Genomics

A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm

1. Sara A Carioscia
2. Kathryn J Weaver
3. Andrew N Bortvin
4. Hao Pan
5. Daniel Ariad
6. Avery Davis Bell
7. Rajiv C McCoy

• Curated by eLife

  Evaluation Summary:

  The authors first develop a new flexible and robust method to detect deviations from Mendelian inheritance in genomic data from gametes. The authors then apply this method to study deviations from Mendelian inheritance in human sperm data, but find no evidence for it. Even though this is a negative result, and overall the results are expected based on previous studies. the reviewers agreed that the research is rigorous and valuable.

  (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

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

1. Akito Y. Kawahara
2. Caroline G. Storer
3. Amanda Markee
4. Jacqueline Heckenhauer
5. Ashlyn Powell
6. David Plotkin
7. Scott Hotaling
8. Timothy P. Cleland
9. Rebecca B. Dikow
10. Torsten Dikow
11. Ryoichi B. Kuranishi
12. Rebeccah Messcher
13. Steffen U. Pauls
14. Russell J. Stewart
15. Koji Tojo
16. Paul B. Frandsen

Reviewed by GigaByte

CRISPR interference identifies vulnerable cellular pathways with bactericidal phenotypes in Mycobacterium tuberculosis

1. Matthew B. McNeil
2. Laura M. Keighley
3. Josephine R. Cook
4. Chen‐Yi Cheung
5. Gregory M. Cook

• Curated by eLife

  Evaluation Summary:

  High-throughput approaches that accurately assess drug target vulberbility in Mycobacterium tuberculosis, the causative agent of tuberculosis, are urgently needed to develop new treatment options for this dreaded disease. This paper applies a CRISPRi based approach to investigate gene essentiality and vulnerability on a diverse set of 96 genes. While the key observations of the study support previous findings, the approach reported here is useful for identification and characterization of novel drug targets. The study will be of interest to microbiologists and those interested in diverse aspects of bacterial metabolism.

  (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

Tethering distinct molecular profiles of single cells by their lineage histories to investigate sources of cell state heterogeneity

1. Anna Minkina
2. Junyue Cao
3. Jay Shendure

• Curated by eLife

  Evaluation Summary:

  The authors use single-cell RNA-sequencing, single-cell ATAC-sequencing, a CRISPR-based lineage tracing system, and a novel computational pipeline to characterize heritable expression changes. Aspects of this work were found to be both impactful and technically sound, but there is a concern with the scalability/generalizability of the approach, the use of the single cell ATAC-sequencing data, and some technical aspects of the computational pipeline. This work will appeal to groups working on lineage tracing and gene regulation.

  (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 #2 agreed to share their name with the authors.)

Reviewed by eLife

Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans

1. Jun Kim
2. David S Jimenez
3. Bhavana Ragipani
4. Bo Zhang
5. Lena A Street
6. Maxwell Kramer
7. Sarah E Albritton
8. Lara H Winterkorn
9. Ana K Morao
10. Sevinc Ercan

• Curated by eLife

  Evaluation Summary:

  This paper is potentially of broad interest to researchers in the chromosome biology field. With specific loading sequences identified, the condensin DC complex studied here provides an elegant system to investigate the in vivo activities of SMC complexes. Combining Hi-C, ChIP-seq and RNA-seq, the authors have a comprehensive suite of assays to probe their questions. However, not all of their major conclusions are currently supported by the data.

  (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

Mapping the single-cell landscape of acral melanoma and analysis of the molecular regulatory network of the tumor microenvironments

1. Zan He
2. Zijuan Xin
3. Qiong Yang
4. Chen Wang
5. Meng Li
6. Wei Rao
7. Zhimin Du
8. Jia Bai
9. Zixuan Guo
10. Xiuyan Ruan
11. Zhaojun Zhang
12. Xiangdong Fang
13. Hua Zhao

• Curated by eLife

  Evaluation Summary:

  He and collaborators analyse eight samples from six patients with acral melanoma through single-cell RNA sequencing. They describe the tumour microenvironment in these tumours, including descriptions of interactions among distinct cell types and potential biomarkers. The study is thoroughly done. In its final form, this study will help to inform our knowledge of the immune infiltration on the poorly studied acral melanoma subtype, the most common type of the disease in several countries in Africa, Asia and Latin America.

  (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

Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing

1. Xuefei Wang
2. Xiangru Shen
3. Shan Chen
4. Hongyi Liu
5. Ni Hong
6. Hanbing Zhong
7. Xi Chen
8. Wenfei Jin

• Curated by eLife

  Evaluation Summary:

  This manuscript is of broad interest to readers interested in heterogeneity in immune cell populations with single-cell RNA sequencing, and for students of human T cell biology. It uses and reanalyses published single-cell RNA sequencing data dataset for this purpose. However, it does not adequately address major technical concerns, and therefore the interpretations are not robustly supported.

  (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

Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

1. Francisco Rodriguez-Algarra
2. Robert A. E. Seaborne
3. Amy F. Danson
4. Selin Yildizoglu
5. Harunori Yoshikawa
6. Pui Pik Law
7. Zakaryya Ahmad
8. Victoria A. Maudsley
9. Ama Brew
10. Nadine Holmes
11. Mateus Ochôa
12. Alan Hodgkinson
13. Sarah J. Marzi
14. Madapura M. Pradeepa
15. Matthew Loose
16. Michelle L. Holland
17. Vardhman K. Rakyan

• Curated by eLife

  Evaluation Summary:

  This manuscript extends the evidence that ribosomal DNA has substantial interindividual variation, and presents evidence that variants are associated with differences in DNA methylation. The authors show that some rDNA types respond to environmental signals during in utero development, whereas others are changed during the aging process - thus broadening the known communication between development/nutrition/aging and the cellular protein synthesis machinery. These findings have relevance for the influence of such epialleles on gene expression and disease risk.

  (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

Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes

1. Léa Pradier
2. Stéphanie Bedhomme

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to microbiologists, clinicians, and public health workers with an interest in the possible impact of antibiotic use and regulations. The scope of the study is unusually high, integrating economic and geographical factors as well as genomic data among others. However, reasonable alternative explanations can be identified such that the data do not strongly favor the preferred hypothesis put forward by the authors.

  (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

A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340

1. Yikun Zhao
2. Yuancong Wang
3. De Ma
4. Guang Feng
5. Yongxue Huo
6. Zhihao Liu
7. Ling Zhou
8. Yunlong Zhang
9. Liwen Xu
10. Liang Wang
11. Han Zhao
12. Jiuran Zhao
13. Fengge Wang

Reviewed by GigaByte