DNA G-Quadruplex-Binding Proteins: An Updated Overview

Round 1

Reviewer 1 Report

G-quadruplex (G4) structures, which are formed at specific G-rich regions in the genome DNA and RNA, are thought to be regulated by DNA and RNA G4 binding proteins. Especially, DNA G4 is thought to related with human disease including cancer and have biologic functions, such as transcriptional regulation, telomere elongation, replication, chromatin remodeling and histone modification. Recently, new methods to identify G4 binding proteins have been developed. As results, a lot of DNA and RNA G4 binding proteins and their functions have been reported. This paper is focused on DNA G4 binding proteins and their functions. Therefore, this review paper is very important to understand their functions and will contribute to develop G4 binding molecules for approaching human diseases. However, further papers are needed to prove the authors' conclusions.

 

Telomere repeat binding factor 2 (TRF2) is one of the telomere and G4 binding protein (J. Am. Chem. Soc. 2012, 134, 11974-11976). Moreover, promoter binding by TRF2 mediates PCGF3 promoter activity via DNA G4 (Biochemistry 2018, 57, 2317-2324). The author should add the information to Table 1 and section 3.3.

 

Cold-inducible RNA-binding protein (CIRBP), which contains RGG domain, binds to DNA G4 (J. Am. Chem. Soc. 2018, 140, 17945-17955). The author should add the information to the section 4.

 

Translocated in liposarcoma/Fused in sarcoma (TLS/FUS), which contains RGG domain, binds to DNA and RNA G4 in telomere and promote histone modification to heterochromatin (Chem. Biol. 2013, 20, 341-350). The author should add the information to Table 1 and section 3.4.

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The Author has submitted an interesting overview of the functional aspects and interactions of G4 binding proteins (G4BPs). She writes about the role of G4BPs in regulation of G4 formation, structural properties of G4BPs and binding modes to G4s. The review is well-written but there are some issues/comments to consider before publication:

Title: In my opinion the title doesn't reflect what paper is about. Even the author uses quotation marks when connecting G4BPs with phrase cellular interactome (see lines 94 to 95: "...of the functional aspects and interactions of G4BPs, what can 94 be referred to as “the cellular interactome” of DNA G4s")

Line 41: Figure 1B is unnecessary and should be removed. The sequence of G4 motif is already described in the text.

Line 44: Figure 1C doesn't show different number of stacking G-tetrads even though this is implied in text ("...and the number of stacking G-tetrads (Figure 1C))

Line 49: This sentence should be rewritten as follows: However, G4 stability and folding kinetics remain a topic of research.

Figure 1: The drawing of intramolecular parallel G4 is wrong. This is the drawing of intramolecular antiparallel (basket) G4.

Line 59: 700000-375000 ∼ 350000 and not 450000

Line 76: The author should elaborate a little bit on "long-range mechanisms".

Line 120: This sentence should be rewritten as follows: To overcome these limitations, a co-binding-mediated protein profiling (CMPP) approach has been recently developed to identify G4BPs in living cells (27).

Line 123: Please consider revising the part of the sentence that talks about "bringing the probes into close proximity of the G4BPs and enables labeling by subsequent photocrosslinking".

Line 128: Use "Another" instead of "An independent".

Line 139: Use "one shouldn't overlook" instead of "it can not be discarded"

Lines 181-184: Two different mechanisms of POT-G4 binding are cited. I would love to read author's opinion on which one is more likely to be the correct one.

Line 198: Space is missing

Line 253: Space is missing

Line 253: delete first "nuclease"

Line 261: Space is missing

Figure 4B: The third drawing that shows groove-binding should be changed because it looks protein is binding between planar G-tetrads.

Line 296: Space is missing

Line 303-304: Author is referring to "several investigations" but only cites one.

Line 323: "Sparse" should be used instead of "insufficient"

Lines 337-356: Founding, Data Availability Statement, Acknowledgements and Conflicts of Interest are missing.

General comment:

At least two review papers that talk about G4BPs have already been published in year 2022 (https://doi.org/10.1007/s12551-022-00952-8 and https://doi.org/10.3390/biom12050648). Only one review is cited in this manuscript (72) and the other one is not. This should be corrected. Also, the author of submitted manuscript clearly states that it has been prepared "at a level accessible to readers who are non-specialists in the topic themselves". I would expect this description to be followed by a redirection to other more detailed reviews. For example: "Readers that are interested in more detailed review should also read an excellent paper by Vanessa Meier‑Stephenson".

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The author has adequately addressed all my comments.