Dyskeratosis congenita and other telomere biology disorders", section on 'Role of telomeres'.)

Chromosomes are numbered in order of decreasing length (ie, chromosome 1 is the longest, followed by chromosome 2). Exceptions are chromosome 21, which is approximately 3 million base pairs shorter than chromosome 22, and the X and Y chromosomes (X is large, Y is very small).

Normal ploidy (number of chromosomes) — Most somatic cells are diploid (2n), containing two sets of 23 chromosomes, for a total of 46 chromosomes (44 autosomes and two sex chromosomes).

There are both normal and pathologic exceptions to diploidy:

●Germ cells (egg and sperm) are haploid, containing one set of 23 chromosomes (22 autosomes and one sex chromosome, either X or Y). The egg can only provide an X chromosome because it is derived from cells with two X chromosomes; the sperm can provide X or Y because it is derived from cells with an X and a Y chromosome.

●Megakaryocytes represent a physiologically normal exception to diploidy. These cells are large platelet-producing cells in the bone marrow; typically they have a ploidy of 32n or 64n, due to multiple rounds of DNA replication without cell division. (See 'Mitosis' below.)

●Certain pathologic numerical chromosome abnormalities can arise during fertilization. As an example, an extra X chromosome in a male causes Klinefelter syndrome. (See "Sex chromosome abnormalities".)

●Cancer cells are often aneuploid; this may occur due to errors in cell division in precancerous somatic cells. (See 'Numerical and structural chromosome variation' below.)

SOMATIC CELL DIVISION

Overview of the cell cycle — The cell cycle refers to a series of stages through which actively dividing cells must pass to distribute genetic material to daughter cells, along with cytoplasmic proteins and organelles, with high fidelity.

The DNA replication phase is referred to as "S" (for synthesis of new DNA) and the phase in which one cell divides into two, with partitioning of material to two daughter cells, is referred to as "M" (for mitosis). Between these phases are the "G" (for gap) phases. Interphase is another term for cells that are not actively undergoing mitosis. These phases are illustrated in the figure (figure 3).

DNA replication (S phase) — DNA replication creates an identical copy of the cell's nuclear genome. It begins with the separation of DNA strands (denaturation), a process facilitated by DNA helicase (figure 4). The weakness of the hydrogen bonds between complementary bases on opposite strands allows denaturation to occur at physiologic temperatures. Replication occurs throughout the genome, converting one complete genome to two complete genomes allows a cell to divide into two daughter cells, each of which has an identical genetic sequence with conservation of sequence information and maintenance of the diploid (2n) DNA content.

Topoisomerases play a critical role in the proper unwinding of DNA during the replication process. Inhibitors of topoisomerase such as topotecan or irinotecan are used as anticancer therapies because they interfere with cell division. (See "Treatment of refractory and relapsed small cell lung cancer", section on 'Irinotecan' and "Systemic therapy for nonoperable metastatic colorectal cancer: Selecting the initial therapeutic approach", section on 'FOLFOX versus FOLFIRI'.)

DNA synthesis creates a new strand of DNA, which is assembled in the 5' to 3' direction. DNA polymerase binds to the 3' end of single strand template DNA and moves in a 3' to 5' direction, adding nucleic acids that are complementary to the template (eg, adding A where there is a T on the template and C where there is a G), joining the bases in the nascent (growing) strand to each other by phosphodiester bonds.

Both strands of the double helix serve as templates. However, because they are antiparallel, one strand has its 3' end exposed and the other has its 5' end exposed:

●The orientation of the antisense strand (3' to 5') is amenable to generation of a continuous new DNA strand that grows in a 5' to 3' direction. This strand is referred to as the leading strand.

●The orientation of the sense strand (5' to 3') is opposite of the direction that the polymerase moves. Thus, messenger RNA (mRNA) synthesis occurs discontinuously, in short fragments (referred to as Okazaki fragments) that are synthesized in a 3' to 5' direction and then joined together by DNA ligase. This strand is termed the lagging strand.

Each newly formed strand base-pairs with its template to produce a new double helical molecule. Thus, each new DNA molecule contains one old and one newly synthesized strand. This is referred to as semi-conservative replication. Special modifications of the original DNA molecule allow the cell to recognize which strand is new, which facilitates correction of errors introduced during the replication process [3,4].

