Genomics

Evolution of binding preferences among whole-genome duplicated transcription factors

1. Tamar Gera
2. Felix Jonas
3. Roye More
4. Naama Barkai

• Curated by eLife

  Evaluation Summary:

  The authors applied original approaches to explore the evolution of transcription factors following duplication and subsequent divergence among duplicates. This paper should generate broad interest among evolutionary biologists as it addresses the long-standing question of how newly evolved transcription factors acquire new binding specificity. By combining genome editing with high-precision DNA binding profiling, this study provides extensive in vivo data showing how the binding profiles of transcription factor paralog pairs diverge.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

1. Jayashree Kumar
2. Lela Lackey
3. Justin M Waldern
4. Abhishek Dey
5. Anthony M Mustoe
6. Kevin M Weeks
7. David H Mathews
8. Alain Laederach

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest to biologists who study RNA structure-function relationships in a broad range of systems, splicing researchers, and RNA structure bioinformaticians. An integrative analysis of RNA structure probing, model-based RNA folding energetics, cryo-EM data, and protein binding sequence motifs serves as the basis for a comprehensive, accurate, and robust framework for predictive models of splicing dynamics in a well-studied system. The modeling is leveraged by in silico mutagenesis that reveals novel insights into the mechanisms and tradeoffs that underlie the impact of disease-associated mutations on alternative splicing.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant

1. Kanika Bansal
2. Sanjeet Kumar

Reviewed by ScreenIT

Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies

1. Masaud Shah
2. Hyun Goo Woo

Reviewed by ScreenIT

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

1. Dawei Cai
2. Siqi Zhu
3. Mian Gong
4. Naifan Zhang
5. Jia Wen
6. Qiyao Liang
7. Weilu Sun
8. Xinyue Shao
9. Yaqi Guo
10. Yudong Cai
11. Zhuqing Zheng
12. Wei Zhang
13. Songmei Hu
14. Xiaoyang Wang
15. He Tian
16. Youqian Li
17. Wei Liu
18. Miaomiao Yang
19. Jian Yang
20. Duo Wu
21. Ludovic Orlando
22. Yu Jiang

• Curated by eLife

  Evaluation Summary:

  This paper represents multiple milestones in our understanding of the evolution and extinction of Pleistocene equids, including revising the timing of extinction and clarifying the evolutionary history of Equus (Sussemionus) ovodovi. The discovery of the late persistence of non-caballine equid taxa in northern China until deep into the late Holocene is particularly important. This finding will be of broad interest to the paleontology, paleoecology, archaeology, paleogenomic communities and should stimulate important future research into equid extinction processes.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest

1. Praveen Anand
2. Patrick J. Lenehan
3. Michiel Niesen
4. Unice Yoo
5. Dhruti Patwardhan
6. Marcelo Montorzi
7. A. J. Venkatakrishnan
8. Venky Soundararajan

Reviewed by ScreenIT

Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

1. Camilla Ugolini
2. Logan Mulroney
3. Adrien Leger
4. Matteo Castelli
5. Elena Criscuolo
6. Maia Kavanagh Williamson
7. Andrew D Davidson
8. Abdulaziz Almuqrin
9. Roberto Giambruno
10. Miten Jain
11. Gianmaria Frigè
12. Hugh Olsen
13. George Tzertzinis
14. Ira Schildkraut
15. Madalee G Wulf
16. Ivan R Corrêa
17. Laurence Ettwiller
18. Nicola Clementi
19. Massimo Clementi
20. Nicasio Mancini
21. Ewan Birney
22. Mark Akeson
23. Francesco Nicassio
24. David A Matthews
25. Tommaso Leonardi

Reviewed by ScreenIT

Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells

1. Alejandro La Greca
2. Nicolás Bellora
3. François Le Dily
4. Rodrigo Jara
5. Ana Silvina Nacht
6. Javier Quilez Oliete
7. José Luis Villanueva
8. Enrique Vidal
9. Gabriela Merino
10. Cristóbal Fresno
11. Inti Tarifa Reischle
12. Griselda Vallejo
13. Guillermo Vicent
14. Elmer Fernández
15. Miguel Beato
16. Patricia Saragüeta

• Curated by eLife

  Evaluation Summary:

  All three reviewers are in agreement that the study is of potential interest in the field of ER/PR signaling and endometrial cancer and that it contains significant amount of genomic data. However, functional data linking PAX2 to the PR/ER pathway are lacking, and the study is limited to a single model cell line and thus has a relatively narrow scope. There is also a concern that ChIP-seq data appear to be from a single, unreplicated experiment.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

1. Ching-Ho Chang
2. Lauren E Gregory
3. Kathleen E Gordon
4. Colin D Meiklejohn
5. Amanda M Larracuente

Reviewed by Review Commons

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

1. José L. Oliver
2. Pedro Bernaola-Galván
3. Francisco Perfectti
4. Cristina Gómez-Martín
5. Silvia Castiglione
6. Pasquale Raia
7. Miguel Verdú
8. Andrés Moya

Reviewed by ScreenIT