So-called junk DNA plays critical role in mammalian development
Knocking out transposon promoter leads to pup death in mice; similar
promoters found in many mammals

Date:
October 18, 2021
Source:
University of California - Berkeley
Summary:
Despite the prevalent view that some 98% of our genome is junk DNA,
new research shows that one piece of junk DNA -- the promoter
of a virus- based transposon -- plays a critical role in cell
proliferation and timing of embryo implantation in mice. The group
found virus-based promoters linked to genes involved in development
in other mammals, including humans, suggesting that transposons
have been broadly repurposed for important regulatory roles.



FULL STORY ========================================================================== Nearly half of our DNA has been written off as junk, the discards of
evolution: sidelined or broken genes, viruses that got stuck in our
genome and were dismembered or silenced, none of it relevant to the
human organism or human evolution.


==========================================================================
But research over the last decade has shown that some of this genetic
"dark matter" does have a function, primarily in regulating the
expression of host genes -- a mere 2% of our total genome -- that code for proteins. Biologists continue to debate, however, whether these regulatory sequences of DNA play essential or detrimental roles in the body or are
merely incidental, an accident that the organism can live without.

A new study led by researchers at University of California, Berkeley,
and Washington University explored the function of one component of this
junk DNA, transposons, which are selfish DNA sequences able to invade
their host genome.

The study shows that at least one family of transposons -- ancient viruses
that have invaded our genome by the millions -- plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died
before birth.

This is the first example of a piece of "junk DNA" being critical to
survival in mammals.

In mice, this transposon regulates the proliferation of cells in the
early fertilized embryo and the timing of implantation in the mother's
uterus. The researchers looked in seven other mammalian species, including humans, and also found virus-derived regulatory elements linked to cell proliferation and timing of embryo implantation, suggesting that ancient
viral DNA has been domesticated independently to play a crucial role in
early embryonic development in all mammals.

According to senior author Lin He, UC Berkeley professor of molecular and
cell biology, the findings highlight an oft-ignored driver of evolution: viruses that integrate into our genome and get repurposed as regulators
of host genes, opening up evolutionary options not available before.



==========================================================================
"The mouse and humans share 99% of their protein coding genes in their
genomes -- we are very similar with each other," He said. "So, what
constitutes the differences between mice and humans? One of the major differences is gene regulation -- mice and humans have the same genes,
but they can be regulated differently. Transposons have the capacity
to generate a lot of gene regulatory diversity and could help us to
understand species-specific differences in the world." Colleague
and co-senior author Ting Wang, the Sanford and Karen Loewentheil
Distinguished Professor of Medicine in the Department of Genetics at the Washington University School of Medicine in St. Louis, Missouri, agrees.

"The real significance of this story is it tells us how evolution works
in the most unexpected manner possible," Wang said. "Transposons were
long considered useless genetic material, but they make up such a big
portion of the mammalian genome. A lot of interesting studies illustrate
that transposons are a driving force of human genome evolution. Yet, this
is the first example that I know of where deletion of a piece of junk DNA
leads to a lethal phenotype, demonstrating that the function of specific transposons can be essential." The finding could have implications
for human infertility. According to first author Andrew Modzelewski,
a UC Berkeley postdoctoral fellow, nearly half of all miscarriages in
humans are undiagnosed or don't have a clear genetic component. Could transposons like this be involved? "If 50% of our genome is non-coding
or repetitive -- this dark matter -- it is very tempting to ask the
question whether or not human reproduction and the causes of human
infertility can be explained by junk DNA sequences," he said.



========================================================================== Embryo implantation He, the Thomas and Stacey Siebel Distinguished Chair Professor at UC Berkeley, studies the 98% or more of our genome that
does not code for proteins. For most of He's career, she has focused
on microRNAs and longer pieces of non-coding RNAs, both of which are
potent gene regulators. Five years ago, however, her team accidentally discovered a microRNA regulator for a transposon family called MERVL
(mouse endogenous retroviral elements) that was involved in cell fate determination of early mouse embryos. The unexpected abundance of
transposon transcription in mouse embryos led He's team to investigate
the developmental functions of transposons, which have taken up residence
in the genomes of nearly every organism on Earth.

In a paper appearing this week in the journal Cell, He and her team
identify the key regulatory DNA involved: a piece of a transposon --
a viral promoter - - that has been repurposed as a promoter for a mouse
gene that produces a protein involved in cell proliferation in the
developing embryo and in the timing of implantation of the embryo. A
promoter is a short DNA sequence that is needed upstream of a gene in
order for the gene to be transcribed and expressed.

Wild mice use this transposon promoter, calledMT2B2, to initiate
transcription of the gene Cdk2ap1 specifically in early embryos to
produce a short protein "isoform" that increases cell proliferation in
the fertilized embryo and speeds its implantation in the uterus. Using CRISPR-EZ, a simple and inexpensive technique that Modzelewski and He
developed several years ago, they disabled the MT2B2 promoter and found
that mice instead expressed the Cdk2ap1 gene from its default promoter
as a longer form of the protein, a long isoform, that had the opposite
effect: decreased cell proliferation and delayed implantation.