DNA replication in eukaryotes occurs with high fidelity, with an estimated error rate of 1 in 10⁹ to 1 in 10¹¹ (can vary by location in the genome). These low error rates reflect the low intrinsic DNA polymerase error rates of 1 in 10⁵ along with the actions of cellular proofreading machinery.

Despite this high degree of fidelity, DNA replication is not perfect, and variations from the template can occur. Errors in DNA replication tend to produce sequence variants, some of which are clinically impactful and others that do not appear to have a deleterious or advantageous effect. (See "Basic genetics concepts: DNA regulation and gene expression", section on 'Sequence variants' and "Basic genetics concepts: DNA regulation and gene expression", section on 'Clinical classification of pathogenicity'.)

Base substitutions are considered synonymous when they do not change the resulting amino acid sequence (figure 5). Other changes can alter the properties of the resulting protein or DNA regulatory region, which may have important clinical implications. (See "Basic genetics concepts: DNA regulation and gene expression", section on 'Genetic variation'.)

●Some individuals carry a pathogenic variant in a gene that encodes one of the proteins that repair mispaired DNA bases, a process known as mismatch repair (MMR). Disease variants in MMR genes are responsible for Lynch syndrome, a hereditary cancer syndrome characterized by colorectal and uterine cancers. (See "Lynch syndrome (hereditary nonpolyposis colorectal cancer): Clinical manifestations and diagnosis", section on 'Genetics'.)

●Some individuals carry a pathogenic variant in a gene that encodes one of the proteins involved in homologous recombination, such as BRCA1 or BRCA2. Disease variants in these homologous recombination repair (HRR) genes compromise the ability of cells to repair double-strand DNA breaks, increasing risks for hereditary breast and ovarian cancer. In individuals with HRR-deficient cancer, therapies that block the base excision repair pathway can be useful therapeutically because they can prevent correction of DNA damage, leading to cell death. (See "Overview of the approach to metastatic breast cancer", section on 'Special considerations'.)

Mitosis — Mitosis (M phase) is the stage of the cell cycle during which somatic cells partition replicated chromosomes and cytoplasmic components to produce two daughter cells. It proceeds in phases regulated by a series of checkpoints that ensure each step is completed before the next one begins (figure 6).

●Prophase – The chromosomes condense dramatically, producing a set of sister chromatids with prominent centromeres. (See 'Parts of the chromosome' above.)

●Metaphase – The nuclear envelope begins to break down, and the mitotic spindle forms from an array of microtubules. The "minus" ends of the microtubules collect at two separate poles, and the free "plus" ends extend towards the chromosomes, where they search out and attach to the centromeric DNA.

●Anaphase – Once every sister chromatid pair is fully attached and aligned in the center of the cell on the metaphase plate, with one chromatid tethered to each pole, the sister chromatids separate and are pulled to opposite poles.

●Telophase and cytokinesis – The mitotic spindle breaks down, the chromosomes decondense, a new nuclear membrane forms around each set of daughter chromosomes, and the cell membrane forms a furrow that separates the daughter cells into two separate cells during cytokinesis.

Errors in mitosis tend to produce larger structural and numerical chromosome variants such as aneuploidy. (See 'Numerical and structural chromosome variation' below.)

While the genotype of the daughter cells is usually identical, the other features and fates of the daughter cells often diverge due to differences in distribution of other cellular contents:

●Symmetric divisions partition most of the cellular contents equally and create two relatively similar daughter cells. Examples include expansion of mature tissues during growth of a tissue.

●Asymmetric divisions create two daughter cells with different properties or different fates. This can occur when cellular contents are partitioned unequally (eg, one daughter cell receives more organelles or a different membrane compartment than the other) or if a stochastic process (random chance) results in divergent fates.

Asymmetric divisions are especially important in stem cell biology because they allow a stem cell to generate one differentiating progeny cell and one replacement stem cell. (See "Overview of hematopoietic stem cells", section on 'Self-renewal versus differentiation'.)

