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User:Hanbong/sandbox

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General Overview of the segmentation gene:

A segmentation gene is a gene involved in the early stages of pattern formation that define repeated units (metameres) in a segmented organism, usually the embryo. Virtually all arthropods, during embryonic stage, develop their body in repeating segments. In drosophila (reference) specifically, they divide the embryo into 14 parasegments. The parasegments are different from segments that are visibility delimited by grooves on the embryo. Rather, they consist of posterior part of an anterior segment and anterior part of the segment behind it. These delimit the boundary of segmentation gene expression. Mutation in segmentation genes can cause phenotypic changes of differing severity depending on its type. They can be classified into 3 groups: Gap genes, Pair-rule gene and Segment-polarity genes.

Gap genes (Image):

Gap genes produce sharp boundaries in the embryos that regulate later gene expression. They were named as such because loss of function mutations in gap genes resulted in large deletions (or gaps) in the neighbouring segments of the embryo. There are at least 6 types of gap genes but the three that are well known are hunchback, knirps, kruppel (references).

The establishment of the boundary happens in two steps. First, maternal driven factors drive expression of specific gap proteins (i.e. bicoid, a maternal effect gene, drive expression of hunchback). Different concentration gradients of gap genes establish stable boundaries. These stable boundaries help delimit and regulate expression of pair rule genes.

Pair-rule genes (Image):

Pair rule genes are genes that are expressed in alternating parasegments of the embryo for a total of 7-8 stripes. Each expression stripe is separated by a region of no expression of equal size. For example, even-skipped genes are expressed in alternating even-numbered parasegments (stripe 2, 4, and so on) while odd-skipped genes are expressed in odd-numbered parasegments (stripe 1, 3, and so on). Mutation in one can cause deletion of either odd-numbered or even-numbered parasegments. The pair rule genes regulate expression of segment polarity genes.


Segment polarity (Image):

Segment polarity genes regulate expression of genes within the segment. For example, within the segment there is the anterior region, which means the region close to the head, and the posterior region, in contrast, is the region close to the tail. Loss of function in a segment polarity gene can result in loss of all anterior or posterior portions in each segment. Essentially they are crucial for pattern formation within each embryonic segment 5, 8. Some of the segment polarity genes are involved in the formation of the most ventral pattern body parts, otherwise the action of some specific genes are also essential for producing specific types of denticle type of the insect6.

e.g. wingless (wg) gene7

Source for Article

Deutsch J. S. (2004). Segments and parasegments in arthropods: a functional perspective. BioEssays : news and reviews in molecular, cellular and developmental biology, 26(10), 1117–1125. https://doi.org/10.1002/bies.20111

Gilbert SF. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates; 2000. The Origins of Anterior-Posterior Polarity. https://www.ncbi.nlm.nih.gov/books/NBK10039/

Larsen, C., Bardet, P. L., Vincent, J. P., & Alexandre, C. (2008). Specification and positioning of parasegment grooves in Drosophila. Developmental biology, 321(2), 310–318. https://doi.org/10.1016/j.ydbio.2008.04.026

Marjorie A. Hoy, in Insect Molecular Genetics (Fourth Edition), 2019

4.14.2 Zygotic-Segmentation Genes

https://doi.org/10.1016/B978-0-12-815230-0.00004-2.

Williams, T. A., & Nagy, L. M. (2017). Linking gene regulation to cell behaviors in the posterior growth zone of sequentially segmenting arthropods. Arthropod structure & development, 46(3), 380–394. https://doi.org/10.1016/j.asd.2016.10.003

Confirmation of sources:

  1. "Segmentation gene - definition from Biology-Online.org". 2009-01-07. Retrieved 2009-12-14.
    1. In the original webpage: "A segmentation gene is a gene involved in the early stages of pattern formation that define repeated units (metameres) in a segmented organism, usually the embryo."
    2. The page cited is not about the segmentation genes, only about the pair-rule.
    3. Primary resource: Hiromi, Y., & Gehring, W. J. (1987). Regulation and function of the Drosophila segmentation gene fushi tarazu. Cell, 50(6), 963–974. https://doi.org/10.1016/0092-8674(87)90523-x
  2. "Segmentation gene - Biology-Online Dictionary". www.biology-online.org. Retrieved 2017-03-03.
  1. In the original webpage: “They are classified into 3 groups: gap genes, pair-rule genes, and segment polarity genes.”
  2. The cited page is the same one as for the first reference and does not include the correct information.
  3. Primary resource: Schroeder, M. D., Pearce, M., Fak, J., Fan, H., Unnerstall, U., Emberly, E., Rajewsky, N., Siggia, E. D., & Gaul, U. (2004). Transcriptional control in the segmentation gene network of Drosophila. PLoS biology, 2(9), E271. https://doi.org/10.1371/journal.pbio.0020271
  1. "Gap gene - Biology-Online Dictionary". www.biology-online.org. Retrieved 2017-03-03.
  1. In the original webpage: “The expression of gap genes result in the formation of gaps in the normal pattern of structure in the embryo.”
  2. Page cannot be found anymore.
  3. Primary resource: Carroll S. B. (1990). Zebra patterns in fly embryos: activation of stripes or repression of interstripes?. Cell, 60(1), 9–16. https://doi.org/10.1016/0092-8674(90)90711-m
  1. "Pair-rule gene - Biology-Online Dictionary". www.biology-online.org. Retrieved 2017-03-03.
  1. In the original webpage: “Expression of pair-rule genes subdivides the embryo into a series of stripes and sets the boundaries of the parasegments.”
  2. Secondary/tertiary resources
  3. Primary resource: Hiromi, Y., & Gehring, W. J. (1987). Regulation and function of the Drosophila segmentation gene fushi tarazu. Cell, 50(6), 963–974. https://doi.org/10.1016/0092-8674(87)90523-x
  1. "Segment polarity gene - Biology-Online Dictionary". www.biology-online.org. Retrieved 2017-03-03.
  1. In the original webpage: “Segment polarity genes define the anterior and posterior polarities within each embryonic parasegment.”
  2. Primary resource:
    1. (5) Schroeder, M. D., Pearce, M., Fak, J., Fan, H., Unnerstall, U., Emberly, E., Rajewsky, N., Siggia, E. D., & Gaul, U. (2004). Transcriptional control in the segmentation gene network of Drosophila. PLoS biology, 2(9), E271. https://doi.org/10.1371/journal.pbio.0020271
    2. Baker N. E. (1987). Molecular cloning of sequences from wingless, a segment polarity gene in Drosophila: the spatial distribution of a transcript in embryos. The EMBO journal, 6(6), 1765–1773. https://doi.org/10.1002/j.1460-2075.1987.tb02429.x (7)

Additional resources:

  1. Bejsovec, A., & Wieschaus, E. (1993). Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos. Development (Cambridge, England), 119(2), 501–517. https://doi.org/10.1242/dev.119.2.501
  2. Baker N. E. (1987). Molecular cloning of sequences from wingless, a segment polarity gene in Drosophila: the spatial distribution of a transcript in embryos. The EMBO journal, 6(6), 1765–1773. https://doi.org/10.1002/j.1460-2075.1987.tb02429.x
  3. Nüsslein-Volhard, C., & Wieschaus, E. (1980). Mutations affecting segment number and polarity in Drosophila. Nature, 287(5785), 795–801. https://doi.org/10.1038/287795a0
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