The result of this knockout was the death at birth of about half the pups.

Modzelewski said that the short form of the protein appears to make
the many embryos of the mouse implant with a regular spacing within the
uterus, preventing crowding. When the promoter is knocked out so that
the long form is present only, the embryos implant seemingly randomly,
some of them over the cervix, which blocks exit of the fully developed
fetus and sometimes kills the mother during the birthing process.

They found thatwithin a 24-hour period prior to embryo implantation,
the MT2B2 promoter ramps up expression of the Cdk2ap1 gene so much that
the short form of the protein makes up 95% of the two isoforms present
in embryos. The long isoform is normally produced later in gestation
when the default promoter upstream of the Cdk2ap1 gene becomes active.

Working with Wanqing Shao, co-first author of the study and a postdoctoral fellow in Wang's group at Washington University, the team searched
through published data on preimplantation embryos for eight mammalian
species -- human, rhesus monkey, marmoset, mouse, goat, cow, pig and
opossum -- to see whether transposons are turned on briefly before
implantation in other species. These online data came from a technique
called single cell RNA sequencing, or scRNA- seq, which records the
levels of messenger RNA in single cells, an indication of which genes
are turned on and transcribed. In all cases, they had to retrieve the
data on non-coding DNA because it is typically removed before analysis,
with the presumption that it's unimportant.

While transposons are generally specific to individual species -- humans
and mice, for example, have largely different sets -- the researchers
found that different species-specific transposon families were turned on briefly before implantation in all eight mammals, including the opossum,
the only mammal in the group that does not employ a placenta to implant
embryos in the uterus.

"What's amazing is that different species have largely different
transposons that are expressed in preimplantation embryos, but the global expression profiles of these transposons are nearly identical among all
the mammalian species," He said.

Colleague and co-senior author Davide Risso,a former UC Berkeley
postdoctoral fellow and now associate professor of statistics at the
University of Padua in Italy, developed a method for linking specific transposons to preimplantation genes so as to weed out the thousands
of copies of related transposons that exist in the genome. This method
is crucial to identifying individual transposon elements with important
gene regulatory activity.

"It's interesting to note that the data that we used were mostly based
on the previous sequencing technology, called SMART-seq, which covers
the full sequence of the RNA molecules. The current popular technique,
10x genomics technology, would not have shown us the different levels
of protein isoforms.

They're blind to them," Risso said.

Viruses are evolutionary reservoir The researchers found that in nearly
all of the eight mammalian species, both short and long Cdk2ap1 isoforms
occur, but are switched on at different times and in different proportions
that correlate with whether embryos implant early, as in mice, or late,
as in cows and pigs. Thus, at the protein level, both the short and
long isoforms appear conserved, but their expression patterns are species-specific.

"If you have a lot of the short Cdk2ap1 isoform, like mice, you implant
very early, while in species like the cow and pig, which have none to
very little of the short isoform, it's up to two weeks or longer for implantation," Modzelewski said.

Wang suspects that the promoter that generates the long form of the
protein could be the mouse's original promoter, but that a virus that integrated into the genome long ago was later adapted as a regulatory
element to produce the shorter form and the opposite effect.

"So, what happened here is a rodent-specific virus came in, and then
somehow the host decided, 'OK, I'm going to use you as my promoter to
express this shorter Cdk2ap1 isoform.' We see the redundancy that's built
into the system, where we can take advantage of whatever nature throws
at us and make it useful," he said. "And then, this new promoter happened
to be stronger than the old promoter. I think this fundamentally changed
the phenotype of rodents; maybe that's what makes them grow faster --
a gift of having a shorter pre- implantation time. So, they probably
gained some fitness benefit from this virus." "Whatever you look at
in biology, you're going to see transposons being used, simply because
there are just so many sequences," Wang added. "They essentially provide
an evolutionary reservoir for selection to act upon." Other co-authors
of the study are Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy
Tjokro and Anne Biton of UC Berkeley; Terry Speed of theWalter and
Eliza Hall Institute of Medical Research in Melbourne, Australia;Aparna
Anand of Washington University and Gabriele Sales of the University of
Padua. The work was supported primarily by the Howard Hughes Medical
Institute faculty scholar award and the National Institutes of Health.

========================================================================== Story Source: Materials provided by
University_of_California_-_Berkeley. Original written by Robert
Sanders. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Andrew J. Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi,
Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna
Anand, Terence P. Speed, Zhenyu Xuan, Ting Wang, Davide Risso,
Lin He. A mouse- specific retrotransposon drives a conserved
Cdk2ap1 isoform essential for development. Cell, 2021; DOI:
10.1016/j.cell.2021.09.021 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/10/211018140504.htm

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