Genomics

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

1. Joshua M. Kirsch
2. Andrew J. Hryckowian
3. Breck A. Duerkop

Reviewed by Arcadia Science

The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

1. Mathieu Hénault
2. Souhir Marsit
3. Guillaume Charron
4. Christian R Landry

• Curated by eLife

  eLife assessment

  This valuable study advances our understanding of the forces that shape the genomic landscape of transposable elements. By exploiting both long-read sequencing of mutation accumulation lines and in vivo transposition assays, the authors offer compelling evidence that structural variation rather than transposition largely shapes transposable element copy number evolution in budding yeast. The work will be of interest to the transposable element and genome evolution communities.

Reviewed by eLife

Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

1. Héctor Castillo
2. Francisco Godoy
3. Clément Gilbert
4. Felipe Aguilera
5. Salvatore Spicuglia
6. Sylvain Marcellini

Reviewed by Review Commons

DNA methylation-environment interactions in the human genome

1. Rachel A Johnston
2. Katherine A Aracena
3. Luis B Barreiro
4. Amanda J Lea
5. Jenny Tung

• Curated by eLife

  eLife assessment

  This important paper uses a genome-wide, massively parallel reporter assay to determine how CpG methylation affects regulatory sequences that control the expression of human genes. The authors provide compelling evidence that methylation not only influences baseline activity of regulatory sequences but also the magnitude of acute responses to environmental stimuli. The findings are of broad interest, and the extensive data set will likely become a key resource for the community.

Reviewed by eLife

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

1. Stephanie H Chen
2. Alyssa M Martino
3. Zhenyan Luo
4. Benjamin Schwessinger
5. Ashley Jones
6. Tamene Tolessa
7. Jason G Bragg
8. Peri A Tobias
9. Richard J Edwards

Reviewed by GigaScience

Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

1. Mohammed Seba
2. Frederic Boccard
3. Stéphane Duigou

• Curated by eLife

  eLife assessment

  This important work combines DNA contact analysis and controlled genome rearrangements to investigate the processes that organize the E. coli chromosome, with a particular focus on how the SMC-related complex MukBEF is regulated. The evidence supporting the conclusions is compelling, with time-resolved experiments and analysis of mutant strains. The work will be of broad interest to chromosome biologists and bacterial cell biologists.

Reviewed by eLife

Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap

1. Mengxue Tian
2. Zhenjia Wang
3. Zhangli Su
4. Etsuko Shibata
5. Yoshiyuki Shibata
6. Anindya Dutta
7. Chongzhi Zang

• Curated by eLife

  eLife assessment

  The paper addresses the mechanism of initiation of DNA replication in human cells by analyzing published data on the location of origins of DNA replication and the location of binding sites in the genome for ORC and MCM2-7 complexes. There are some useful analyses of existing data but there are concerns regarding the conclusion that there might be alternative mechanisms for determining the location of origins of DNA replication in human cells compared to the well known mechanism known from many eukaryotic systems, including yeast, Xenopus, C. elegans and Drosophila. The lack of overlap between binding sites for ORC1 and ORC2, which are known to form a complex in human cells, is a particular concern and points to the evidence for the accurate localization of their binding sites in the genome being incomplete.

Reviewed by eLife

Discovering non-additive heritability using additive GWAS summary statistics

1. Samuel Pattillo Smith
2. Gregory Darnell
3. Dana Udwin
4. Julian Stamp
5. Arbel Harpak
6. Sohini Ramachandran
7. Lorin Crawford

• Curated by eLife

  eLife assessment

  This study provides a valuable investigation into whether phenotypic variance due to interactions between genetic variants can be measured using genome-wide association summary statistics. The authors present a method, i-LDSC, that uses statistics on the correlations between genotypes at different loci (linkage disequilibrium) to estimate the phenotypic variance explained by both additive genetic effects and pairwise interactions. While the authors present extensive simulations on the performance of their method and empirical results indicating the presence of epistasis (as they define epistasis) it is unclear how their method and results relate to the traditional definitions of additive and non-additive genetic effects, which are different from the authors' definitions.

Reviewed by eLife

Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

1. Yeming Xie
2. Fengying Ruan
3. Yaning Li
4. Meng Luo
5. Chen Zhang
6. Zhichao Chen
7. Zhe Xie
8. Zhe Weng
9. Weitian Chen
10. Wenfang Chen
11. Yitong Fang
12. Yuxin Sun
13. Mei Guo
14. Juan Wang
15. Shouping Xu
16. Hongqi Wang
17. Chong Tang

• Curated by eLife

  eLife assessment

  This paper reports the development of SCA-seq, a new method derived from PORE-C for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. Most of the conclusions are supported by convincing data. SCA-seq has the potential to become a useful tool to the scientific communities to interrogate genome structure-function relationships.

Reviewed by eLife

Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings

1. Amruta Tendolkar
2. Anyi Mazo-Vargas
3. Luca Livraghi
4. Joseph J Hanly
5. Kelsey C Van Horne
6. Lawrence E Gilbert
7. Arnaud Martin

• Curated by eLife

  eLife assessment

  This valuable paper examines the Bithorax complex in several butterfly species, in which the complex is contiguous and not split, as it is in the well-studied fruit fly Drosophila. Based on genetic screens and genetic manipulations of a boundary element involved in segment-specific regulation of Ubx, the authors provide convincing evidence for their conclusions, which could be strengthened by additional data and analyses in the future. The data presented are relevant for those interested in the evolution and function of Hox genes and of gene regulation in general.

Reviewed by eLife