Genomics

NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

1. Luke Saville
2. Li Wu
3. Jemaneh Habtewold
4. Yubo Cheng
5. Babita Gollen
6. Liam Mitchell
7. Matthew Stuart-Edwards
8. Travis Haight
9. Majid Mohajerani
10. Athanasios Zovoilis

Reviewed by Review Commons

Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

1. Reese Richardson
2. Heliodoro Tejedor Navarro
3. Luis A Nunes Amaral
4. Thomas Stoeger

• Curated by eLife

  eLife assessment

  This study investigated the factors related to understudied genes in biomedical research. It showed that understudied genes are largely abandoned at the writing stage, and it identified a number of biological and experimental factors that influence which genes are selected for investigation. The study is an important contribution to this branch of meta-research, and the evidence in support of the findings is solid.

Reviewed by eLife

Structural variation discovery in wheat using PacBio high‐fidelity sequencing

1. Zhiliang Zhang
2. Jijin Zhang
3. Lipeng Kang
4. Xuebing Qiu
5. Song Xu
6. Jun Xu
7. Yafei Guo
8. Zelin Niu
9. Beirui Niu
10. Aoyue Bi
11. Xuebo Zhao
12. Daxing Xu
13. Jing Wang
14. Changbin Yin
15. Fei Lu

Reviewed by PREreview

Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations

1. Maria L Adelus
2. Jiacheng Ding
3. Binh T Tran
4. Austin C Conklin
5. Anna K Golebiewski
6. Lindsey K Stolze
7. Michael B Whalen
8. Darren A Cusanovich
9. Casey E Romanoski

• Curated by eLife

  eLife assessment

  This is a fundamental resource of snRNA-seq and and chromatin accessibility data from human aortic endothelial cells (ECs), treated with relevant perturbations such as IL1b, TGFB2, or si-EGR. The authors show that ECs can be categorized by distinct subpopulations of differing plasticity. The support for the existence of these subpopulations is compelling, supported also by three publicly available scRNA-seq datasets, and differential enrichment of coronary artery disease associated SNPs in open chromatin in these subpopulations.

Reviewed by eLife

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

1. Magnus Wolf
2. Bruno Lopes da Silva Ferrette
3. Raphael T. F. Coimbra
4. Menno de Jong
5. Marcel Nebenfuehr
6. David Prochotta
7. Yannis Schöneberg
8. Konstantin Zapf
9. Jessica Rosenbaum
10. Hannah A. Mc Intyre
11. Julia Maier
12. Clara C.S. de Souza
13. Lucas M. Gehlhaar
14. Melina J. Werner
15. Henrik Oechler
16. Marie Wittekind
17. Moritz Sonnewald
18. Maria A. Nilsson
19. Axel Janke
20. Sven Winter

• Curated by GigaByte

  Editors Assessment:

  The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.

  **This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

1. Joshua M. Kirsch
2. Andrew J. Hryckowian
3. Breck A. Duerkop

Reviewed by Arcadia Science

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

1. Mathieu Hénault
2. Souhir Marsit
3. Guillaume Charron
4. Christian R Landry

• Curated by eLife

  eLife assessment

  This valuable study advances our understanding of the forces that shape the genomic landscape of transposable elements. By exploiting both long-read sequencing of mutation accumulation lines and in vivo transposition assays, the authors offer compelling evidence that structural variation rather than transposition largely shapes transposable element copy number evolution in budding yeast. The work will be of interest to the transposable element and genome evolution communities.

Reviewed by eLife

Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

1. Héctor Castillo
2. Francisco Godoy
3. Clément Gilbert
4. Felipe Aguilera
5. Salvatore Spicuglia
6. Sylvain Marcellini

Reviewed by Review Commons

DNA methylation-environment interactions in the human genome

1. Rachel A Johnston
2. Katherine A Aracena
3. Luis B Barreiro
4. Amanda J Lea
5. Jenny Tung

• Curated by eLife

  eLife assessment

  This important paper uses a genome-wide, massively parallel reporter assay to determine how CpG methylation affects regulatory sequences that control the expression of human genes. The authors provide compelling evidence that methylation not only influences baseline activity of regulatory sequences but also the magnitude of acute responses to environmental stimuli. The findings are of broad interest, and the extensive data set will likely become a key resource for the community.

Reviewed by eLife

Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR

1. Feroz Akhtar
2. Joselin Hernandez Ruiz
3. Ya-Guang Liu
4. Roy G. Resendez
5. Denis Feliers
6. Liza D. Morales
7. Alvaro Diaz-Badillo
8. Donna M. Lehman
9. Rector Arya
10. Juan Carlos Lopez-Alvarenga
11. John Blangero
12. Ravindranath Duggirala
13. Srinivas Mummidi

• Curated by eLife

  eLife assessment

  CCL2 is a chemokine known to have relevant immune cell chemoattractant properties, and it is believed to play a role in several chronic inflammatory diseases. The RNA-binding protein HuR controls the stability and translation of CCL2 mRNA. This paper presents solid evidence that a relatively common genetic variant tied to several disease phenotypes affects the interaction between the mRNA of CCL2 and the RNA-binding protein HuR. As CCL2 is believed to be relevant for leukocyte migration in various conditions, including chronic inflammation and cancer, this is an important finding that may be relevant to a broad audience.

Reviewed by eLife