Molecular Biology

In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles

1. Zahra Seraj
2. Ximena Zottig
3. Chun-Ying Huang
4. Anna B Loveland
5. Stephen Diggs
6. Emily Sholi
7. Nikolaus Grigorieff
8. Andrei A Korostelev

• Curated by eLife

  eLife Assessment

  In this important work, it is demonstrated that certain high-resolution cryo-EM structures can be obtained by using concentrated cell extracts without purification. The compelling results with the mammalian ribosomes demonstrate the utility of this approach for this molecule and complexes with elongation factor 2. Moreover, this work also demonstrates the utility of 2D template matching for particle picking for structure determination by single-particle averaging pipelines.

Reviewed by eLife

EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology

1. Alan Monziani
2. Juan Pablo Unfried
3. Todor Cvetanovic
4. Igor Ulitsky

• Curated by eLife

  eLife Assessment

  This paper provides important findings towards understanding the role of the lncRNA EPB41L4A-AS1 in a human cell line. The data is generally convincing, supported by extensive and clever integrative analysis. The work provides insights into how this lncRNA regulates gene expression via complex mechanisms; however the biological relevance awaits validation in other models.

Reviewed by eLife

FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

1. Ananya Palo
2. Talina Mohapatra
3. Anamika Singh
4. Shithij Thalakkat
5. Suryasikha Mohanty
6. Rajeeb Kumar Swain
7. Manjusha Dixit

• Curated by eLife

  eLife Assessment

  This useful study by Palo et al proposes that FRG1 functions as a negative regulator of Nonsense-Mediated mRNA decay (NMD) by associating with the exon junction complex (EJC) and destabilizing UPF1 independently of DUX4. The authors present solid evidence to dissect the relationship between FRG1 and DUX4 in NMD. However, the evidence to support the claim that FRG1 is a component of the EJC or the NMD machinery is incomplete.

Reviewed by eLife

Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

1. Gabriela Giordano
2. Robin Buratowski
3. Célia Jeronimo
4. Christian Poitras
5. François Robert
6. Stephen Buratowski

• Curated by eLife

  eLife Assessment

  This important work demonstrates the role of physically linking the core and CTD kinase modules of TFIIH via separate domains of subunit Tfb3 in confining RNA Polymerase II Serine 5 CTD phosphorylation to promoter regions of transcribed genes in budding yeast. The main findings, resulting from analyses of viable Tfb3 mutants in which the linkage between TFIIH core and kinase modules has been severed, are supported by solid evidence from in vitro and in vivo experiments. There is an intriguing possibility that the Tfb3-mediated connection between core and kinase modules of TFIIH is an evolutionary addition to an ancestral state of physically unconnected enzymes, which could be examined more rigorously with additional evolutionary analyses.

Reviewed by eLife

Impacts of DNA Methylation on H2A.Z Deposition and Nucleosome Stability

1. Rochelle M Shih
2. Yasuhiro Arimura
3. Hide A Konishi
4. Hironori Funabiki

• Curated by eLife

  eLife Assessment

  This study provides valuable mechanistic insight into the mutually exclusive distributions of the histone variant H2A.Z and DNA methylation by testing two hypotheses: (i) that DNA methylation destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin remodelling complexes. Through a series of well-designed and carefully executed experiments, findings are presented in support of both hypotheses. However, the evidence in support of either hypothesis is incomplete, so that the proposed mechanisms underlying the enrichment of H2A.Z on unmethylated DNA remain somewhat speculative.

Reviewed by eLife

Specialization of ubiquitin ligases to distinct nucleic acid sensors

1. Ibrahim Syed
2. Sheng Chen
3. David J. Peeler
4. Paul F. McKay
5. Marco A. Briones-Orta
6. Jennifer A. Bohn
7. Robin J. Shattock
8. Daniel Gonçalves-Carneiro

Reviewed by Review Commons

The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements

1. Andria Koulle
2. Oluwaseun Ogundele
3. Devina Shah
4. India Baker
5. Maya Lopez
6. David Lando
7. Nicola Reynolds
8. Ramy Ragheb
9. Ernest D Laue
10. Brian Hendrich

• Curated by eLife

  eLife Assessment

  This work offers important insights into the protein CHD4's function in chromatin remodeling and gene regulation in embryonic stem cells, supported by extensive biochemical, genomic, and imaging data. The use of an inducible degron system allows precise functional analysis, and the datasets generated represent a key resource for the field. The revised study offers compelling evidence and makes a significant contribution to understanding CHD4's role in epigenetic regulation. This work will be of interest to the epigenetics and stem biology fields.

Reviewed by eLife

A novel high-throughput single-cell DNA sequencing method reveals hidden genomic heterogeneity in the unicellular eukaryote Leishmania

1. Gabriel H Negreira
2. Pieter Monsieurs
3. Jean-Claude Dujardin
4. Malgorzata A Domagalska

• Curated by eLife

  eLife Assessment

  This important study, which tackles the challenge of analyzing genome integrity and instability in unicellular pathogens by introducing a novel single-cell genomics approach, presents compelling evidence that this new tool outperforms standard whole-genome amplification techniques. While thorough and rigorous, the work's impact would increase by providing scripts and data, as well as a description of the biological relevance that would make this method more appealing to the broad community studying genetic heterogeneity in diverse organisms.

Reviewed by eLife

HP1β and H3K9me3 Regulate Olfactory Receptor Choice and Transcriptional Identity

1. Martín Escamilla-del-Arenal
2. Rachel Duffié
3. Hani Shayya
4. Valentina Loconte
5. Axel Ekman
6. Lena Annika Street
7. Adan Horta
8. Daniele Canzio
9. Kevin Monahan
10. Carolyn Larabell
11. Marko Jovanovic
12. Stavros Lomvardas

Reviewed by PREreview

Translational response to mitochondrial stresses is orchestrated by tRNA modifications

1. Sherif Rashad
2. Shadi Al-Mesitef
3. Abdulrahman Mousa
4. Yuan Zhou
5. Daisuke Ando
6. Guangxin Sun
7. Tomoko Fukuuchi
8. Yuko Iwasaki
9. Jingdong Xiang
10. Shane R Byrne
11. Jingjing Sun
12. Masamitsu Maekawa
13. Daisuke Saigusa
14. Thomas J Begley
15. Peter C Dedon
16. Kuniyasu Niizuma

Reviewed by PREreview