Genetics

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

ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins

1. Mathew Thayer
2. Michael B Heskett
3. Leslie G Smith
4. Paul T Spellman
5. Phillip A Yates

• Curated by eLife

  eLife assessment

  This important study expands generally upon our understanding of the role of hnRNP proteins in lncRNA function through analysis of ASAR genes that are present on all chromosomes and of profound significance. The findings provide convincing evidence linking ASARs with the phenomenon of RNA retention on chromosomes, including X inactivation, thereby providing an expanded context for studies in these areas. This manuscript will be of interest to researchers studying gene regulation and the interactions and functional roles of hnRNP and lncRNAs.

Reviewed by eLife

mtDNA “nomenclutter” and its consequences on the interpretation of genetic data

1. Vladimir Bajić
2. Vanessa Hava Schulmann
3. Katja Nowick

Reviewed by Peer Community in Evolutionary Biology

Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington’s disease

1. Doo Eun Choi
2. Jun Wan Shin
3. Sophia Zeng
4. Eun Pyo Hong
5. Jae-Hyun Jang
6. Jacob M Loupe
7. Vanessa C Wheeler
8. Hannah E Stutzman
9. Ben Kleinstiver
10. Jong-Min Lee

• Curated by eLife

  eLife assessment

  This proof-of-concept study focuses on an A->G DNA base editing strategy that converts CAG repeats to CAA repeats in the human HTT gene, which causes Huntington's disease (HD). These studies are conducted in human HEK293 cells engineered with a 51 CAG canonical repeat and in HD knock-in mice harboring 105+ CAG repeats. The findings of this study are valuable for the HD field, applying state-of-the-art techniques. However, the key experiments have yet to be performed in neuronal systems or brains of these mice: actual disease-rectifying effects relevant to patients have yet to observed, leaving the work incomplete.

Reviewed by eLife

SCC3 is an axial element essential for homologous chromosome pairing and synapsis

1. Yangzi Zhao
2. Lijun Ren
3. Tingting Zhao
4. Hanli You
5. Yongjie Miao
6. Huixin Liu
7. Lei Cao
8. Bingxin Wang
9. Yi Shen
10. Yafei Li
11. Ding Tang
12. Zhukuan Cheng

• Curated by eLife

  eLife assessment

  This fundamental study elucidates the function of the cohesin subunit SCC3 in maintaining homologous chromosome pairing and synapsis during meiosis. The observation of sterility in the SCC3 weak mutant prompted an investigation of abnormal chromosome behavior during anaphase I, and the discovery that SCC3's loading onto meiotic chromosomes is REC8-dependent. The convincing evidence presented in this study contributes to our understanding of meiosis in rice and attracts cell biologists, reproductive biologists, and plant geneticists.

Reviewed by eLife