DNA Protection Inches from Cytoplasm to Nucleus

In germline cells, PIWI proteins silence jumping gene mRNA post-transcriptionally by cutting them into piRNAs. These piRNAs bind to a nuclear PIWI protein to repress jumping genes at the transcriptional level. [Ramesh Pillai/EMBL]

Inching along, a DNA-preserving mechanism can ultimately defeat the transposon, a danger that jumps. This mechanism is part of a larger process through which tiny pieces of RNA protect reproductive cells from jumping genes that could, if unrestrained, so alter DNA as to cause sterility.

These tiny pieces of RNA are called PIWI-interacting RNAs (piRNAs), a class of 24- to 30-nt RNAs that are exclusively expressed in animal gonads. How piRNAs are made has been unclear, but recent work by EMBL Grenoble and CEA Grenoble scientists indicates that they arise from an “inchworming” process, one in which target messenger RNA is nibbled into fragments, effectively silencing a jumping gene post-transcriptionally.

But that’s not all: Once the messenger RNA fragments are nibbled free, they bind with PIWI proteins and move to the nucleus, interfering with jumping genes directly, at the transcriptional level.

These findings appeared July 9 in the journal Cell Reports, in an article entitled, “PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis.” The article describes how the EMBL Grenoble and CEA Grenoble scientists tracked the action of piRNA by inserting an artificial jumping gene into a fruit fly germ cell. Because the artificial reporters were prepared with unique sequences, the scientists were able to follow piRNA biogenesis. In doing so, they discovered two distinct mechanisms for recruiting transcripts into the primary processing pathway.

“First, reporter RNA carrying a piRNA-trigger sequence (PTS) from the 5′ end of a fly cluster transcript get processed in a directional manner into thousands of overlapping primary piRNAs,” the scientists wrote in Cell Reports. “Second, cytosolic PIWI slicing of a target not only generates secondary piRNAs but also results in further processing of the transcript into non-overlapping primary piRNAs. These piRNAs are loaded into a nuclear PIWI, thus establishing a link between cytosolic silencing and transcriptional repression.”

Essentially, piRNA bound to a jumping gene messenger RNA in the cell’s cytoplasm and to the PIWI protein, which then cut the first section from the jumping gene mRNA to silence it. But this was only the start of the process. The PIWI protein and piRNA then continued to work their way along the jumping gene, cutting off 30 letters of code at a time and converting these into new piRNAs. The new piRNAs were then loaded onto a PIWI protein that was able to travel to the cell nucleus, where the piRNAs could recognize the jumping gene within the DNA, enabling the PIWI protein to silence it.

The scientists are now investigating whether the piRNAs follow the same “inchworm” process within mammalian cells, to take them a step closer to understanding the process within humans.

“We expected simply to see the jumping gene being silenced in the cytoplasm, so were really surprised to see it get converted into new piRNAs that were specifically loaded onto the PIWI protein that silences transposons in the nucleus,” explained Ramesh Pillai, from EMBL Grenoble. “Creating copies clearly increases the number of piRNAs that are able to recognize that particular jumping gene, as they retain the ‘memory’ of the original. This means that once the PIWI protein from the nucleus is loaded with the new piRNAs, it’s able to target the right gene in the DNA and silence it more efficiently.”