Molecular Biology

Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status

1. Ilhame Diboun
2. Sachin Wani
3. Stuart H Ralston
4. Omar ME Albagha

• Curated by eLife

  Evaluation Summary:

  Paget disease of bone (PDB) results in focal areas of disorganized bone, leading to bone deformities and fragility. There is substantial interest in finding circulating biomarkers that might be of use for possible diagnostic applications and towards this end, these authors identified novel DNA methylation patterns in peripheral blood mononuclear cells that are able to differentiate PDB cases from controls with a high level of accuracy. This prediction model has functional relevance as these candidate methylation sites and regions are associated with osteological and immunologic processes and in the longer term, has future clinical potential.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Targeting circPTPN12/miR-21-5p/ΔNp63α pathway as a therapeutic strategy for human endometrial fibrosis

1. Minmin Song
2. Guangfeng Zhao
3. Haixiang Sun
4. Simin Yao
5. Zhenhua Zhou
6. Peipei Jiang
7. Qianwen Wu
8. Hui Zhu
9. Huiyan Wang
10. Chenyan Dai
11. Jingmei Wang
12. Ruotian Li
13. Yun Cao
14. Haining lv
15. Dan Liu
16. Jianwu Dai
17. Yan Zhou
18. Yali Hu

• Curated by eLife

  Evaluation Summary:

  The study by Song and colleagues explores the role of circRNAs in fibrosis of the endometrium. The paper is of interest for scientists working in the field of endometrial fibrosis and most likely can have implications for other endometrial disorders characterised by fibrotic tissues. The study unravel the molecular mechanism underlying the disease and the thorough experimental part fully support the author's claim.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

RSC primes the quiescent genome for hypertranscription upon cell-cycle re-entry

1. Christine E Cucinotta
2. Rachel H Dell
3. Keean CA Braceros
4. Toshio Tsukiyama

• Curated by eLife

  Evaluation Summary:

  Cucinotta et al. describe mechanisms that support an intense burst of transcription from many genes within minutes of nutrient repletion as Saccharomyces cerevisiae cells emerge from quiescence. They focus primarily on the role of the nucleosome remodeler RSC in managing chromatin architecture over promoters during quiescence and as cells re-enter the cell cycle using a broad range of genome-wide measurements that strongly support the conclusions. This important process of cell cycle re-entry from quiescence is understudied but impacts areas as diverse as development and carcinogenesis in multicellular organisms to long-term survival and adaptation of microorganisms to environmental cues, so the results will be of interest to a broad audience.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

The trypanosome Variant Surface Glycoprotein mRNA is stabilized by an essential unconventional RNA-binding protein

1. Larissa Melo do Nascimento
2. Franziska Egler
3. Katharina Arnold
4. Nina Papavisiliou
5. Christine Clayton
6. Esteban Erben

Reviewed by Review Commons

Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ

1. Yang Zhang
2. Gerd Bobe
3. Cristobal L Miranda
4. Malcolm B Lowry
5. Victor L Hsu
6. Christiane V Lohr
7. Carmen P Wong
8. Donald B Jump
9. Matthew M Robinson
10. Thomas J Sharpton
11. Claudia S Maier
12. Jan F Stevens
13. Adrian F Gombart

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive study of the effect of xanthohumol and TXN, a xanthohumol derivative, on different pathologies related to the metabolic syndrome. It clearly shows the therapeutic potential of these substances, which has a high translational potential since currently, there are is a lack of effective therapies.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia

1. Jimmy Lee
2. Tom Hughes
3. Mei-Ho Lee
4. Hume Field
5. Jeffrine Japning Rovie-Ryan
6. Frankie Thomas Sitam
7. Symphorosa Sipangkui
8. Senthilvel K. S. S. Nathan
9. Diana Ramirez
10. Subbiah Vijay Kumar
11. Helen Lasimbang
12. Jonathan H. Epstein
13. Peter Daszak

Reviewed by ScreenIT, NCRC

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

1. Matthew T Parker
2. Katarzyna Knop
3. Vasiliki Zacharaki
4. Anna V Sherwood
5. Daniel Tomé
6. Xuhong Yu
7. Pascal GP Martin
8. Jim Beynon
9. Scott D Michaels
10. Geoffrey J Barton
11. Gordon G Simpson

• Curated by eLife

  Evaluation Summary:

  In this study, the authors examined the function of the RNA-binding protein FPA through analyzing its protein interactome and its global impact on gene expression using a combined approach of Nanopore DRS, Helicos DRS, and short-read Illumina RNA-Seq. The combined datasets and new computational approaches developed by the authors permitted them to identify the predominant role of FPA in promoting poly(A) site choice. The authors further revealed that FPA mediates widespread premature cleavage and polyadenylation of transcripts of NLR genes, important plant immune regulators. Overall, this study suggests that control of transcription termination processes mediated by FPA provides an additional layer of the regulatory dynamics of NLRs in plant immune responses.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail

1. Brandon R Lowe
2. Rajesh K Yadav
3. Ryan A Henry
4. Patrick Schreiner
5. Atsushi Matsuda
6. Alfonso G Fernandez
7. David Finkelstein
8. Margaret Campbell
9. Satish Kallappagoudar
10. Carolyn M Jablonowski
11. Andrew J Andrews
12. Yasushi Hiraoka
13. Janet F Partridge

Reviewed by eLife

PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis

1. Heesun Kim
2. Yue-He Ding
3. Shan Lu
4. Mei-Qing Zuo
5. Darryl Conte
6. Meng-Qiu Dong
7. Craig C. Mello

• Curated by eLife

  Summary: In this paper you describe experiments showing that PIE-1 is sumoylated at K68, and that K68 sumoylation plays a role in PIE-1 interaction with HDA-1 and its sumoylation, which leads to its activation. The reviewers found the sumoylation dependence of PIE-1 function in piRNA silencing to be of interest, but raised major issues that need to be addressed. In particular, more mechanistic insights into how sumoylation of PIE-1 at K68 enhances HDA-1 sumoylation and regulation are required.

  This is a co-submission with the manuscript https://www.biorxiv.org/content/10.1101/2020.08.17.254466v2

Reviewed by eLife

HDAC1 SUMOylation promotes Argonaute-directed transcriptional silencing in C. elegans

1. Heesun Kim
2. Yue-He Ding
3. Gangming Zhang
4. Yong-Hong Yan
5. Darryl Conte
6. Meng-Qiu Dong
7. Craig C Mello

• Curated by eLife

  Summary: In this paper, your studies showed that sumoylation of HDA-1, a type 1 HDAC, at two C-terminal Lys residues plays a role in establishing transcriptional silencing of piRNA-regulated genes in C. elegans through enhanced NuRD complex interaction and histone H3 deacetylation. The reviewers all found the link between HDA-1 sumoylation and silencing to be interesting, but raised a number of issues that need to be addressed.

  This is a co-submission with the manuscript https://www.biorxiv.org/content/10.1101/2020.08.17.254466v2

Reviewed by eLife