Ancient 'genomic parasites' spurred evolution of pregnancy in mammals

Ancient 'genomic parasites' spurred evolution of pregnancy in mammals
Number of genes that gained or lost expression in the uterus during the evolution of pregnancy at three major points in mammalian evolution. Credit: Vincent Lynch, Cell Reports

An international team of scientists has identified large-scale genetic changes that marked the evolution of pregnancy in mammals.

They found thousands of genes that evolved to be expressed in the uterus in early mammals, including many that are important for maternal-fetal communication and suppression of the immune system. Surprisingly, these genes appear to have been recruited and repurposed from other tissue types by transposons - ancient mobile genetic elements sometimes thought of as genomic parasites.

The study, published online in Cell Reports on Jan. 29, sheds light on how organisms evolve new morphological structures and functions.

"For the first time, we have a good understanding of how something completely novel evolves in nature, of how this new way of reproducing came to be," said study author Vincent Lynch, PhD, assistant professor of human genetics at the University of Chicago. "Most remarkably, we found the that likely underlie the evolution of pregnancy are linked to domesticated transposable elements that invaded the genome in early mammals. So I guess we owe the evolution of pregnancy to what are effectively genomic parasites."

To study genetic changes during the evolution of pregnancy in mammals, Lynch and his colleagues used high-throughput sequencing to catalog genes expressed in the uterus of several types of living animals - placental mammals (a human, monkey, mouse, dog, cow, pig, horse and armadillo), a marsupial (opossum), an egg-laying mammal (platypus), a bird, a reptile and a frog. Then they used computational and evolutionary methods to reconstruct which genes were expressed in ancestral mammals.

The researchers found that as the first mammals evolved - and resources for fetal development began to come more from the mother and less from a yolk - hundreds of genes that are important for cellular signaling, metabolism and uterine development started to be expressed in the uterus. As the eggshell was lost and live-birth evolved in the common ancestor to marsupials and placental mammals, more than 1,000 genes were turned on, many of which were strongly linked to the establishment of maternal-fetal communication. As prolonged pregnancy evolved in , hundreds of genes began to be expressed that greatly strengthened and elaborated maternal-fetal communication, as well as locally suppressing the maternal immune system in the uterus - thus protecting the developing fetus.

The team also identified hundreds of genes that were turned off as these lineages evolved, many of which had been involved in egg shell formation.

"We found lots of genes important for maintaining hormone signaling and mediating maternal-fetal communication, which are essential for pregnancy, evolved to be expressed in the uterus in early ," Lynch said. "But immune suppression genes stand out. The fetus is genetically distinct from the mother. If these immune genes weren't expressed in the uterus, the fetus would be recognized by the mother's immune system as foreign and attacked like any other parasite."

In addition to function, Lynch and his colleagues investigated the origin of these genes. They found most already had roles in other organ and tissue systems such as the brain, digestive and circulatory systems. But during the evolution of pregnancy, these genes were recruited to be expressed in the uterus for new purposes. They evolved regulatory elements that allowed them to be activated by progesterone, a hormone critical in reproduction.

The team found that this process was driven by ancient transposons - stretches of non-protein coding DNA that can change their position within the genome. Sometimes called "jumping genes," transposons are generally thought to be genomic parasites that serve only to replicate themselves. Many of the ancient mammalian transposons possessed progesterone binding sites that regulate this process. By randomly inserting themselves into other places in the genome, transposons appear to have passed on this activation mechanism to nearby genes.

"Genes need some way of knowing when and where to be expressed," Lynch said. "Transposable elements appear to have brought this information, allowing old genes to be expressed in a new location, the uterus, during pregnancy. Mammals very likely have a progesterone-responsive because of these ."

Lynch and his colleagues note their findings represent a novel explanation for how entirely new biological structures and functions arise. Rather than genes gradually evolving uterine expression one at a time, transposable elements coordinated large-scale, genome-wide changes that allowed numerous to be activated by the same signal - in this case, progesterone, which helped drive the evolution of pregnancy.

"It's easy to imagine how evolution can modify an existing thing, but how new things like evolve has been much harder to understand," Lynch said. "We now have a new mechanistic explanation of this process that we've never had before."


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Invasion of genomic parasites triggered modern mammalian pregnancy

More information: "Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy," Cell Reports , 2015.
Journal information: Cell Reports

Citation: Ancient 'genomic parasites' spurred evolution of pregnancy in mammals (2015, January 29) retrieved 19 August 2019 from https://phys.org/news/2015-01-ancient-genomic-parasites-spurred-evolution.html
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JVK
Jan 29, 2015
Excerpt: "We now have a new mechanistic explanation of this process that we've never had before."

There is no new mechanistic explanation of molecular mechanisms. This is a thinly disguised refutation of mutation-driven evolution. The molecular epigenetics of nutrient-dependent RNA-mediated cell type differentiation via amino acid substitutions have not changed.

