Genomics

Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice

1. Elizaveta V Bashkirova
2. Nell Klimpert
3. Kevin Monahan
4. Christine E Campbell
5. Jason Osinski
6. Longzhi Tan
7. Ira Schieren
8. Ariel Pourmorady
9. Beka Stecky
10. Gilad Barnea
11. Xiaoliang Sunney Xie
12. Ishmail Abdus-Saboor
13. Benjamin M Shykind
14. Bianca J Marlin
15. Richard M Gronostajski
16. Alexander Fleischmann
17. Stavros Lomvardas

• Curated by eLife

  eLife assessment

  This is an important paper that revises the canonical model of how olfactory sensory neurons choose which odor receptor to express. The data presented in the paper are convincing and the model proposed is provocative and likely to enable future work.

Reviewed by eLife

A reference assembly for the legume cover crop hairy vetch (Vicia villosa)

1. Tyson Fuller
2. Derek M. Bickhart
3. Lisa M. Koch
4. Lisa Kissing Kucek
5. Shahjahan Ali
6. Haley Mangelson
7. Maria J. Monteros
8. Timothy Hernandez
9. Timothy P. L. Smith
10. Heathcliffe Riday
11. Michael L. Sullivan

• Curated by GigaByte

  Editors Assessment:

  The hairy vetch Vicia villosa is an annual legume widely used as a cover crop due to its ability to withstand harsh winters. Here a new a 2.03GB reference-quality genome is presented, assembled from PacBio HiFi long-sequence reads and Hi-C scaffolding. After adding some more methodological details and long-terminal repeat (LTR) assembly index (LAI) analysis the assembly quality and metrics look quite convincing as a chromosome-scale assembly. This resource hopefully providing the foundation for a genetic improvement program for this important cover crop and forage species.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

1. Andrew J. C. Russell
2. Jackson A. Weir
3. Naeem M. Nadaf
4. Matthew Shabet
5. Vipin Kumar
6. Sandeep Kambhampati
7. Ruth Raichur
8. Giovanni J. Marrero
9. Sophia Liu
10. Karol S. Balderrama
11. Charles R. Vanderburg
12. Vignesh Shanmugam
13. Luyi Tian
14. Catherine J. Wu
15. Charles H. Yoon
16. Evan Z. Macosko
17. Fei Chen

Reviewed by PREreview

DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes

1. Akihiro Kuno
2. Yoshihisa Ikeda
3. Shinya Ayabe
4. Kanako Kato
5. Kotaro Sakamoto
6. Sayaka R. Suzuki
7. Kento Morimoto
8. Arata Wakimoto
9. Natsuki Mikami
10. Miyuki Ishida
11. Natsumi Iki
12. Yuko Hamada
13. Megumi Takemura
14. Yoko Daitoku
15. Yoko Tanimoto
16. Tra Thi Huong Dinh
17. Kazuya Murata
18. Michito Hamada
19. Masafumi Muratani
20. Atsushi Yoshiki
21. Fumihiro Sugiyama
22. Satoru Takahashi
23. Seiya Mizuno

Reviewed by Review Commons

The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer

1. Johannes Engelken
2. Matthias Altmeyer
3. Renty B. Franklin

Reviewed by PREreview

Regulation of nuclear transcription by mitochondrial RNA in endothelial cells

1. Kiran Sriram
2. Zhijie Qi
3. Dongqiang Yuan
4. Naseeb Kaur Malhi
5. Xuejing Liu
6. Riccardo Calandrelli
7. Yingjun Luo
8. Alonso Tapia
9. Shengyan Jin
10. Ji Shi
11. Martha Salas
12. Runrui Dang
13. Brian Armstrong
14. Saul J Priceman
15. Ping H Wang
16. Jiayu Liao
17. Rama Natarajan
18. Sheng Zhong
19. Zhen Bouman Chen

• Curated by eLife

  eLife assessment

  This work is fundamental in providing compelling evidence of mitochondria-encoded RNAs playing a role in controlling nuclear gene expression. How mitochondria and the nucleus communicates is an important but yet not well-appreciated area of biology. Using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by this team, the authors found that mitochondria-encoded RNAs play an unexpected role in regulating nuclear gene expressions in endothelial cells and intriguingly, depletion or overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and supported by experimental confirmation, bulk-RNA-seq, and snRNA and scRNA-seq data and will be of interest to the field studying RNA regulation, gene expression and cell biology.

Reviewed by eLife

Exploring the genetic architecture of ecophysiological traits in microbial ecology using statistical analysis of the properties of protein sequences: application to the glycogen accumulating organism (GAO) phenotype

1. Rohan B. H. Williams
2. Irina Bessarab
3. Michael J. Wise
4. Krithika Arumugam

Reviewed by Arcadia Science

Parallel gene size and isoform expansion of ancient neuronal genes

1. Matthew J. McCoy
2. Andrew Z. Fire

Reviewed by preLights

Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis

1. Jun Hu
2. Zhe Zhang
3. Sai Xiao
4. Yalei Cao
5. Yinghong Chen
6. Jiaming Weng
7. Hui Jiang
8. Wei Li
9. Jia-Yu Chen
10. Chao Liu

• Curated by eLife

  eLife assessment

  This study provides important information on the biogenesis of eccDNAs during spermatogenesis. The data presented are solid and supportive of the concussion that eccDNAs in spermatogenic cells are not derived from miotic recombination hotspots but rather represent oligonucleosomal DNA fragments from apoptotic male germ cells, whose ends are ligated through microhomology-mediated end-joining. This work is of interest to researchers working on germ cell biology and cancer biology.

Reviewed by eLife

A Database of Restriction Maps to Expand the Utility of Bacterial Artificial Chromosomes

1. Eamon Winden
2. Alejandro Vasquez-Echeverri
3. Susana Calle-Casteneda
4. Yumin Lian
5. Juan Pablo Hernández-Ortiz
6. David C. Schwartz

• Curated by GigaByte

  **Editors Assessment: **

  While Bacterial Artificial Chromosomes libraries were once a key resource for building the human genome project over time they have been rendered relatively obsolete by long-read technologies. In the era of CRISPR-Cas systems pairing this data with one of the many guide-RNA libraries to find targets for manipulation with CRISPR tools is bringing back BACs advantages for genomics. With this in mind the authors have developed a BAC restriction map database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of available restriction enzymes. Alongside a set of Python functions to reconstruct the database and more easily access it (which were debugged and had improved documentation added during review). The presented data should be valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte