Everyone knows the old saying that “when life gives you lemons, make lemonade”, but what are you supposed to do when life gives you a genome full of retroviral ncRNAs? Nature seems to think it should evolve elaborate regulatory elements for your complex development.
Two-thirds of the 10,000 long intergenic noncoding RNAs (lincRNA) found so far contain transposable elements (TEs), which create a large pool for species-specific diversity. One limitation to the study of TE lincRNA is that their repetitive nature has meant that TE lincRNAs are studied as functional families and not individual members. Now a team from Stanford build on their past screen human pluripotency-associated transcripts (HPATs) to show that a little individuality can unlock the secrets of human embryonic stem cell pluripotency.
Here’s what they found:
- HPAT1-HPAT23 code for TE derived lincRNA.
- Singe-cell analysis showed that HPAT2, HPAT3, and HPAT5 regulate pluripotency genes and are expressed in the inner cell mass (ICM).
- siRNA knockdown showed that they modulate human embryonic stem cell fate during preimplantation.
- The expression of these lincRNAs isn’t just a consequence of open chromatin during transition from one cell fate to another.
- ChIP-seq revealed that HPAT2, HPAT3, and HPAT5 loci are bound by the pluripotency factor NANOG and are activated in a methylation dependent manner.
Next, given that it had the most pronounced effects and some interestingly unique sequence, the team decided to hone in on the role of HPAT5 in human embryonic stem cells:
- A protein microarray revealed that HPAT5 is bound by microRNA processing machinery.
- A luciferase reporter assay showed that retroviral sequence in HPAT5 has gained a single base pair to create a miRNA response element targeted by the let-7 microRNA family, which modulates pluripotency.
- By using CRISPR/Cas9 to KO HPAT5, they created stem cells that had increased let-7 expression and a lower iPSC reprogramming efficiency. Overexpression of exogenous let-7 in the HPAT5 KO line triggered differentiation.
- Further knockdown and overexpression studies revealed that let-7 miRNA expression is inversely associated with HPAT5 expression.
Co-lead author Jens Durruthy-Durruthy shares, “Previously retroviral elements were considered to be a class that all functioned in basically the same way. Now we’re learning that they function as individual elements with very specific and important roles in our cells. It’s fascinating to imagine how, during the course of evolution, primates began to recycle these viral leftovers into something that’s beneficial and necessary to our development.”
Co-lead and co-senior author Vittorio Sebastiano concludes, “We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit. In this manner, they may even have contributed species-specific characteristics and fundamental cell processes, even in humans.”
Learn more about the pluripotent powers of retroviral lincRNA over at Nature Genetics, November 2015.