New Worlds: New animal ‘molecular fingerprint’ emerges from gene regulation survey

There are nearly eight million different species of animals around the globe that show striking diversity.

By JUDY SIEGEL-ITZKOVICH
A scientist looks through a microscope (photo credit: INGIMAGE)
A scientist looks through a microscope
(photo credit: INGIMAGE)
An international team of biologists has identified the molecular signature of the animal kingdom, providing genetic evidence for an animal classification that has been used for nearly 300 years. Their research, just published in the prestigious journal Nature, offers a historic dataset for the field, serving developmental biologists, evolutionary biologists and computational biologists.
The study was led by biology Prof. Itai Yanai of the Technion-Israel Institute of Technology, in cooperation with research teams in Australia, Germany, the US and Israel. The research team investigated a diverse set of animal species, applying a powerful technique called CEL-Seq, developed in 2012 by Dr. Tamar Hashimshony in the Yanai lab. CEL-Seq makes it possible to monitor the activity of all genes in individual cells, and the team used it to analyze gene regulation in 70 embryos in each of 10 species.
The researchers found a striking pattern of universality across the species. Between phases of similar genes turned ‘on’ at the beginning and the end of development, a mid-developmental transition was discovered.
This new regulatory pattern explains how the differences among animals develop and evolve, which allows biology to now have molecular means to define the specific properties of groups of species.
Their work further defines a category of animal life that has been underdefined since 1735 when Swedish botanist Carl Linnaeus, recognized as the father of the biological classification of organisms, proposed a twoname classification system for the world’s plants. He also classified animals into “families” based on similarities and differences in body “plans.” The work offers new information on how, at the molecular and genetic levels, animals of different body designs – whether they have a true spinal column (mammals) or just a nerve cord (chordates) – have evolved to be different and why.
There are nearly eight million different species of animals around the globe that show striking diversity.
For example, animals span five orders of magnitude of adult body sizes. Yanai’s team launched this research by asking what is common to all animals. To tackle this question, they chose 10 of the most different animals one could choose – a fish, worm, fly, water bear, sponge and five others, each of a different phylum (a term coined by German naturalist Ernst Haeckel in the 19th century to describe a group of animals with the same body plan). About 35 phyla are typically recognized, however it remains controversial with contention over whether this is a meaningful classification and, if so, what attributes are the same, or different across all animals.
“We selected species representing 10 different animal phyla,” said Yanai. “For each phyla, we determined the gene expression profile of all genes from the development of the fertilized egg to the free-living larvae and found a surprising pattern of gene expression conservation in all species occurring at a pivotal, transitional period in development.”
By studying the molecular programs of development in 10 very different animals, the researchers found that all of the animals they studied express two distinct “modules” (a set of genes – similar across the organisms – that are turned “on”) of genetic expression.
During the transition between the modules, mechanisms of cell signaling and regulation occur.
With this new information, the researchers proposed a definition for phylum as “a set of species sharing the same signals and transcription factor networks during the mid-developmental transition.” In other words, they clarified the definition by suggesting that those organisms sharing a phylum, formerly by virtue of body design alone, also share a unique and similar genetic and molecular transition that other species do not.
To demonstrate their proposal, the researchers developed an “hourglass model” that captures gene expression differences between species. The inverse hourglass model shows the origin of phyla compared with the hourglass model that demonstrates “within phylum evolution.”
Embryonic development is called the “phylotypic” stage. This is when the embryo begins to assume recognizable features typical of vertebrates. The phylotypic stage represents a general layout on which specialized features – such as the turtle’s shell, the pig’s snout, or your large brain – can be mounted later in development.
The researchers proposed that during the transition period, properties specific to each phylum are genetically encoded. Their emerging dataset, they said, will be useful in studying the hallmarks of animal body plan formation from the embryonic stage.
As with many scientific discoveries, the researchers suggest that their work “raises more questions than it answers.” For example, “what molecular pathways underlie phyletic transition in each phylum? Why are the phyletic-transition mechanisms so relatively susceptible to change? Is the coupling of the conserved modules universal to all multicellular life?” “The transition we identified may be a hallmark of development only in animals,” the researchers concluded.
“Future work may show that this is a general characteristic of development in all multicellular organisms."