The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors

Round 1

Reviewer 1 Report

In the manuscript “The importance of networking: plant Polycomb repressive complex 2 and its interactors” the authors summarized the recently identified PRC2 partners and the underlying mechanisms of the protein interactions. The paper is quite comprehensive and could be useful for plant epigenetic studies. However, I still have some concerns about the manuscript:

1. The understanding of plant PcG and H3K27me3 repression is greatly improved during recent years, not only the PRC2 partners but also the unique mechanism compared to the animal counterparts. So, in order to make the manuscript more attractive and significant, the authors may put the breakthroughs like the role of H3.10 in H3K27me3 transgenerational memory and the identification of new H3K27me3 readers EBS and SHL in the beginning introduction part. Although they are not direct PRC2 partners, they could make the review more comprehensive and incisive.

2. Several ncRNAs perform as PRC2 interactors, like COLDAIR and COLDWRAP in PRC2 recruitment and APOLO in PcG-mediated gene repression. This could also be included in the manuscript.

3. Please provide reference to demonstrate JAZs and NINJA are DNA binding proteins.

4. In line 457-458, Trx proteins are not only for H3K4me3, but also H3K36me3, histone acetylation as well as chromatin remodeling.

5. Please rephrase line 48 and 626, them here is unsuitable.

Author Response

Response to Reviewer 1 comments

In the manuscript “The importance of networking: plant Polycomb repressive complex 2 and its interactors” the authors summarized the recently identified PRC2 partners and the underlying mechanisms of the protein interactions. The paper is quite comprehensive and could be useful for plant epigenetic studies. However, I still have some concerns about the manuscript:

We would like to thank Reviewer 1 for her/his positive comments about our review.

1. The understanding of plant PcG and H3K27me3 repression is greatly improved during recent years, not only the PRC2 partners but also the unique mechanism compared to the animal counterparts. So, in order to make the manuscript more attractive and significant, the authors may put the breakthroughs like the role of H3.10 in H3K27me3 transgenerational memory and the identification of new H3K27me3 readers EBS and SHL in the beginning introduction part. Although they are not direct PRC2 partners, they could make the review more comprehensive and incisive.

We agree with the reviewer that the suggested breakthrough will add value to our review and have added them in the introduction part.

2. Several ncRNAs perform as PRC2 interactors, like COLDAIR and COLDWRAP in PRC2 recruitment and APOLO in PcG-mediated gene repression. This could also be included in the manuscript.

Thanks for this comment. We have added a new section at the end about ncRNA-PRC2 interactions titled, “PRC2 interaction with long non-coding RNAs”.

3. Please provide reference to demonstrate JAZs and NINJA are DNA binding proteins.

Thanks to the reviewer for this comment as indeed JAZ proteins and NINJA do not possess a DNA binding domain and there is no direct evidence of DNA binding activity. Nevertheless, they interact and influence many transcription factors (e.g. MYC2), playing key roles in gene repression (Fernández-Calvo et al., 2011), acting as repressors. Therefore, we have decided to change the title of the section to “PRC2 interaction with activators and repressors”. We hope that this will increase accuracy of the message of this section.

4. In line 457-458, Trx proteins are not only for H3K4me3, but also H3K36me3, histone acetylation as well as chromatin remodeling.

Thanks for this comment. It is true that Trithorax proteins have been involved with diverse molecular functions. However, specifically, ATX1 is shown to catalyse H3K4me3 activity. Therefore, we have rephrased this sentence to make it more clearer.

5. Please rephrase line 48 and 626, them here is unsuitable. 

Rephrased both lines.

Reviewer 2 Report

This review is an extremely useful collation of the now considerable amount of information on  PRC interactors.

There are a few minor details:

-Line 47 The following key reference is missing

Shu J. et al. Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. Plant Direct 2019, Jan 31;3(1)

-Line 94 Here Drosophila PRE and mammalian PRC binding sites need to be discriminated/defined. It is inaccurate to name the mammalian binding sites as PREs. It would be beneficial to add the references for one or two recent reviews on this topic.

-Line382 the placement of the 4.2 “RETINOBLASTOMA RELATED” in the  section 4  “PRC2 interaction with DNA replication components” does not seem appropriate. RBR1 has several functions, the key one is in the control of G1 to S phase progression, as mentioned in the text. However a direct control of RBR1 in replication has not been shown,  unlike in Drosophila where RB interacts with the ORC complex. In plants so far, RBR1 has only a role in  transcriptional control on replication genes. Therefore, I think it would be more appropriate to move the 4.2 “RBR1” paragraph to section 6 “Other PRC2 interactors”.

-Line 418 for 4.4 a title “DNA polymerases” instead of “EARLY IN SHORT DAYS” would be more accessible to the general reader.

Author Response

Response to Reviewer 2 comments

This review is an extremely useful collation of the now considerable amount of information on PRC interactors.

We thank reviewer 2 for her/his very positive comment.

There are a few minor details:

-Line 47 The following key reference is missing Shu J. et al. Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. Plant Direct 2019, Jan 31;3(1)

Thanks for pointing this out. We have added this reference.

-Line 94 Here Drosophila PRE and mammalian PRC binding sites need to be discriminated/defined. It is inaccurate to name the mammalian binding sites as PREs. It would be beneficial to add the references for one or two recent reviews on this topic. 

Thanks for pointing this out. We have corrected it and appropriate references have now been added.

-Line382 the placement of the 4.2 “RETINOBLASTOMA RELATED” in the section 4 “PRC2 interaction with DNA replication components” does not seem appropriate. RBR1 has several functions, the key one is in the control of G1 to S phase progression, as mentioned in the text. However a direct control of RBR1 in replication has not been shown, unlike in Drosophila where RB interacts with the ORC complex. In plants so far, RBR1 has only a role in transcriptional control on
replication genes. Therefore, I think it would be more appropriate to move the 4.2 “RBR1” paragraph to section 6 “Other PRC2 interactors”.

Following the reviewer 2’s recommendation, the RBR1 part has now been moved into the “Other PRC2 interactors” section.

-Line 418 for 4.4 a title “DNA polymerases” instead of “EARLY IN SHORT DAYS” would be more accessible to the general reader.

The title has accordingly been modified.

Reviewer 3 Report

An excellent review that gathered information about interaction of Polycomb repressive complexes of Arabidopsis with its fucntional partners including transcription factors, chromatin-related proteins, the replicational and proteasomal proteins etc. The review is well-structured and contains detailed description of protein interactions at the level of expression regulation, protein degradation, DNA replication and other aspects of cell physiology. 

Very minor comments: 

Drosophila - name of the genus, use italic. 

Remove extra spacing between paragraphs in secton 1. 

Line 615: «The Plant Cells» - use small first letters

Author Response

Response to reviewer 3 comments

An excellent review that gathered information about interaction of Polycomb repressive complexes of Arabidopsis with its fucntional partners including transcription factors, chromatin-related proteins, the replicational and proteasomal proteins etc. The review is well-structured and contains detailed
description of protein interactions at the level of expression regulation, protein degradation, DNA replication and other aspects of cell physiology.

We would like to thank review 3 for her/his positive comments.

Very minor comments:
Drosophila - name of the genus, use italic.

Corrected

Remove extra spacing between paragraphs in secton 1.

corrected

Line 615: «The Plant Cells» - use small first letters

Corrected