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

    This article has 19 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  2. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

    This article has 19 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  3. Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies

    This article has 6 authors:
    1. Jorge Blanco Mendana
    2. Margaret Donovan
    3. Lindsey Gengelbach O'Brien
    4. Benjamin Auch
    5. John Garbe
    6. Daryl M Gohl
    This article has been curated by 1 group:
    • 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

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  4. Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

    This article has 7 authors:
    1. Mehul Vora
    2. Jonathan Dietz
    3. Zachary Wing
    4. Karen George
    5. Jun Kelly Liu
    6. Christopher Rongo
    7. Cathy Savage-Dunn
    This article has been curated by 1 group:
    • 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

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  5. Non-linear transcriptional responses to gradual modulation of transcription factor dosage

    This article has 7 authors:
    1. Júlia Domingo
    2. Mariia Minaeva
    3. John A Morris
    4. Sam Ghatan
    5. Marcello Ziosi
    6. Neville E Sanjana
    7. Tuuli Lappalainen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important work develops a new protocol to experimentally perturb target genes across a quantitative range of expression levels in cell lines. The evidence supporting their new perturbation approach is compelling, and the computational analyses to better understand dosage response relationships between genes are convincing. The study will be of broad interest to scientists in the fields of functional genomics and biotechnology. However, the evidence supporting the conclusions can be further improved.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  6. Intrahost dynamics, together with genetic and phenotypic effects predict the success of viral mutations

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

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  7. Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

    This article has 4 authors:
    1. Luke J Dillard
    2. Gina M Calabrese
    3. Larry D Mesner
    4. Charles R Farber
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study provides a framework for applying single-cell transcriptome data and network analysis from genetically diverse mouse cells to identify novel driver genes underlying the role of genetic loci associated with bone mineral density. The evidence supporting the identification of the driver genes and the conclusion of the paper is convincing. Overall, this approach may be broadly applicable and of interest to researchers investigating the genetics of complex diseases.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  8. De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

    This article has 19 authors:
    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

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  9. Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis

    This article has 17 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  10. Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression

    This article has 4 authors:
    1. Shengze Yao
    2. Yesu Jeon
    3. Barry Kesner
    4. Jeannie T Lee
    This article has been curated by 1 group:
    • 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

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
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