Genomics

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

Is tumor mutational burden predictive of response to immunotherapy?

1. Carino Gurjao
2. Dina Tsukrov
3. Maxim Imakaev
4. Lovelace J Luquette
5. Leonid A Mirny

• Curated by eLife

  eLife Assessment

  This useful study examines relationships between tumor mutational burden and the response to immunotherapy, using new data sets along with publicly available data sets. The authors conclude that tumor mutational burden cut-offs are unreliable proxies for predicting the response to therapy, underpinned by solid evidence, but with several caveats and assumptions that leave the central question subject to further inquiry. In summary, this is an interesting study that adds to a growing body of work investigating the particular conditions governing the effectiveness of immunotherapy.

Reviewed by eLife

Increased inflammatory signature in myeloid cells of non-small cell lung cancer patients with high clonal hematopoiesis burden

1. Hyungtai Sim
2. Hyun Jung Park
3. Geun-Ho Park
4. Yeon Jeong Kim
5. Woong-Yang Park
6. Se-Hoon Lee
7. Murim Choi

• Curated by eLife

  eLife Assessment

  This valuable article represents a significant body of work that addresses some novel aspects of the biology of lung cancer, the overall influence of CHIP and its impacts on responses to therapy. While a high clonal hematopoiesis (CHIP) burden was previously linked with an inflammatory phenotype in other disease settings, the authors demonstrate with solid evidence that this is also true for lung cancer. CHIP is complex and more data will be required to substantiate more evidence with regard perhaps to specific mutations in certain situations and how this might influence therapy choices.

Reviewed by eLife

Functional characteristics and computational model of abundant hyperactive loci in the human genome

1. Sanjarbek Hudaiberdiev
2. Ivan Ovcharenko

• Curated by eLife

  eLife Assessment

  This valuable study explores the sequence characteristics and conservation of high-occupancy target loci, regions in the human genome such as promoters and enhancers that are bound by a multitude of transcription factors. The computational analyses presented in this study are solid. This study would be a helpful resource for researchers performing ChIP-seq based analyses of transcription factor binding.

Reviewed by eLife

Expression of most retrotransposons in human blood correlates with biological aging

1. Yi-Ting Tsai
2. Nogayhan Seymen
3. I Richard Thompson
4. Xinchen Zou
5. Warisha Mumtaz
6. Sila Gerlevik
7. Ghulam J Mufti
8. Mohammad M Karimi

• Curated by eLife

  eLife Assessment

  The study by Tsai et al. employed multi-omics approaches, including transcriptomic, methylomic, and single-cell RNA-seq, and provided a solid and comprehensive analysis of the correlation between retrotransposable element (RTE) expression and biological aging in human blood. Their findings highlight the differential roles of RTE families, providing valuable insights for understanding the mechanisms of human aging.

Reviewed by eLife