Endomitosis (mitosis without cytokinesis) produces polyploid cells with >2N DNA content. This is the normal process by which megakaryocytes (precursors of platelets) are formed in the bone marrow. The average ploidy of megakaryocytes is 16N, consistent with three cycles of endomitosis per cell. (See "Megakaryocyte biology and platelet production", section on 'Size and ploidy'.)

MEIOSIS — Meiosis is a specialized type of cell division that produces haploid (1n) daughter cells to form the gametes (egg and sperm), which in turn combine with the gametes of a genetically distinct individual to produce offspring that are genetically different from both parents.

●Meiosis starts similarly to mitosis, with DNA replication followed by chromosome condensation, pairing, synapsis (alignment of homologous chromosomal regions), and recombination, followed by segregation to two daughter cells. This first step, which separates homologous chromosomes, is referred to as meiosis I (MI). MI involves the critical step that results in reduction of chromosome number, making meiosis distinct from mitosis. While mitosis ends with the production of two diploid daughter cells, in meiosis there is a second cell division without an intervening DNA replication step, producing four haploid daughter cells (figure 7). This second stage in which sister chromatids are separated is referred to as meiosis II.

●Another major difference from mitosis is that in meiosis, chromosomal segments are exchanged between the sister chromatids via the process of recombination (also called meiotic crossing over) during meiosis I. Homologous chromosome regions from the maternally derived and paternally derived chromosomes are traded, and the new material is incorporated (figure 8). This results in new haplotypes (combinations of genes on a single chromosome) that were not present in the maternal or paternal cells.

●Independent assortment, where pairs of homologous chromosomes are divided randomly so the haploid cell contains a mixture of the organism's maternal and paternal chromosomes and genes, is another critical part of meiosis (figure 9A). Recombination further enhances diversity as pieces of the DNA are broken and then recombined. Errors can happen if this recombination has a breakpoint across a gene. The closer two alleles or genes are, the lower the recombination rate is. When there are two or more loci that do not appear to randomly associate, they are said to be in linkage disequilibrium. (See "Genetics: Glossary of terms", section on 'Linkage disequilibrium'.)

●During oocyte formation, cell division is asymmetric, such that only one of the resulting cells becomes an oocyte; the three other cells become polar bodies that eventually degenerate. The hormonal and anatomical regulation spermatogenesis is discussed separately. (See "Male reproductive physiology".)

Recombination coupled with independent assortment of chromosomes yields further variation in the final genotype of the gametes. Together with sexual reproduction, these forces ensure genetic diversity in the population.

However, errors in the fidelity of these processes can cause structural variations that may be present in the offspring. Examples include trisomies due to nondisjunction of paired sister chromatids, or duplications or deletions due to defective recombination events. (See 'Numerical and structural chromosome variation' below and "Genomic disorders: An overview".)

NUMERICAL AND STRUCTURAL CHROMOSOME VARIATION — Variation in chromosome number or structure can occur in the germline or in somatic cells, similar to variation at the DNA/nucleotide level. (See "Basic genetics concepts: DNA regulation and gene expression", section on 'Genetic variation'.)

●Germline – Abnormalities of chromosome segregation in the germline can lead to autosomal trisomies such as trisomy 21 or sex-chromosome abnormalities such as Turner syndrome or Klinefelter syndrome. (See "Down syndrome: Clinical features and diagnosis" and "Clinical manifestations and diagnosis of Turner syndrome" and "Clinical features, diagnosis, and management of Klinefelter syndrome".)

●Somatic – Abnormal chromosome number or structure affecting somatic cells is characteristic of many types of malignancies. (See "Acute myeloid leukemia: Cytogenetic abnormalities".)

There are a number of different categories of large-scale chromosomal variations that include the following numerical and structural abnormalities:

Aneuploidies — Aneuploidies refer to an abnormal chromosome number (extra copy or missing copy of one or more chromosomes). These typically occur during cell division, either through non-disjunction of paired chromosomes in meiosis I or meiosis II (figure 9A-B) or through mitotic changes such as checkpoint errors, anaphase lag, or mitosis without cytokinesis.

Sex chromosome aneuploidies are more common than autosomal aneuploidies. This may be because epigenetic mechanisms limit the phenotypic consequences of sex chromosome aneuploidies and/or because they are less likely to impact essential gene functions.

