Reviewer #1 (Public Review):
In Drosophila germline, most piRNA loci use a non-canonical mechanism to transcribe piRNA precursors at the presence of H3K9me3, which depends on an HP1a paralog called Rhino/HP1d that specifically binds piRNA loci. How does Rhino find the right loci to bind? The current model in the field posits that maternally deposited piRNAs provide a specificity cue for Rhino. Now, Baumgartner et al. from Brennecke Group described a novel factor, the ZAD zinc-finger protein CG2678/Kipferl, that appears to provide another key specificity input to a subset of Rhino's chromatin binding, specifically in differentiated female germline (but not in males or stem/progenitor cell types in the female germline). Using genetics, genomics, genome editing, microscopy and biochemical approaches, Baumgartner et al. propose that Kipferl binds a G-rich DNA motif and, at the presence of local H3K9me3, recruits and/or stabilizes the binding of Rhino to these loci and then convert them from transcriptionally inert heterochromatin to piRNA-producing loci. Overall, the text is well written, the figure is clear, and the data is of high quality. With some additional experiments and text edits, this work represents a significant contribution to the field and should attract readers working on piRNA, transposon, satellite DNA, zinc-finger proteins, HP1 and heterochromatin.
Specific concerns
1. The genetic hierarchy between Kipferl and Rhino requires further clarification. Authors seem to propose a simple model where Kipferl acts genetically upstream of Rhino. This simple hierarchy is at odds with several observations. First, the center of Kipferl binding generally has less Kipferl binding without Rhino (Fig 5D). In some cases, Kipferl binding is completely gone without Rhino (Fig 7E middle, bottom). The text describes the loss of Kipferl spreading without Rhino but should also mention this reduction/loss in Kipferl binding. The effect of rhino-/- on Kipferl's chromatin binding should be shown along with wildtype level of Kipferl enrichment in Fig 5C for proper comparison. How should readers understand the effect of Rhino on Kipferl? What is the prominent Kipferl domain in rhino-/- in Fig 5B? Second, the broad binding of Kipferl is gone in rhino-/-, does it mean Kipferl requires Rhino to spread? Or, could Rhino (that is recruited by maternally deposited Piwi/piRNA) recruit Kipferl to neighboring sites, which look like a spreading phenomenon? Most importantly, the argument of Kipferl recruiting Rhino should be directly demonstrated by a sufficiency test in addition to the presented evidence of necessity. Could authors tether Kipferl in H3K9me3-decorated regions to see if Rhino is recruited and vice versa? Observations like 42AB in Fig 5E make one wonder if Rhino also recruits Kipferl, so their relationship is not simply Kipferl recruiting or acting upstream of Rhino, as described throughout this manuscript. Clarifying the relationship between Kipferl and Rhino is essential as it is a central claim made.
2. DNA binding of Kipferl remains putative. Since the 4th zinc-finger is shown to impact Kipferl localization via interaction with Rhino, it remains formally possible that the first three zinc-fingers control Kipferl localization via protein-protein interaction rather than direct DNA binding. Unless direct biochemical evidence of Kipferl binding DNA is available, the DNA binding of Kipferl should be toned down and described as putative and requires further investigation in text.
3. The relative contribution of maternally deposited piRNAs versus Kipferl in recruiting Rhino is unaddressed. Prior work from multiple groups including Mohn et al. 2014 Cell from the same group of this manuscript suggested a role of maternally deposited piRNAs in determining a subset of H3K9me3 domains as Rhino binding sites. Is Kipferl or maternally deposited piRNA a better predictor of Rhino binding? This manuscript proposes that Kipferl binds a simple G-rich motif and at the presence of H3K9me3 recruits Rhino binding. The readers are left wondering where maternally deposited piRNAs fit in the model of Rhino recruitment, which should be tested or discussed in text, as maternally deposited piRNA is seen as the key determinant of Rhino binding before this work.



