Genomics

Genome-wide mapping of native co-localized G4s and R-loops in living cells

1. Ting Liu
2. Xing Shen
3. Yijia Ren
4. Hongyu Lu
5. Yu Liu
6. Chong Chen
7. Lin Yu
8. Zhihong Xue

• Curated by eLife

  eLife assessment

  This study describes a useful antibody-free method to map both G-quadruplexes and R-loops in vertebrate cells independently of the BG4 and S9.6 antibodies. It also reveals that the helicase Dhx9 can affect the self-renewal and differentiation capacities of mESCs, perhaps by regulating co-localized G4s and R-loops. The datasets provided might constitute a good starting point for future functional studies, and although the strength of the evidence that DHX9 interferes with the ability of mESCs to differentiate by regulating directly the stability of either G4s or R-loops has been improved compared to a previous version, it is still incomplete.

Reviewed by eLife

Regulatory genome annotation of 33 insect species

1. Hasiba Asma
2. Ellen Tieke
3. Kevin D Deem
4. Jabale Rahmat
5. Tiffany Dong
6. Xinbo Huang
7. Yoshinori Tomoyasu
8. Marc S Halfon

• Curated by eLife

  eLife assessment

  In the revised version of this important study, the authors present a convincing pipeline for insect genome regulatory annotation across 33 insect genomes spanning 5 orders. Despite technical limitations in the field owing to the lack of comprehensive knowledge of enhancer content in any system, the authors employ several independent downstream analyses to support the validity of their enhancer predictions for a subset of these genomes. Taken together, the revised results suggest that this prediction pipeline may have uses in identifying functional enhancers across large phylogenetic distances. Reviewers note caveats that an experimental validation is not yet available in the field to validate a large class of newly identified enhancers across such evolutionary distances, and other pipelines might be of use to compare. This work will be of interest to the computational genomics, evolutionary biology, and gene regulation fields.

Reviewed by eLife

Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling

1. Chen Weng
2. Jonathan S. Weissman
3. Vijay G. Sankaran

Reviewed by Arcadia Science

Essentiality and dynamic expression of the human tRNA pool during viral infection

1. Noa Aharon-Hefetz
2. Michal Schwartz
3. Orna Dahan
4. Noam Stern-Ginossar
5. Yitzhak Pilpel

Reviewed by Review Commons

Dynamics and Regulatory Roles of RNA m6A Methylation in Unbalanced Genomes

1. Shuai Zhang
2. Xinyu Liu
3. Ruixue Wang
4. Junhan Wang
5. Ludan Zhang
6. Lin Sun

• Curated by eLife

  eLife assessment

  This valuable study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, using aneuploid Drosophila as a model, and suggests that the dosage compensation complex and m6A act in a feedback loop. The evidence is incomplete due to technical concerns, as quantitative assessments are being made using non-quantitative methods, and the study would be improved by further functional studies. If strengthened, the study will be of interest to RNA and developmental biologists.

Reviewed by eLife

Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow

1. Sila Gerlevik
2. Nogayhan Seymen
3. Shan Hama
4. Warisha Mumtaz
5. I Richard Thompson
6. Seyed R Jalili
7. Deniz E Kaya
8. Alfredo Iacoangeli
9. Andrea Pellagatti
10. Jacqueline Boultwood
11. Giorgio Napolitani
12. Ghulam J Mufti
13. Mohammad M Karimi

• Curated by eLife

  eLife assessment

  This manuscript uses public datasets of myelodysplastic syndrome (MDS) patients to undertake a multi-omics analysis of clinical, genomic, and transcriptomic datasets. Useful findings are provided by way of interesting correlations of specific mutations with inflammation and differing clinical outcomes. The evidence is solid and interesting, and the manuscript is of substantive value to hematologists and clinical immunologists.

Reviewed by eLife

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

1. Mehul Vora
2. Jonathan Dietz
3. Zachary Wing
4. Jun Liu
5. Christopher Rongo
6. Cathy Savage-Dunn

• Curated by eLife

  eLife assessment

  This study presents valuable findings that will allow for a better understanding of the targets of SMAD and Schnurri, transcription factors that act downstream in the BMP signalling pathway. The evidence presented in this manuscript is solid, but because the claims of a SMA-3/SMA-9 complex are not experimentally supported, they should be toned down. Revising the discussion to give a broader context of BMP-driven body size control would help the readers put this work in a larger context. This work will be of broad interest to colleagues studying BMP signalling across phyla.

Reviewed by eLife

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

1. Lenore Pipes
2. Rasmus Nielsen

• Curated by eLife

  eLife assessment

  This potentially important work presents a tool for performing phylogenetic taxonomic classification of DNA sequences. In terms of methodology, the work is compelling. The authors perform a benchmark experiment against current state-of-the-art tools using real and simulated datasets to demonstrate where the novel tool stands in the context of existing methods. However, the experimentation is still incomplete. It would benefit from a more thorough exploration of existing methods as well as data sets that better represent real-world use cases.

Reviewed by eLife

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

1. Shaohua Gu
2. Yuanzhe Shao
3. Karoline Rehm
4. Laurent Bigler
5. Di Zhang
6. Ruolin He
7. Ruichen Xu
8. Jiqi Shao
9. Alexandre Jousset
10. Ville-Petri Friman
11. Xiaoying Bian
12. Zhong Wei
13. Rolf Kümmerli
14. Zhiyuan Li

• Curated by eLife

  eLife assessment

  This important study presents a novel pipeline for the large-scale genomic prediction of members of the non-ribosomal peptide group of pyoverdines based on a dataset from nearly 2000 Pseudomonas genomes. The advance presented in this study is based on convincing evidence. This study of bacterial siderophores has broad theoretical and practical implications beyond a singular subfield.

Reviewed by eLife

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

1. Yiming Xu
2. Wanqiu Wang
3. Jiefeng Huang
4. Minjie Xu
5. Binhu Wang
6. Yingsong Wu
7. Yongzhong Xie
8. Jianbo Jian

• Curated by GigaByte

  Editors Assessment:

  RAD-Seq (Restriction-site-associated DNA sequencing) is a cost-effective method for single nucleotide polymorphism (SNP) discovery and genotyping. In this study the authors performed a kinship analysis and pedigree reconstruction for two different cattle breeds (Angus and Xiangxi yellow cattle). A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping using RAD-Seq. Producing a SNP panel with 7305 SNPs capturing the maximum difference between paternal and maternal genome information, and being able to distinguish between the F1 and F2 generation with 90% accuracy. Peer review helped highlight better the practical applications of this work. The combination of the efficiency of RNA-seq and advances in kinship analysis here can helpfully help improve breed management, local resource utilization, and conservation of livestock.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte