Genomics

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

Non-linear transcriptional responses to gradual modulation of transcription factor dosage

1. Júlia Domingo
2. Mariia Minaeva
3. John A Morris
4. Sam Ghatan
5. Marcello Ziosi
6. Neville E Sanjana
7. Tuuli Lappalainen

• 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

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

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

1. Luke J Dillard
2. Gina M Calabrese
3. Larry D Mesner
4. Charles R Farber

• 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

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

Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity

1. Khund Sayeed
2. Sreeja Parameswaran
3. Matthew J. Beucler
4. Lee E. Edsall
5. Andrew VonHandorf
6. Audrey Crowther
7. Omer Donmez
8. Matthew Hass
9. Scott Richards
10. Carmy Forney
11. Hayley K. Hesse
12. Sydney H. Jones
13. Katelyn A. Dunn
14. Jay Wright
15. Merrin Man Long Leong
16. Laura A. Murray-Nerger
17. Vijay K. Yechoor
18. Ben E. Gewurz
19. Kenneth M. Kaufman
20. John B. Harley
21. Bo Zhao
22. William E. Miller
23. Leah C. Kottyan
24. Matthew T. Weirauch

• Curated by eLife

  eLife Assessment

  This interesting study presents valuable information on how human cytomegalovirus (HCMV) infection disrupts the activity of the TEAD1 transcription factor, leading to widespread chromatin alterations. However, the precise mechanisms underlying this disruption and the extent to which these chromatin changes influence HCMV replication remain unclear. The study is supported by solid evidence, which would be made stronger by including functional analyses. This work will be of interest to virology, chromosome biology and transcriptional co-regulation fields.

Reviewed by eLife