Genomics

Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning

1. Gemma E May
2. Christina Akirtava
3. Matthew Agar-Johnson
4. Jelena Micic
5. John Woolford
6. Joel McManus

• Curated by eLife

  eLife assessment

  Protein abundance is the result of many layers of regulation, including at the levels of transcription, mRNA stability, translation and protein degradation. Many transcripts contain short upstream ORFs (uORFS), but their effects on the translation of the main ORFs are difficult to predict as they are sometimes negative, positive and of different magnitudes. Here, the authors identify features of uORFs using massively parallel reporter assays, and these features help predict uORF effects on translation of main ORFs. The results will be an important resource for the community of researchers using this model organism and for the molecular and cell biology community in general as they allow to better understand how genes are regulated. There are also areas in which the authors' claims or conclusions are not fully justified and require either additional statistical analysis or new experimentation.

Reviewed by eLife

Multi-omics analysis identifies LBX1 and NHLH1 as central regulators of human midbrain dopaminergic neuron differentiation

1. Borja Gomez Ramos
2. Jochen Ohnmacht
3. Nikola de Lange
4. Aurélien Ginolhac
5. Elena Valceschini
6. Aleksandar Rakovic
7. Rashi Halder
8. François Massart
9. Christine Klein
10. Roland Krause
11. Marcel H. Schulz
12. Thomas Sauter
13. Rejko Krüger
14. Lasse Sinkkonen

Reviewed by Review Commons

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

1. J. William O. Ballard
2. Matt A. Field
3. Richard J. Edwards
4. Laura A.B. Wilson
5. Loukas G. Koungoulos
6. Benjamin D. Rosen
7. Barry Chernoff
8. Olga Dudchenko
9. Arina Omer
10. Jens Keilwagen
11. Ksenia Skvortsova
12. Ozren Bogdanovic
13. Eva Chan
14. Robert Zammit
15. Vanessa Hayes
16. Erez Lieberman Aiden

Reviewed by GigaScience

The mutational signatures of poor treatment outcomes on the drug-susceptible Mycobacterium tuberculosis genome

1. Yiwang Chen
2. Qi Jiang
3. Mijiti Peierdun
4. Howard E Takiff
5. Qian Gao

• Curated by eLife

  eLife assessment

  In this useful study, a GWAS-type analysis is applied to clinical Mycobacterium tuberculosis isolates to discover genetic polymorphisms linked to poor tuberculosis outcomes. The evidence for the detected associations is still incomplete, as the corresponding polymorphisms are not adequate to power a prediction model for infection outcome, although key host factors - including patient age, sex, and duration of diagnostic delay (which have stronger predictive value) - appear to enhance predictive capacity.

Reviewed by eLife

Genome assembly of the deep-sea coral Lophelia pertusa

1. Santiago Herrera
2. Erik E. Cordes

Reviewed by GigaByte

The first genome assembly of the amphibian nematode parasite ( Aplectana chamaeleonis )

1. Lei Han
2. Tianlu Liu
3. Fengping He
4. Zhijun Hou

Reviewed by GigaByte

Whole-genome sequencing of Chinese native goat offers biological insights into cashmere fiber formation

1. Hu Han
2. Man-Man Yang
3. Jiang Dan
4. Xing-Ju Zhang
5. Qiang Wei
6. Tao Chen
7. Qi-Ju Wang
8. Cheng-Ye Yang
9. Bater Wulan
10. Ting-Ting Zhang
11. Gang Gen
12. Mengkedala
13. Bin Li
14. Wei-Dong Deng
15. Ze-Pu Miao
16. Ran Wang
17. Qing-Feng Zhang
18. Lin Li
19. Sheng-Yu Chao
20. Ming Fang
21. Yong Li

Reviewed by GigaScience

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

1. Benjamin Guinet
2. David Lepetit
3. Sylvain Charlat
4. Peter N Buhl
5. David G Notton
6. Astrid Cruaud
7. Jean-Yves Rasplus
8. Julia Stigenberg
9. Damien M de Vienne
10. Bastien Boussau
11. Julien Varaldi

• Curated by eLife

  eLife assessment

  This important manuscript employs a rigorous and multi-pronged comparative genomics approach to unravel how lifestyle modulates the acquisition and domestication of viral genetic elements in the genomes of hymenopteran insects. Using an extensive dataset of over 120 hymenopteran genomes, the authors provide convincing evidence that endoparasitism (where parasite development occurs within hosts) facilitates the uptake and domestication of double-stranded DNA viral elements.

Reviewed by eLife

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

1. William Matlock
2. Samuel Lipworth
3. Kevin K Chau
4. Manal AbuOun
5. Leanne Barker
6. James Kavanagh
7. Monique Andersson
8. Sarah Oakley
9. Marcus Morgan
10. Derrick W Crook
11. Daniel S Read
12. Muna Anjum
13. Liam P Shaw
14. Nicole Stoesser
15. REHAB Consortium

• Curated by eLife

  eLife assessment

  This important study presents valuable findings on the dissemination of plasmids. In an analysis of five major Enterobacterales genera, the authors convincingly demonstrate that similar plasmids are shared between genera, species, and clones, both within and between ecological niches. Given the size of the dataset and the very detailed level of analysis this study importantly contributes to insights into to the flow of plasmids, including those carrying antimicrobial resistance genes, across niches.

Reviewed by eLife

Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

1. Jeff Jiajing Zhou
2. Jin Sun Cho
3. Han Han
4. Ira L Blitz
5. Wenqi Wang
6. Ken WY Cho

• Curated by eLife

  eLife assessment

  In this manuscript, the authors investigate the role of histone deacetylases in the spatial epigenetic control of zygotic gene expression in early gastrulation. They discover HDAC1 binding is maternally-controlled and that inhibition of histone acetylation blocks gastrulation and disrupts cell lineage integrity, tied to both positive and negative regulatory effects on gene transcription in space and time. The study contributes to a growing body of evidence that highlights a central role of histone acetylation-deacetylation dynamics in epigenetic regulation of gene expression and cell fating in early tissue patterning of the embryo.

Reviewed by eLife