Genetics

Dimensionality reduction of genetic data using contrastive learning

1. Filip Thor
2. Carl Nettelblad

Reviewed by Arcadia Science

Sibling similarity can reveal key insights into genetic architecture

1. Tade Souaiaia
2. Hei Man Wu
3. Clive Hoggart
4. Paul F O'Reilly

• Curated by eLife

  eLife assessment

  The authors present a solid statistical framework for using sibling phenotype data to assess whether there is evidence for de-novo or rare variants causing extreme trait values. Their valuable method is promising and will be of interest to researchers studying complex trait genetics.

Reviewed by eLife

Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

1. James Boocock
2. Noah Alexander
3. Leslie Alamo Tapia
4. Laura Walter-McNeill
5. Shivani Prashant Patel
6. Chetan Munugala
7. Joshua S Bloom
8. Leonid Kruglyak

• Curated by eLife

  eLife assessment

  This manuscript describes the mapping of natural DNA sequence variants that affect gene expression and its noise, as well as cell cycle timing, using as input single-cell RNA-sequencing of progeny from crosses between wild yeast strains. The method represents an important advance in the study of natural genetic variation. The findings, especially given the follow-up validation of the phenotypic impact of a mapped locus of major effect, provide convincing support for the rigor and utility of the method.

Reviewed by eLife, Arcadia Science

Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon

1. James Lee
2. Leman Simpson
3. Yi Li
4. Samuel Becker
5. Fan Zou
6. Xin Zhang
7. Lu Bai

• Curated by eLife

  eLife assessment

  This important study investigates the relationship between transcription factor condensate formation, transcription, and 3D gene clustering of the MET regulon in the model organism S. cerevisiae. The authors provide solid experimental evidence that transcription factor condensates enhance transcription of MET-regulated genes, but evidence for the role of Met4 IDRs and Met4-containing condensates in mediating target gene clustering in the MET regulon is not as strong. This paper will be of interest to molecular biologists working on chromatin and transcription, although its impact would be strengthened by further investigation.

Reviewed by eLife

Tbx1 haploinsufficiency causes brain metabolic and behavioral anomalies in adult mice which are corrected by vitamin B12 treatment

1. Marianna Caterino
2. Debora Paris
3. Giulia Torromino
4. Michele Costanzo
5. Gemma Flore
6. Annabella Tramice
7. Elisabetta Golini
8. Silvia Mandillo
9. Diletta Cavezza
10. Claudia Angelini
11. Margherita Ruoppolo
12. Andrea Motta
13. Elvira De Leonibus
14. Antonio Baldini
15. Elizabeth Illingworth
16. Gabriella Lania

Reviewed by Review Commons

A CRISPR ‐Cas9‐based system for the dose‐dependent study of DNA double‐strand break sensing and repair

1. Morgane Auboiron
2. Jocelyn Coiffard
3. Sylvain Kumanski
4. Olivier Santt
5. Benjamin Pardo
6. María Moriel‐Carretero

Reviewed by Review Commons

Resetting of H3K4me2 during mammalian parental-to-zygote transition

1. Chong Wang
2. Yong Shi
3. Jia Guo
4. Kaiyue Hu
5. Yaqian Wang
6. Yang Li
7. Jiawei Xu

• Curated by eLife

  eLife assessment

  This study presents an important finding of dynamic reprogramming of global H3K4me2 during mouse oocyte-to-embryo transition. While the H3K4me2 epigenome data is convincing, the interpretation and the potential mechanistic claims of the authors are incomplete in the current shape with the primary concerns regarding the contribution of Kdm1b or Kdm1a, as well as the specificity of the inhibitor and the antibody. The work will be of interest to researchers interested in epigenetic reprogramming.

Reviewed by eLife

The role of heterochronic gene expression and regulatory architecture in early developmental divergence

1. Nathan D Harry
2. Christina Zakas

• Curated by eLife

  eLife assessment

  This important study examines the extent to which distinct developmental pathways that result in alternative morphs correlate with transcriptome differences in a marine annelid, Streblospio benedicti. The strengths of the study include the experimental design and dense temporal sampling, which together provide convincing evidence that the two morphs can be clearly distinguished at the transcriptome level, despite relatively modest overall differences. The work will be of particular interest to students of the evolution of development.

Reviewed by eLife

Deficiency of IQCH causes male infertility in humans and mice

1. Tiechao Ruan
2. Ruixi Zhou
3. Yihong Yang
4. Junchen Guo
5. Chuan Jiang
6. Xiang Wang
7. Gan Shen
8. Siyu Dai
9. Suren Chen
10. Ying Shen

• Curated by eLife

  eLife assessment

  This valuable study describes mice with a knock out of the IQ motif-containing H (IQCH) gene, to model a human loss-of-function mutation in IQCH associated with male sterility. While the evidence for interaction between IQCH and potential RNA binding proteins is limited, the human infertility is reproduced in the mouse, making it a compelling model. The paper could be of interest to cell biologists and male reproductive biologists working on the sperm flagellar cytoskeleton and mitochondrial structure.

Reviewed by eLife

Target-specific requirements for RNA interference can arise through restricted RNA amplification despite the lack of specialized pathways

1. Daphne R Knudsen-Palmer
2. Pravrutha Raman
3. Farida Ettefa
4. Laura De Ravin
5. Antony M Jose

• Curated by eLife

  eLife assessment

  This valuable study shows how an intersecting network of regulators acting on genes with differences in their RNA metabolism explains why the loss of some regulators of RNAi in C. elegans can selectively impair the silencing of some target genes. The evidence presented is convincing, as the authors use a combination of computational modeling and RNAi assays to support their conclusions.

Reviewed by eLife