●Monosomy – Monosomy refers to loss of a whole chromosome or chromosome material. Autosomal monosomies (loss of a non-sex-linked chromosome), are incompatible with life unless accompanied by mosaicism. Turner syndrome (monosomy X or XO) is caused by the loss of one X chromosome and is compatible with life.

●Trisomy – Trisomy refers to gain of a whole chromosome or chromosome material.

Trisomy 21 (Down syndrome) is the only trisomy for a whole human autosome in which affected individuals frequently survive into adulthood. Trisomy 18 (Edwards syndrome) and trisomy 13 (Patau syndrome) pregnancies can survive to term, but life expectancy is significantly shortened in most cases. (See "Down syndrome: Clinical features and diagnosis" and "Congenital cytogenetic abnormalities".)

Sex chromosome trisomies include 47,XXY (Klinefelter syndrome); 47,XYY, which is generally an incidental finding or may produce alterations in learning or attention; and 47,XXX (triple X syndrome), which generally produces mild neurocognitive effects [5]. (See "Causes of primary hypogonadism in males", section on 'Klinefelter syndrome' and "The child with tall stature and/or abnormally rapid growth", section on '47,XYY (Jacobs) syndrome'.)

Structural aberrations — Chromosome aberrations (also known as "structural changes") typically result from either chromosome recombination errors during meiosis (for germline aberrations) or abnormal chromosomal segregation during meiosis or mitosis (for germline or somatic aberrations).

Deletions and duplications — Chromosomal deletion refers to loss of a portion of a chromosome; typically many genes are affected. Duplication occurs when a region of the chromosome is present twice, resulting in extra copies of the genes in the duplicated region. As an example, duplication of the PMP22 gene can cause Charcot-Marie-Tooth disease type IA. (See "Charcot-Marie-Tooth disease: Genetics, clinical features, and diagnosis".)

In some cases, the number of times a segment of DNA is duplicated can expand in successive generations, causing children to develop diseases such as Huntington disease earlier than their parents. This phenomenon is referred to as anticipation. (See "Huntington disease: Genetics and pathogenesis", section on 'Clinical genetics' and "Inheritance patterns of monogenic disorders (Mendelian and non-Mendelian)", section on 'Anticipation'.)

Inversions — A chromosome inversion occurs when a region of a chromosome is excised and reinserted into the chromosome in the opposite orientation (eg, a switch in the order of genes ABCDEF to ABDCEF). The breakpoints of the chromosome inversion may interrupt a critical gene. An inversion in the F8 gene is a common cause of hemophilia A [6]. (See "Genetics of hemophilia A and B".)

Translocations — A chromosomal translocation occurs when a portion of one chromosome becomes fused with a portion of a non-homologous chromosome (a chromosome other than the paired sister chromatid) (figure 10). Balanced translocations are not associated with any net gain or loss of chromosomal material; unbalanced translocations can be associated with gains or losses of chromosomal material.

Translocations can result in an inappropriately positioned regulatory sequence and aberrant gene expression, or juxtaposition of two coding sequences, to produce novel fusion genes. A commonly used example of the latter is the translocation associated with chronic myeloid leukemia (CML). This is a reciprocal translocation between chromosomes 9 and 22 [t(9;22)(q34;q11)], referred to as the Philadelphia chromosome (figure 11); it generates a new BCR-ABL fusion gene that encodes a hyperfunctional tyrosine kinase with uncontrolled activity that leads to dysregulated clonal cellular expansion [7,8]. (See "Cellular and molecular biology of chronic myeloid leukemia".)

Ring chromosomes — Ring chromosomes can form when the two ends of a chromosome become fused, creating a circular structure. This can occur following chromosome breakage and loss of material at the ends of both the 'p' and 'q' arms of the same chromosome, which then become joined together.

Centromere defects — The centromere is the constriction in a condensed chromosome that is used as an attachment site for kinetochore microtubules during metaphase (see 'Mitosis' above). Acentric (lacking a centromere) or dicentric (having two centromeres) chromosomes or isochromosomes can result through abnormal repair of chromosome breakage or non-homologous recombination errors (figure 12). Isochromosomes (chromosomes in which one arm is the mirror image of the other arm) can be dicentric.

