Genomics

Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans

1. Hailey Sounart
2. Enikő Lázár
3. Yuvarani Masarapu
4. Jian Wu
5. Tibor Várkonyi
6. Tibor Glasz
7. András Kiss
8. Erik Borgström
9. Andrew Hill
10. Aleksandra Jurek
11. Anezka Niesnerová
12. Henrik Druid
13. Olaf Bergmann
14. Stefania Giacomello

Reviewed by ScreenIT

The human FLT1 regulatory element directs vascular expression and modulates angiogenesis pathways in vitro and in vivo

1. Julian Stolper
2. Holly K. Voges
3. Michael See
4. Neda Rahmani Mehdiabadi
5. Gulrez Chahal
6. Mark Drvodelic
7. Michael Eichenlaub
8. Tanya Labonne
9. Benjamin G. Schultz
10. Alejandro Hidalgo
11. Lazaro Centanin
12. Jochen Wittbrodt
13. Enzo R. Porrello
14. David A. Elliott
15. Mirana Ramialison

• Curated by eLife

  Evaluation Summary:

  This paper aims to identify enhancers controlling human cardiovascular development. The authors identified a set of highly conserved regulatory elements bioinformatically and tested one of these in vivo, in medaka, and in vitro, in hESC differentiated into endothelial cells. They find deletion of this enhancer had no significant effect on the expression of FLT1 mRNA in the human cell line or on the formation of tube formation. However, deletion of the orthologous enhancer in medaka showed phenotypic effects in blood clot formation. Together, the data provide insights into the function of an enhancer controlling FLT1. This manuscript will be of interest to scientists interested in gene regulation, vascular biology and developmental biology.

  (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

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