Genomics

The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

1. Torsten Günther
2. Jacob Chisausky
3. Ángeles M Galindo-Pellicena
4. Eneko Iriarte
5. Oscar Cortes Gardyn
6. Paulina G Eusebi
7. Rebeca García-González
8. Irene Ureña
9. Marta Moreno-García
10. Alfonso Alday
11. Manuel Rojo
12. Amalia Pérez
13. Cristina Tejedor Rodríguez
14. Iñigo García Martínez de Lagrán
15. Juan Luis Arsuaga
16. José-Miguel Carretero
17. Anders Götherström
18. Colin Smith
19. Cristina Valdiosera

• Curated by eLife

  eLife Assessment

  Using genomic data from ancient and modern samples, this important study investigates the genomic history of cattle in Iberia, focusing on the admixture between domestic cattle and their wild ancestors, aurochs. The authors present convincing evidence for interbreeding between domestic cattle and wild aurochs since the Neolithic period, although the evidence of sex-biased introgression is weak. The authors also show that the aurochs ancestry in cattle stabilized at ~20% since ~4000 years ago and continues into modern breeds; however, the aurochs ancestry is not heightened in a modern breed of Spanish fighting bulls that are bred for aggressiveness. The work will be of interest to evolutionary biologists and quantitative geneticists who seek to understand the genomic history and genetic basis of trait variation of domesticated animals.

Reviewed by eLife

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

1. Kira Breunig
2. Xuifen Lei
3. Mauro Montalbano
4. Gabriela DA Guardia
5. Shiva Ostadrahimi
6. Victoria Alers
7. Adam Kosti
8. Jennifer Chiou
9. Nicole Klein
10. Corina Vinarov
11. Lily Wang
12. Mujia Li
13. Weidan Song
14. W Lee Kraus
15. David S Libich
16. Stefano Tiziani
17. Susan T Weintraub
18. Pedro AF Galante
19. Luiz O Penalva

• Curated by eLife

  eLife Assessment

  This study reports valuable insights into the interactome of the RNA-binding protein SERBP1 and possible links through PARylation to diverse processes, including splicing, cell division, and ribosome biogenesis. The diversity of processes SERBP1 may regulate means this work would be of very broad interest to the cell biology community. The proteomics data are solid, but the functional connection to downstream processes and the link to Alzheimer's disease, while compelling, still require further examination. These latter data currently rely on a very limited set of experiments and patient samples with questionable quality of preservation and methodology.

Reviewed by eLife

Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies

1. Jorge Blanco Mendana
2. Margaret Donovan
3. Lindsey Gengelbach O'Brien
4. Benjamin Auch
5. John Garbe
6. Daryl M Gohl

• Curated by eLife

  eLife Assessment

  This useful study presents a genetically encoded barcoding system that could advance transcriptomic studies and that has the potential for further applications, such as in high-throughput population-scale behavioral measurements. The evidence supporting the claims of the authors is solid and highlights both the usefulness and the limitations of the approach.

Reviewed by eLife

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

1. Mehul Vora
2. Jonathan Dietz
3. Zachary Wing
4. Karen George
5. Jun Kelly Liu
6. Christopher Rongo
7. Cathy Savage-Dunn

• Curated by eLife

  eLife Assessment

  Modulation of BMP signalling affects body size in the nematode Caenorhabditis elegans, and this paper examines the effects on C. elegans body size brought about by the modulation of BMP signalling. Thw study provides valuable analyses of ChIP-seq and RNA-Seq data to understand the function of SMA-3 (Smad) and SMA-9 (Schnurri) in this model. The authors provide compelling evidence that the BMP-dependent body size effect could be due to defects in cuticle collagen secretion, a finding of interest to those studying organismal growth and epidermal function.

