Genetics

Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations

1. Wei-Ping Li
2. Jia-Ying Su
3. Yu-Chi Chang
4. Yun-Lin Wang
5. Hung-Lun Chiang
6. Yu-Tung Hsieh
7. Yi-Hsuan Chiang
8. Yen-Ling Ko
9. Bing-Jen Chiang
10. Cheng-Han Yang
11. Yen-Tsung Huang
12. Chien-Ling Lin

• Curated by eLife

  eLife assessment

  To elucidate the precise function of variants in the UTRs, the authors established and conducted a massively parallel poly(ribo)some profiling method to compare ribosome associations and effects of genetic variants. The approach and results are valuable, as this is a new approach to studying UTRs. However, the experimental and analytic validation seems to be incomplete, as the results are less robust than expected.

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

Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals

1. Lisa Baumgartner
2. Jonathan J Ipsaro
3. Ulrich Hohmann
4. Dominik Handler
5. Alexander Schleiffer
6. Peter Duchek
7. Julius Brennecke

• Curated by eLife

  eLife assessment

  This fundamental work has completed our understanding of the singular binding profile of the Rhino HP1 protein to chromatin, a key step in converting certain genomic regions into piRNA source loci. The evidence supporting the conclusions is compelling. Phylogenetic analyses, structure prediction, rigorous biochemical assays and in vivo genetics emphasize the importance of the Rhino chromodomain in the recognition of both a histone mark and a DNA-binding protein, and highlight the importance of a single chromodomain residue in the protein-protein interaction.

Reviewed by eLife

The retrotransposon - derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity

1. Thomas W.P. Wood
2. William S. Henriques
3. Harrison B. Cullen
4. Mayra Romero
5. Cecilia S. Blengini
6. Shreya Sarathy
7. Julia Sorkin
8. Hilina Bekele
9. Chen Jin
10. Seungsoo Kim
11. Alexei Chemiakine
12. Rishad C. Khondker
13. José V.V. Isola
14. Michael B. Stout
15. Vincenzo A. Gennarino
16. Binyam Mogessie
17. Devanshi Jain
18. Karen Schindler
19. Yousin Suh
20. Blake Wiedenheft
21. Luke E. Berchowitz

Reviewed by Arcadia Science

Insights into Immune Gene Prediction and Function Through the Evolutionary History of ADF Gene Family

1. Huan Chen
2. Brad Day

Reviewed by Arcadia Science

Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties

1. Wenfan Ke
2. Miki Fujioka
3. Paul Schedl
4. James B Jaynes

• Curated by eLife

  eLife assessment

  This valuable work investigates the role of boundary elements in the formation of 3D genome architecture. The authors established a specific model system that allowed them to manipulate boundary elements and examine the resulting genome topology. The work yielded the first demonstration of the existence of stem and circle loops in a genome and confirms a model which had been posited based on extensive prior genetic work, providing insights into how 3D genome topologies affect enhancer-promoter communication. The evidence is solid, although the degree of generalization remains uncertain.

Reviewed by eLife

Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion

1. Xinyang Bing
2. Wenfan Ke
3. Miki Fujioka
4. Amina Kurbidaeva
5. Sarah Levitt
6. Mike Levine
7. Paul Schedl
8. James B Jaynes

• Curated by eLife

  eLife assessment

  This valuable work presents elegant experimental data from the Drosophila embryo supporting the notion that interactions among specific loci, called boundary elements, contribute to topologically associated domain (TAD) formation and gene regulation. The evidence supporting boundary:boundary pairing as a determinant of 3D structures is compelling; however, an inability to deplete loop extruders formally leaves open a possible contribution of loop extrusion. This study will be of interest to the nuclear structure community, particularly those using Drosophila as a model.

Reviewed by eLife

Poseidon – A framework for archaeogenetic human genotype data management

1. Clemens Schmid
2. Ayshin Ghalichi
3. Thiseas C. Lamnidis
4. Dhananjaya B. A. Mudiyanselage
5. Wolfgang Haak
6. Stephan Schiffels

• Curated by eLife

  eLife assessment

  This paper describes an important software framework for the curation, retrieval, and analysis of ancient human genomic data and their associated metadata, overcoming long-standing coordination and harmonization issues in ancient human genomics. The resource is built on compelling and sometimes exceptional principles of software engineering and reproducibility, and the authors make an excellent case that their resource will be of practical use to many researchers studying human history using DNA. The main issues include natural uncertainties regarding future funding and maintenance of this resource, as well as deviation from established standards in other areas of genomics.

Reviewed by eLife