Genomics

Machine learning sequence prioritization for cell type-specific enhancer design

1. Alyssa J Lawler
2. Easwaran Ramamurthy
3. Ashley R Brown
4. Naomi Shin
5. Yeonju Kim
6. Noelle Toong
7. Irene M Kaplow
8. Morgan Wirthlin
9. Xiaoyu Zhang
10. BaDoi N Phan
11. Grant A Fox
12. Kirsten Wade
13. Jing He
14. Bilge Esin Ozturk
15. Leah C Byrne
16. William R Stauffer
17. Kenneth N Fish
18. Andreas R Pfenning

• Curated by eLife

  Evaluation Summary:

  This manuscript describes an exciting new approach for tagging and isolation of unique neuronal subpopulations, which has traditionally been challenging without the incorporation of expensive and time consuming transgenic animal colonies. While the manuscript highlights a specific test case of this technology with neurons expressing Parvalbumin, in theory this method could be applied to any neuronal or even non-neuronal cell type. Further, this approach could be applied to other model organisms for which transgenic technologies are limited, thereby facilitating research in other species.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Cohesin-dependence of neuronal gene expression relates to chromatin loop length

1. Lesly Calderon
2. Felix D Weiss
3. Jonathan A Beagan
4. Marta S Oliveira
5. Radina Georgieva
6. Yi-Fang Wang
7. Thomas S Carroll
8. Gopuraja Dharmalingam
9. Wanfeng Gong
10. Kyoko Tossell
11. Vincenzo de Paola
12. Chad Whilding
13. Mark A Ungless
14. Amanda G Fisher
15. Jennifer E Phillips-Cremins
16. Matthias Merkenschlager

• Curated by eLife

  Evaluation Summary:

  Neurons use activity-responsive gene programs to shape cell specific identity and respond appropriately to environmental stimuli. By combining elegant protein degradation and cell-specific knockout approaches with transcriptional profiling and chromatin structure analysis, this manuscript delineates the contributions of cohesin (a key protein responsible for genome structure and organization), in activity-dependent gene expression programs and stimulus-dependent chromatin reorganization. These results demonstrate that cohesin is required for full expression of key genes required for the maturation and activation of cortical excitatory neurons, and reveal a tight correlation between cohesin effects and the genomic distance of higher order chromatin loops.

  (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

Parent-of-origin effects propagate through networks to shape metabolic traits

1. Juan F Macias-Velasco
2. Celine L St Pierre
3. Jessica P Wayhart
4. Li Yin
5. Larry Spears
6. Mario A Miranda
7. Caryn Carson
8. Katsuhiko Funai
9. James M Cheverud
10. Clay F Semenkovich
11. Heather A Lawson

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to scientists studying metabolism and those interested in the evolution of genomic imprinting. The authors show how parent-of-origin effects in crosses between inbred strains of mice can arise from epistasis between imprinted and unimprinted loci. They consider scenarios for the interactions of imprinted and unimprinted genes in adipocytes.

  (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

Epigenetic machinery is functionally conserved in cephalopods

1. Filippo Macchi
2. Eric Edsinger
3. Kirsten C. Sadler

Reviewed by Review Commons

Dictionary learning for integrative, multimodal and scalable single-cell analysis

1. Yuhan Hao
2. Tim Stuart
3. Madeline H. Kowalski
4. Saket Choudhary
5. Paul Hoffman
6. Austin Hartman
7. Avi Srivastava
8. Gesmira Molla
9. Shaista Madad
10. Carlos Fernandez-Granda
11. Rahul Satija

Reviewed by ScreenIT

Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells

1. Samantha M. Barnada
2. Andrew Isopi
3. Daniela Tejada-Martinez
4. Clément Goubert
5. Sruti Patoori
6. Luca Pagliaroli
7. Mason Tracewell
8. Marco Trizzino

Reviewed by Review Commons

Confirming Multiplex Q-PCR Use in COVID-19 with Next Generation Sequencing: Strategies for Epidemiological Advantage

1. Rob E. Carpenter
2. Vaibhav Tamrakar
3. Harendra Chahar
4. Tyler Vine
5. Rahul Sharma

Reviewed by ScreenIT

Robust and annotation-free analysis of alternative splicing across diverse cell types in mice

1. Gonzalo Benegas
2. Jonathan Fischer
3. Yun S Song

• Curated by eLife

  Evaluation Summary:

  The manuscript presents a potentially interesting new method to study alternative splicing at the single-cell level in the mouse. With further testing and benchmarking, this method would be of interest to researchers working with single-cell data and/or interested in 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

Profiling of the most reliable mutations from sequenced SARS-CoV-2 genomes scattered in Uzbekistan

1. Mirzakamol S. Ayubov
2. Zabardast T. Buriev
3. Mukhammadjon K. Mirzakhmedov
4. Abdurakhmon N. Yusupov
5. Dilshod E. Usmanov
6. Shukhrat E. Shermatov
7. Khurshida A. Ubaydullaeva
8. Ibrokhim Y. Abdurakhmonov

Reviewed by ScreenIT

A trans- acting long non-coding RNA represses flowering in Arabidopsis

1. Yu Jin
2. Maxim Ivanov
3. Anna Nelson Dittrich
4. Andrew D. L. Nelson
5. Sebastian Marquardt

Reviewed by Review Commons