Genomics

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

1. Jie Lin
2. Yujian Wen
3. Ji Tang
4. Xuecong Zhang
5. Huanlin Zhang
6. Hao Zhu

• Curated by eLife

  eLife Assessment

  This valuable study uses tools of population and functional genomics to examine long non-coding RNAs (lncRNAs) in the context of human evolution. Analyses of computationally predicted human-specific lncRNAs and their genomic targets lead to the development of hypotheses regarding the potential roles of these genetic elements in human biology. Compared to previous versions, the conclusions regarding evolutionary acceleration and adaptation have become more solid by more fully taking data and literature on human/chimpanzee genetics and functional genomics into account.

Reviewed by eLife

Nuclear genome profiling of two Mexican orchids of the genus Epidendrum

1. Miguel A. Alcalá-Gaxiola
2. Gerardo A. Salazar
3. Eric Hágsater
4. Mónica A. Flores-Iniestres
5. Lidia I. Cabrera
6. Aldo I. Aviña-Rivera
7. Pedro Mercado-Ruaro
8. Susana Magallon
9. Carolina Granados Mendoza
10. Aleida Núñez-Ruiz
11. Gloria Soldevila
12. Araxi Urrutia
13. Rubi N. Meza-Lázaro

Reviewed by Review Commons

Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites

1. Yatendra Kumar
2. Dipta Sengupta
3. Elias T Friman
4. Robert S Illingworth
5. Manon Soleil
6. Zheng Fan
7. Hua Wang
8. Kristian Helin
9. Matthieu Gerard
10. Wendy A Bickmore

• Curated by eLife

  eLife Assessment

  This fundamentally significant study provides the first genome-wide characterization of H3K115 acetylation and identifies a striking and previously unappreciated association of this globular-domain histone modification with fragile nucleosomes at CpG island promoters, active enhancers, and CTCF binding sites. While the work is largely descriptive and correlative in nature the evidence is compelling. The authors present multiple, orthogonal genomic and biochemical analyses that consistently support their central conclusions.

Reviewed by eLife

Stranded short nascent strand sequencing reveals the topology of DNA replication origins in Trypanosoma brucei

1. Slavica Stanojcic
2. Bridlin Barckmann
3. Pieter Monsieurs
4. Lucien Crobu
5. Simon George
6. Yvon Sterkers

• Curated by eLife

  eLife Assessment

  The authors use sequencing of nascent DNA (DNA linked to an RNA primer, “SNS-Seq”) to localise DNA replication origins in Trypanosoma brucei, so this work will be of interest to those studying either Kinetoplastids or DNA replication. The paper presents the SNS-seq results for only part of the genome, and there are significant discrepancies between the SNS-Seq results and those from other, previously-published results obtained using other origin mapping methods. The reasons for the differences are unknown and from the data available, it is not possible to assess which origin-mapping method is most suitable for origin mapping in T. brucei. Thus at present, the evidence that origins are distributed as the authors claim - and not where previously mapped - is inadequate.

Reviewed by eLife

Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

1. Abdulkadir Elmas
2. Hillary M. Layden
3. Jacob D. Ellis
4. Luke N. Bartlett
5. Xian Zhao
6. Reika Kawabata-Iwakawa
7. Hideru Obinata
8. Scott W. Hiebert
9. Kuan-lin Huang

Reviewed by GigaScience

CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

1. Lanlan Ji
2. An Wang
3. Shreyash Sonthalia
4. Seungmae Seo
5. Daniel Q Naiman
6. Laurent Younes
7. Carlo Colantuoni
8. Donald Geman

• Curated by eLife

  eLife Assessment

  This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

Reviewed by eLife

Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

1. Joyner Cruz
2. William Y Sun
3. Alexandra Verbeke
4. Iswar K Hariharan

• Curated by eLife

  eLife Assessment

  This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to reduce heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila and allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their compelling analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

Reviewed by eLife

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

1. Sarah L.F. Martin
2. Renato La Torre
3. Bram Danneels
4. Ave Tooming-Klunderud
5. Morten Skage
6. Spyridon Kollias
7. Ole Kristian Tørresen
8. Mohsen Falahati Anbaran
9. Elisabeth Stur
10. Kjetill S. Jakobsen
11. Michael D. Martin
12. Torbjørn Ekrem

Reviewed by GigaScience

Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy

1. Koseki J. Kobayashi-Kirschvink
2. Shreya Gaddam
3. Taylor James-Sorenson
4. Emanuelle Grody
5. Johain R. Ounadjela
6. Baoliang Ge
7. Ke Zhang
8. Jeon Woong Kang
9. Ramnik Xavier
10. Peter T. C. So
11. Tommaso Biancalani
12. Jian Shu
13. Aviv Regev

Reviewed by Arcadia Science

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons

1. Alec Barrett
2. Erdem Varol
3. Alexis Weinreb
4. Seth R Taylor
5. Rebecca M McWhirter
6. Cyril Cros
7. Berta Vidal
8. Manasa Basaravaju
9. Abigail Poff
10. John A Tipps
11. Maryam Majeed
12. Chen Wang
13. Emily A Bayer
14. Molly Reilly
15. Eviatar Yemini
16. HaoSheng Sun
17. Oliver Hobert
18. David M Miller
19. Marc Hammarlund

• Curated by eLife

  eLife Assessment

  This paper uses a new computational method that integrates bulk sequencing and single-cell sequencing data to provide refined gene expression datasets for 52 neuron classes in C. elegans. The paper's findings are convincing, presenting an approach that alleviates a key shortcoming of single-cell RNA sequencing. While the datasets have some limitations that the authors acknowledge, the new methodology and refined datasets will be important resources for those interested in understanding how gene expression shapes neuronal morphology and physiology.

Reviewed by eLife