Genomics

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.

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.

Editors Assessment:

This Data Release paper presents the genome of the whippet breed of dog. Demonstrating a streamlined laboratory and bioinformatics workflows with PacBio HiFi long-read whole-genome sequencing that enables the generation of a high-quality reference genome within one week. The genome study being a collaboration between an academic biodiversity institute and a medical diagnostic company. The presented method of working and workflow providing examples that can be used for a wide range of future human and non-human genome projects. The final is 2.47 Gbp assembly being of high quality - with a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. This reference being scaffolded into 39 chromosome-length scaffolds and the annotation resulting in 28,383 transcripts. The results also looked at the Myostatin gene which can be used for breeding purposes, as these heterozygous animals can have an advantage in dog races. The reviewers making the authors clarify this part a little better with additional results. Overall this study demonstrating how rapidly animal genome research can be carried out through close and streamlined time management and collaboration.

This evaluation refers to version 1 of the preprint