Ecological variation continues to links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Feedback loops link nutrient uptake to chromatin loops via thermodynamic cycles of protein biosynthesis and degradation. The cycles lead to ecological adaptations via nutrient-dependent changes in the microRNA/messenger RNA balance.

The changes link RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species, including the cell types of the mammalian placenta.

Jan 29, 2015
The biologically uninformed continue to yell: MUTATIONS! (JVK, DEC 18, 2014)


I'll let your own words do the talking, JVK, since you have YET AGAIN introduced that term to a thread.

ROTFLMAO!

JVK
Jan 29, 2015
This is a link to the open access article. There is no mention of genomic parasites.
http://www.cell.c...901105-X

See also: Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals http://www.nature...917.html

What is a transposon? Did transposons evolve into microRNAs?

Origin and Evolution of Human microRNAs From Transposable Elements http://www.ncbi.n...1894593/

If transposable elements evolved into microRNAs, they link nutrient-dependent changes in the microRNA/messenger RNA balance and to....

A universal trend of amino acid gain and loss in protein evolution http://www.nature...306.html

I linked amino acid substitutions to cell type differentiation in
Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Jan 30, 2015
This is a link to the open access article. There is no mention of genomic parasites.
http://www.cell.c...901105-X


JVK, the paper is FULL of references to transposons. These started out as 'genetic parasites', but while their jumping around and replication within the genome were typically detrimental they occasionally produced beneficial results so our genomes evolved tolerate them and then manage them.

Study author Vincent Lynch even calls them 'genomic parasites': "Most remarkably, we found the genetic changes that likely underlie the evolution of pregnancy are linked to domesticated transposable elements that invaded the genome in early mammals. So I guess we owe the evolution of pregnancy to what are effectively genomic parasites."

JVK
Jan 30, 2015
MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates http://dx.doi.org....1001214

Whether you claim they are transposons, trans-regulators, or genomic parasites, microRNAs drive tissue-specific changes in cell type differentiation via RNA-mediated amino acid substitutions.

Nutrient-dependent changes in the microRNA/messenger RNA balance are the driving force underlying developmental remodeling across hundreds of genes. Referring to microRNAs as genomic parasites is a way to discuss biologically-based cause and effect with science idiots, like the journalist who wrote this article.

See the article from The Scientist, for comparison: http://www.the-sc...egnancy/

JVK
Jan 31, 2015
Clarificaton: The microRNAs control what they call "genomic parasites." We've been through all of this before. See:

http://phys.org/n...nes.html Imperfect system is all that protects you from genetic parasites out to destroy your genes

"The pathway's main weapons against transposons are PIWI proteins and small RNA molecules called piRNAs."

The nutrient-dependent pheromone-controlled microRNA/messenger RNA balance enables
"..."genetic variation and diversity, which is important for a species to reproduce and..." to ecologically adapt.

JVK
Jan 31, 2015
...transposons. These started out as 'genetic parasites' ...


Additional clarification. Only the biologically uninformed will take the ridiculous representation of "genomic parasites" and run it into the ground before realizing the misrepresentation is based on the pseudoscientific nonsense touted by evolutionary theorists who are now charged to defend themselves against claims of "rapid evolution." Those claims are supported by experimental evidence.

The experimental evidence links ecological variation to RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types of all individuals in all species via conserved molecular mechanisms. The detailed mechanisms link the epigenetic landscape to the physical landscape of DNA in organized genomes via the biophysically constrained chemistry of nutrient-dependent protein folding and fixation of amino acid substitutions via the species-specific physiology of reproduction.

JVK
Jan 31, 2015
Links to this article are posted on two yahoo groups:

human-ethology@yahoogroups.com (I was banned by Jay R. Feierman)
Evolutionary-Psychology (I was banned by Robert Karl Stonjek)

I welcome comments from participants in those groups because science idiots like Andrew Jones (see his review of my 2013 published work) helped to get me banned.
http://www.socioa...ew/24367

Nearly every participant in those two groups -- and others in other groups -- have been critical of my model, which links nutrient-dependent amino acid substitutions to the pheromone-controlled physiology of reproduction in species from microbes to man via conserved molecular mechanisms. http://www.ncbi.n...24693353

The mechanisms were detailed in our 1996 Hormones and Behavior review: http://www.hawaii...ion.html

We now have the concept of "genomic parasites" for comparison.

Jan 31, 2015
Whether you claim they are transposons, trans-regulators, or genomic parasites, microRNAs drive tissue-specific changes


JVK, you confused DNA and RNA yet again.

The ARTICLE YOU CITED is about transposable elements (also known as TEs or transposons). Tranposons are DNA. In contrast, MicroRNAs are RNA.

Here's a definition from Wikipedia.
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.


Oh, that's right, you claim that "serious scientists do not use definitions" - no wonder you confused DNA and RNA again!

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