Reviewed by eLife

Intrahost dynamics, together with genetic and phenotypic effects predict the success of viral mutations

1. Cedric C.S. Tan
2. Marina Escalera-Zamudio
3. Alexei Yavlinsky
4. Lucy van Dorp
5. Francois Balloux

Reviewed by PREreview

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

1. Carolina Heloisa de Souza Borges
2. Ricardo Utsunomia
3. Alessandro Varani
4. Marcela Uliano-Silva
5. Lieschen Valeria G. Lira
6. Arno J. Butzge
7. John F. Gomez Agudelo
8. Shisley Manso
9. Milena V. Freitas
10. Raquel B. Ariede
11. Vito A. Mastrochirico-Filho
12. Carolina Penaloza
13. Agustín Barria
14. Fábio Porto-Foresti
15. Fausto Foresti
16. Ricardo Hattori
17. Yann Guiguen
18. Ross D. Houston
19. Diogo Teruo Hashimoto

Reviewed by GigaScience

Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis

1. Jongkeun Park
2. WonJong Choi
3. Do Young Seong
4. Seungpil Jeong
5. Ju Young Lee
6. Hyo Jeong Park
7. Dae Sun Chung
8. Kijong Yi
9. Uijin Kim
10. Ga-Yeon Yoon
11. Hyeran Kim
12. Taehoon Kim
13. Sooyeon Ko
14. Eun Jeong Min
15. Hyun-Soo Cho
16. Nam-Hyuk Cho
17. Dongwan Hong

• Curated by eLife

  eLife Assessment

  The study provides valuable insight into the biological significance of SARS-CoV-2 by using a series of computational analyses of viral proteins. While the evidence is solid, the reviewers noted a lack of clarity about the objectives of the analyses. While impactful for the field, the manuscript would benefit from improved presentation.

Reviewed by eLife

Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression

1. Shengze Yao
2. Yesu Jeon
3. Barry Kesner
4. Jeannie T Lee

• Curated by eLife

  eLife Assessment

  This valuable study addresses the potential roles of the master regulator of X chromosome inactivation, the Xist long non-coding RNA, in the regulation of autosomal genes. Using data from mouse cells, the authors propose that Xist can coat specific autosomal promoters, which in turn leads to the attenuation of their transcriptional activity. The evidence from individual genes is interesting, and the model aligns with recently published results from humans. However, despite some improvements during revision, the data and statistical analyses in the current study are not yet strong enough to allow for conclusive inferences, leaving the evidence for mouse cells behaving like human cells incomplete. The topic of the work is of broad interest, in particular to colleagues studying gene regulation and noncoding RNAs.

Reviewed by eLife

Genome-wide identification of stable RNA-chromatin interactions

1. Xingzhao Wen
2. Sheng Zhong

• Curated by eLife

  eLife Assessment

  This study provides a valuable look at genome-wide RNaseA-resistant RNA-DNA interactions in human embryonic stem cells. The research indicated that RNase treatment maintained long-range RNA-chromatin connections characterized by significant sequence conservation while abolishing permissive interactions. Interestingly, coding and non-coding RNA transcripts exhibited differing sensitivity to RNase treatment. Although the study findings reveal an intriguing RNase-inaccessible regulatory RNA-chromatin interactome, conclusions about the identity and regulatory significance of RNase-resistant RNA-chromatin interactions are incomplete and would benefit from more rigorous approaches that include additional computational and experimental controls.

Reviewed by eLife

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

1. Arkadiy K Golov
2. Alexey A Gavrilov
3. Noam Kaplan
4. Sergey V Razin

• Curated by eLife

  eLife Assessment

  Identifying chromatin interactions with high sensitivity and resolution at the genome-wide scale continues to be technically challenging. This study introduces findings based on the improved MNase-based proximity ligation method, MChIP-C, which enables genome-wide measurement of chromatin interactions at single-nucleosome resolution. The evidence presented in this manuscript is convincing, and the technological advancements will be valuable for the study of 3D genome architecture.

Reviewed by eLife