Copy number variants — A copy number variant (CNV) refers to a nucleotide sequence, typically of greater than 1000 bases to millions of bases in length, which varies in copy number between different individuals. A deleted region is termed a loss; regions that are duplicated one or more times are termed duplications or gains. CNVs may cause clinically relevant phenotypic effects related to changes in gene expression, or they may be clinically silent. (See "Genomic disorders: An overview".)

TOOLS TO EVALUATE CHROMOSOMAL VARIATION — Techniques used to evaluate chromosomal variation include the following:

●Karyotyping – Karyotyping refers to a traditional process of preparing a chromosome spread from dividing cells. In some cases, a mitogen is used to cause cells to enter mitosis. Karyotype analysis requires substantial expertise to identify and analyze specific chromosomes and chromosomal regions. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Chromosomal analysis'.)

●FISH – Fluorescence in situ hybridization (FISH) is a technique that uses fluorescent probes, typically to identify unique chromosome regions. FISH can be performed on mitotic or interphase cells, making it especially useful for assaying somatic tissues. (See 'Overview of the cell cycle' above.)

●Array CGH – Array comparative genome hybridization (array CGH, also referred to as chromosomal microarray) is a method of assaying for copy number variations (CNVs) that uses hybridization of patient DNA to an array of normal or control DNA. The size of the probes on the array can be modified to assay small changes (as small as single nucleotides) to larger regions of DNA. Most microarrays are also performed with single nucleotide polymorphism (SNP) analysis that enables detection of regions of loss of heterozygosity and uniparental isodisomy; these are referred to as SNP arrays. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Array comparative genomic hybridization' and "Genomic disorders: An overview", section on 'Array comparative genomic hybridization'.)

●Whole genome sequencing – Whole genome sequencing is gaining traction as a method to evaluate chromosomal variation. One example is the use of whole genome sequencing to make a genetic diagnosis in critically ill children in the intensive care unit. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications", section on 'Diagnosis of complex diseases'.)

SUMMARY

●Basic biology – Chromosome structure facilitates packaging of a massive amount of DNA (nearly two meters in length if stretched end-to-end) into the cell nucleus, a compaction to nearly one 1-millionth of the original length. Each chromosome has a central constriction (the centromere) flanked by two arms (p [the short arm] and q [the long arm]). Telomeres are the regions at the end of the chromosome arms that protect them from loss of chromosomal material or fusion with another chromosome. (See 'Chromosome organization' above and 'Parts of the chromosome' above.)

●Ploidy – Most somatic cells are diploid (2n), containing two sets of 23 chromosomes, for a total of 46 chromosomes (44 autosomes and two sex chromosomes). The germ cells (egg and sperm) are haploid. Examples of normal (physiologic) and pathologic increases in chromosome number are provided above. (See 'Normal ploidy (number of chromosomes)' above.)

●DNA replication – DNA is replicated during the S (synthesis) phase of the cell cycle. Both strands of the double helix serve as templates. The fidelity of DNA replication is extremely high. (See 'DNA replication (S phase)' above.)

●Mitosis – Cellular components, including replicated chromosomes, are partitioned to daughter cells during mitosis. Mitosis proceeds in phases regulated by a series of checkpoints that ensure each step is completed before the next one begins (figure 6). (See 'Mitosis' above.)

●Meiosis – Meiosis is the specialized cell division process by which haploid (1n) germ cells (egg and sperm) are formed. Recombination and independent assortment during meiosis and sexual reproduction ensure genetic diversity in the population. (See 'Meiosis' above.)

●Chromosomal variation – Categories of large-scale chromosomal variations include aneuploidies, deletions, inversions, translocations, and copy number variants. Abnormalities of chromosome segregation in the germline can lead to autosomal trisomies such as trisomy 21 or sex-chromosome abnormalities such as Turner syndrome or Klinefelter syndrome. Abnormal chromosome number or structure affecting somatic cells is characteristic of many cancers. (See 'Numerical and structural chromosome variation' above.)

●Evaluation – Chromosomal abnormalities can be evaluated clinically using a number of tools including karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (array CGH), single nucleotide polymorphism (SNP) arrays, and whole genome sequencing. (See 'Tools to evaluate chromosomal variation' above.)