Genomics

The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells

1. Keisuke Shoji
2. Yusuke Umemura
3. Susumu Katsuma
4. Yukihide Tomari

Reviewed by Review Commons

Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance

1. Fares Z Najar
2. Evan Linde
3. Chelsea L Murphy
4. Veniamin A Borin
5. Huan Wang
6. Shozeb Haider
7. Pratul K Agarwal

• Curated by eLife

  eLife assessment

  Najar et al., present a method for the identification of the emergence of new variants prior to the accompanying surge in cases by examining the trend of accumulated non-synonymous mutations from the original Wuhan 2020 SARS-CoV-2 strain. This is an interesting idea but requires additional evidence to establish this as a robust tool for predictions.

Reviewed by eLife

Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns

1. Simon Grund Sørensen
2. Amruta Shrikhande
3. Gustav Alexander Poulsgaard
4. Mikkel Hovden Christensen
5. Johanna Bertl
6. Britt Elmedal Laursen
7. Eva R Hoffmann
8. Jakob Skou Pedersen

• Curated by eLife

  eLife assessment

  This paper will be of interest to researchers in the field of genomic medicine and cancer mutagenesis. It presents predictive models with potential clinical applications that can identify patients with specific gene dysfunction based on characteristic patterns of mutation. The key findings are well supported.

Reviewed by eLife

Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project

1. Emmelien Vancaester
2. Mark Blaxter

Reviewed by Arcadia Science

Structure-guided isoform identification for the human transcriptome

1. Markus J Sommer
2. Sooyoung Cha
3. Ales Varabyou
4. Natalia Rincon
5. Sukhwan Park
6. Ilia Minkin
7. Mihaela Pertea
8. Martin Steinegger
9. Steven L Salzberg

• Curated by eLife

  eLife assessment

  This study applies AlphaFold to the CHESS selection of transcripts with the goal of generating predicted 3D protein structures and a quality measure of folding, the pLDDT score. From these data, the authors build a database for result exploration, documented by several examples, including proteins, where the authors propose the pLDDT score as a measure of presumed superior biological functionality over other isoforms. These results will be highly relevant for anyone working with proteins that occur in different isoforms.

Reviewed by eLife

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

1. Hjörleifur Einarsson
2. Marco Salvatore
3. Christian Vaagensø
4. Nicolas Alcaraz
5. Jette Bornholdt
6. Sarah Rennie
7. Robin Andersson

• Curated by eLife

  eLife assessment

  This paper by Einarsson and colleagues presents a comprehensive analysis on how human genetic variability impacts both gene expression and promoter. Using a new resource of CAGE data in lymphoblastoid cell lines from 108 individuals, they uncover a series of features that distinguish promoters with highly variable expression across individuals from those exhibiting low variability. The authors propose various explanations for the observed results. A few additional analyses and a more pragmatic interpretation of their data may help consolidate or refine the models proposed.

Reviewed by eLife

Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice

1. Yanis Zekri
2. Romain Guyot
3. Inés Garteizgogeascoa Suñer
4. Laurence Canaple
5. Amandine Gautier Stein
6. Justine Vily Petit
7. Denise Aubert
8. Sabine Richard
9. Frédéric Flamant
10. Karine Gauthier

• Curated by eLife

  eLife assessment

  The manuscript by Yanis Zekri et al identifies the direct T3 target genes that are important in thyroid hormone signaling in brown adipose tissue (BAT). The findings reported in this manuscript are significant and fundamental to our understanding of thyroid hormone action in response to environmental changes. The strength of the evidence presented with the novel methodological approaches used makes the manuscript exceptional in the area of BAT biology and T3 regulation of adaptive thermogenesis.

Reviewed by eLife

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

1. Rebeca San Martin
2. Priyojit Das
3. Jacob T Sanders
4. Ashtyn M Hill
5. Rachel Patton McCord

• Curated by eLife

  eLife assessment

  This manuscript is of interest to researchers investigating genetic mechanisms of aging and transcriptional regulation of developmental processes in mesenchyme-derived tissues. In this study, fibroblast cell lines from patients with and without Hutchinson-Gilford Progeria were compared to pinpoint the molecular mechanisms leading to the phenotypes of persons with this condition. The identification of five major dysregulated functional hubs in fibroblast cell lines derived from Hutchinson-Gilford Progeria Syndrome (HGPS) patients provides a unique opportunity for others working on this disorder to utilize animal models to validate the authors' hypotheses.

Reviewed by eLife

Mouse B2 SINE elements function as IFN-inducible enhancers

1. Isabella Horton
2. Conor J Kelly
3. Adam Dziulko
4. David M Simpson
5. Edward B Chuong

• Curated by eLife

  eLife assessment

  This paper will be of interest to scientists studying species-specific immune responses and those studying how transposable elements rewire transcriptional regulatory networks. The work describes a new class of TEs that may act as enhancers of immune genes in mice. A combination of computational and experimental data supports most but not all conclusions in the paper.

Reviewed by eLife

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

1. Awais Khan
2. Sarah B. Carey
3. Alicia Serrano
4. Huiting Zhang
5. Heidi Hargarten
6. Haley Hale
7. Alex Harkess
8. Loren Honaas

Reviewed by GigaByte