What Is Synapsis? Definition and Function

Prophase I of meiosis I in a lily cell.
Prophase I of meiosis I in a lily cell.

Ed Reschke / Getty Images

Synapsis or syndesis is the lengthwise pairing of homologous chromosomes. Synapsis mainly occurs during prophase I of meiosis I. A protein complex called the synaptonemal complex connects the homologues. The chromatids intertwine, breaking apart and exchanging pieces with one other in a process called crossing-over. The cross-over site forms an "X" shape called a chiasma. Synapsis organizes homologues so they can be separated in meiosis I. Crossing-over during synapsis is a form of genetic recombination that ultimately produces gametes that have information from both parents.

Key Takeaways: What Is Synapsis?

  • Synapsis is the pairing of homologous chromosomes prior to their separation into daughter cells. It is also known as syndesis.
  • Synapsis occurs during prophase I of meiosis I. In addition to stabilizing the homologous chromosomes so they separate correctly, synapsis facilitates the exchange of genetic material between the chromosomes.
  • Crossing-over occurs during synapsis. An x-shaped structure called a chiasma forms where the arms of chromosomes overlap. The DNA breaks at the chiasma and the genetic material from one homologue swaps with that from the other chromosome.

Synapsis in Detail

When meiosis starts, each cell contains two copies of each chromosome—one from each parent. In prophase I, the two different versions of each chromosome (homologues) find each other and connect so they can line up parallel to each other on the metaphase plate and ultimately be separated to form two daughter cells. A ribbon-like protein framework called the synaptonemal complex forms. The synaptonemal complex appears as a central line flanked by two lateral lines, which are attached to homologous chromosomes. The complex holds a synapsis in a fixed state and provides the framework for chiasma formation and the exchange of genetic material in crossing-over. The homologous chromosomes and synaptonemal complex form a structure called a bivalent. When crossing-over is complete, the homologous chromosomes separate into chromosomes with recombinant chromatids.

Crossing-over in meiosis
Synapsis occurs when homologous chromosomes line up and form chiasma for crossing-over.  FancyTapis / Getty Images

Synapsis Functions

The main functions of synapsis in humans are to organize homologous chromosomes so they can divide properly and ensure genetic variability in offspring. In some organisms, crossing-over during synapsis appears to stabilize bivalents. However, in fruit flies (Drosophila melanogaster) and certain nematodes (Caenorhabditis elegans) synapsis is not accompanied by meiotic recombination.

Chromosome Silencing

Sometimes problems occur during synapsis. In mammals, a mechanism called chromosome silencing removes defective meiotic cells and "silences" their genes. Chromosome silencing initiates at the sites of double-strand breaks in the DNA helix.

Common Questions About Synapsis

Textbooks typically simplify descriptions and illustrations of synapsis to help students understand the basic concepts. However, this sometimes leads to confusion.

The most common question students ask is whether synapsis only occurs at single points on homologous chromosomes. Actually, chromatids may form many chiasmas, involving both sets of homologue arms. Under an electron microscope, the pair of chromosomes appears entangled and crossed at multiple points. Even sister chromatids may experience crossing-over, although this does not result in genetic recombination because these chromatids have identical genes. Sometimes synapsis occurs between non-homologous chromosomes. When this happens, a chromosome segment detaches from one chromosome and attaches to another chromosome. This results in a mutation called a translocation.

Another question is whether synapsis ever occurs during prophase II of meiosis II or whether it can occur during prophase of mitosis. While meiosis I, meiosis II, and mitosis all include prophase, synapsis is restricted to prophase I of meiosis because this is the only time homologous chromosomes pair with each other. There are certain rare exceptions when crossing-over occurs in mitosis. It can occur as an accidental chromosome pairing in asexual diploid cells or as an important source of genetic variation in some types of fungi. In humans, mitotic crossing-over may allow mutation or cancer gene expression that would otherwise be suppressed.


  • Dernburg, A.F.; McDonald, K.; Moulder, G.; et al. (1998). "Meiotic recombination in C. elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis". Cell. 94 (3): 387–98. doi:10.1016/s0092-8674(00)81481-6
  • Ellnati, E.; Russell, H.R.; Ojarikre, O.A.; et al. (2017). "DNA damage response protein TOPBP1 regulates X chromosome silencing in the mammalian germ line". Proc. Natl. Acad. Sci. U.S.A. 114 (47): 12536–12541. doi:10.1073/pnas.1712530114
  • McKee, B, (2004). "Homologous pairing and chromosome dynamics in meiosis and mitosis". Biochim Biophys Acta. 1677 (1–3): 165–80. doi:10.1016/j.bbaexp.2003.11.017.
  • Page, J.; de la Fuente, R,; Gómez, R.; et al. (2006). "Sex chromosomes, synapsis, and cohesins: a complex affair". Chromosoma. 115 (3): 250–9. doi:10.1007/s00412-006-0059-3
  • Revenkova, E.; Jessberger, R. (2006). "Shaping meiotic prophase chromosomes: cohesins and synaptonemal complex proteins". Chromosoma. 115 (3): 235–40. doi:10.1007/s00412-006-0060-x
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Helmenstine, Anne Marie, Ph.D. "What Is Synapsis? Definition and Function." ThoughtCo, Aug. 29, 2020, thoughtco.com/synapsis-definition-and-function-4795794. Helmenstine, Anne Marie, Ph.D. (2020, August 29). What Is Synapsis? Definition and Function. Retrieved from https://www.thoughtco.com/synapsis-definition-and-function-4795794 Helmenstine, Anne Marie, Ph.D. "What Is Synapsis? Definition and Function." ThoughtCo. https://www.thoughtco.com/synapsis-definition-and-function-4795794 (accessed March 30, 2023).