Genomics

Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis

1. Ohad Yogev
2. Omer Weissbrod
3. Giorgia Battistoni
4. Dario Bressan
5. Adi Naamti
6. Ilaria Falciatori
7. Ahmet C. Berkyurek
8. Roni Rasnic
9. Myra Hosmillo
10. Shaul Ilan
11. Iris Grossman
12. Lauren McCormick
13. Christopher C. Honeycutt
14. Timothy Johnston
15. Matthew Gagne
16. Daniel C. Douek
17. Ian Goodfellow
18. Gregory J. Hannon
19. Yaniv Erlich

Reviewed by Rapid Reviews Infectious Diseases, ScreenIT

Independent acquisition of short insertions at the RIR1 site in the spike N‐terminal domain of the SARS‐CoV‐2 BA.2 lineage

1. Samuele Greco
2. Marco Gerdol

Reviewed by ScreenIT

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation

1. Iromi Wanigasuriya
2. Sarah A. Kinkel
3. Tamara Beck
4. Ellise A. Roper
5. Kelsey Breslin
6. Heather J. Lee
7. Andrew Keniry
8. Matthew E. Ritchie
9. Marnie E. Blewitt
10. Quentin Gouil

• Curated by eLife

  Evaluation Summary:

  This study assess the role of SMCHD1 provided by the oocyte at fertilization in the regulation of Xist expression in the embryo. They also provide preliminary analysis of the downstream effects of faulty Xist expression, on X chromosome silencing. This work has implications in epigenetics and embryonic development and aims at an audience interested in gene dosage regulation in mammals. Although of potential interest, some further analytical and experimental work is needed to understand how SMHCD1 works on the early stages of X inactivation.

  (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

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

1. Weihong Qi
2. Yi-Wen Lim
3. Andrea Patrignani
4. Pascal Schläpfer
5. Anna Bratus-Neuenschwander
6. Simon Grüter
7. Christelle Chanez
8. Nathalie Rodde
9. Elisa Prat
10. Sonia Vautrin
11. Margaux-Alison Fustier
12. Diogo Pratas
13. Ralph Schlapbach
14. Wilhelm Gruissem

Reviewed by GigaScience

Evolution of Delta variant by non-Spike signature co-appearing mutations: trailblazer of COVID-19 disease outcome

1. Anindita Banerjee
2. Anup Mazumder
3. Jayita Roy
4. Agniva Majumdar
5. Ananya Chatterjee
6. Nidhan K Biswas
7. Mamta Chawla Sarkar
8. Arindam Maitra
9. Shanta Dutta
10. Saumitra Das

Reviewed by ScreenIT

Characterization of sequence determinants of enhancer function using natural genetic variation

1. Marty G Yang
2. Emi Ling
3. Christopher J Cowley
4. Michael E Greenberg
5. Thomas Vierbuchen

• Curated by eLife

  Evaluation Summary:

  This manuscript describes a useful dataset for those interested in regulatory variation. The large scale of variants surveyed offers the potential to look for dependencies between nearby TF binding events at the same accessible site, and will likely be useful to those interested in dissecting sequence determinants of transcription-factor binding genome-wide.

  (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

Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

1. Yang Liu
2. Marcello DiStasio
3. Graham Su
4. Hiromitsu Asashima
5. Archibald Enninful
6. Xiaoyu Qin
7. Yanxiang Deng
8. Pino Bordignon
9. Marco Cassano
10. Mary Tomayko
11. Mina Xu
12. Stephanie Halene
13. Joseph E. Craft
14. David Hafler
15. Rong Fan

Reviewed by ScreenIT

Genetic surveillance of SARS-CoV-2 M ^pro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

1. Jonathan T. Lee
2. Qingyi Yang
3. Alexey Gribenko
4. B. Scott Perrin
5. Yuao Zhu
6. Rhonda Cardin
7. Paul A. Liberator
8. Annaliesa S. Anderson
9. Li Hao

Reviewed by ScreenIT

Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

1. Le Xiong
2. Erik A Tolen
3. Jinmi Choi
4. Sergiy Velychko
5. Livia Caizzi
6. Taras Velychko
7. Kenjiro Adachi
8. Caitlin M MacCarthy
9. Michael Lidschreiber
10. Patrick Cramer
11. Hans R Schöler

• Curated by eLife

  Evaluation Summary:

  The manuscript by Xiong et al provides high resolution kinetic information on transcriptional events and enhancer activity after loss of Oct4. The authors conclude that Oct4 mainly acts as an activator whereas Sox2 maintains chromatin accessibility. These results are of interest for stem cell biologists and developmental biologists.

  (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 #3 agreed to share their name with the authors.

Reviewed by eLife

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

1. Derek M. Bickhart
2. Lisa M. Koch
3. Timothy P. L. Smith
4. Heathcliffe Riday
5. Michael L. Sullivan

Reviewed by GigaByte