Genomics

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

Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps

1. Cedric C.S. Tan
2. Lucy van Dorp
3. Francois Balloux

Reviewed by Rapid Reviews Infectious Diseases

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

Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions

1. Weiting Zhang
2. Karl Petri
3. Junyan Ma
4. Hyunho Lee
5. Chia-Lun Tsai
6. J Keith Joung
7. Jing-Ruey Joanna Yeh

• Curated by eLife

  eLife assessment

  This useful paper reports on two simple methods for improving the efficiency of prime editing, a prominent gene editing technique. In combination with published modifications, the strategies described in this study may lead to significant improvements in editing efficiencies. The data are solid, and the methods will be of broad interest to anyone using gene editing.

Reviewed by eLife

The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

1. Christine E. Schnitzler
2. E. Sally Chang
3. Justin Waletich
4. Gonzalo Quiroga-Artigas
5. Wai Yee Wong
6. Anh-Dao Nguyen
7. Sofia N. Barreira
8. Liam B. Doonan
9. Paul Gonzalez
10. Sergey Koren
11. James M. Gahan
12. Steven M. Sanders
13. Brian Bradshaw
14. Timothy Q. DuBuc
15. Febrimarsa
16. Danielle de Jong
17. Eric P. Nawrocki
18. Alexandra Larson
19. Samantha Klasfeld
20. Sebastian G. Gornik
21. R. Travis Moreland
22. Tyra G. Wolfsberg
23. Adam M. Phillippy
24. James C. Mullikin
25. Oleg Simakov
26. Paulyn Cartwright
27. Matthew Nicotra
28. Uri Frank
29. Andreas D. Baxevanis

Reviewed by preLights

Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids

1. Anneri Lötter
2. Tuan A Duong
3. Julia Candotti
4. Eshchar Mizrachi
5. Jill L Wegrzyn
6. Alexander A Myburg

Reviewed by GigaScience

SGLT2 transcriptomic expression atlas supports a kidney-centric role for empagliflozin’s benefits in heart failure

1. Omar Mourad
2. Shabana Vohra
3. Sara S Nunes

Reviewed by PREreview