Molecular biology

  • Article
    | Open Access

    Termination of eukaryotic RNA polymerase III (Pol III)-mediated transcription occurs when the polymerase reaches a stretch of four or more deoxythymidine nucleotides (poly-dT) on the non-template strand. Here, the authors present the 3.6 Å cryo-EM structure of a human Pol III pre-termination complex (PTC) that was assembled on a 7 dT-containing DNA template and discuss the mechanism of poly-dT-dependent transcription termination of Pol III.

    • Haifeng Hou
    • , Yan Li
    •  & Yanhui Xu
  • Article
    | Open Access

    NPH3 is required for auxin-dependent plant phototropism. Here Reuter et al. show that NPH3 is a plasma membrane-bound phospholipid-binding protein and that in response to blue light, NPH3 is phosphorylated and associates with 14-3-3 proteins which leads to dissociation from the plasma membrane.

    • Lea Reuter
    • , Tanja Schmidt
    •  & Claudia Oecking
  • Article
    | Open Access

    Here the authors identify PHF3 SPOC domain as a reader of the phosphorylated RNA polymerase II (Pol II) C-terminal domain. They show that PHF3 clusters with Pol II complexes in cells, drives phase separation of Pol II in vitro, and regulates neuronal gene expression and neuronal differentiation.

    • Lisa-Marie Appel
    • , Vedran Franke
    •  & Dea Slade
  • Article
    | Open Access

    Heterologous expression of recombinant proteins often results in misfolding, aggregation and degradation. Here, we show an in vivo dual-biosensor system that simultaneously assesses protein translation and protein folding, thereby enabling rapid screening of expression strains as well as mutant libraries.

    • Ariane Zutz
    • , Louise Hamborg
    •  & Alex Toftgaard Nielsen
  • Article
    | Open Access

    Endogenous retroviruses (ERVs) compose a significant portion of mammalian genomes; however, how ERVs are regulated is not well known. Here the authors performed a genome-wide sgRNA screen to identify Morc3 as a mediator of ERV silencing. They show Morc3 associates with the H3.3 chaperone Daxx, and that loss of Morc3 leads to reduced H3.3 at ERVs.

    • Sophia Groh
    • , Anna Viktoria Milton
    •  & Gunnar Schotta
  • Article
    | Open Access

    Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.

    • Zhihua Kang
    • , Pan Fu
    •  & Bing Xia
  • Article
    | Open Access

    Both ubiquitin and NEDD8 can be phosphorylated, but the biological role of NEDD8 phosphorylation remains unclear. Here, the authors identify similarities and differences of ubiquitin and NEDD8 phosphorylation, showing that phosphorylated NEDD8 has a distinct interactome and regulates HSP70 proteins.

    • Katrin Stuber
    • , Tobias Schneider
    •  & Martin Scheffner
  • Article
    | Open Access

    Exercise induces structural and functional adaptations in skeletal muscle that involve transcriptomic remodeling, including of miRNA expression. Here the authors examine the expression of miRNAs in human muscle following exercise training and investigate the functions of miR-19b-3p on glucose metabolism in cells and mouse muscle.

    • Julie Massart
    • , Rasmus J. O. Sjögren
    •  & Anna Krook
  • Article
    | Open Access

    A localized Wnt3a signal has been shown to induce asymmetric division of mouse embryonic stem cells. Here the authors develop SET-seq, an approach to jointly profile epigenome and transcriptome in the same single cell and use it to provide mechanistic insights into the gene regulatory programs for maintaining and resetting stem cell fate during differentiation.

    • Zhongxing Sun
    • , Yin Tang
    •  & Dong Fang
  • Article
    | Open Access

    Movement of the ribosome along an mRNA requires the universally-conserved translocase (EF-G in bacteria) that couples GTP hydrolysis to directed movement. Here the authors use time-resolved Cryo-EM to visualize the GTPase-powered step on native translocating ribosomes and capture key translocation intermediates.

    • Valentyn Petrychenko
    • , Bee-Zen Peng
    •  & Niels Fischer
  • Article
    | Open Access

    Application of adenine base editors (ABE) has been precluded by low activity. Here the authors show the generation of a human cell based ABE directional screening system and identification of ABE variant (NG-ABEmax-KR) exhibiting a significant increase in activity for human and mouse genome manipulation.

    • Junhao Fu
    • , Qing Li
    •  & Feng Gu
  • Article
    | Open Access

    During meiosis, chromosomes undergo dramatic changes in morphology and intranuclear positioning. Here the authors mapped the 3D genome architecture throughout mouse spermatogenesis by Hi-C of sorted cells to reveal the contributions of transcriptional activity and mechanical force in modulating homolog alignment and recombination.

    • Wu Zuo
    • , Guangming Chen
    •  & Qian Bian
  • Article
    | Open Access

    ADP-ribosylation is regulated by HPF1 and ARH3, but the cellular target spectrum of these enzymes is not fully understood. Here, the authors use quantitative proteomics to define the HPF1- and ARH3-dependent ADP-ribosylome, providing evidence that mono-ADP-ribosylation of serine predominates in cells.

    • Ivo A. Hendriks
    • , Sara C. Buch-Larsen
    •  & Michael L. Nielsen
  • Article
    | Open Access

    RNA polymerase III (Pol III) employs termination-associated reinitiation-recycling to express high amounts of tRNAs, which involves the essential C11 subunit. Here the authors determine the functions of various C11 domains, finding that the N-terminal domain (NTD) stimulates termination, reinitiation-recycling requires an NTD-linker, and the C-terminal domain stimulates RNA 3′-cleavage.

    • Saurabh Mishra
    • , Shaina H. Hasan
    •  & Richard J. Maraia
  • Article
    | Open Access

    The molecular mechanism by which clock neurons transmit timing information to non-clock neurons is poorly understood. Here, the authors show that circadian clocks drive rhythmic expression of hundreds of genes in mushroom body neurons and drive calcium rhythms via NF1-cAMP/PKAC1 signalling in Drosophila.

    • Pedro Machado Almeida
    • , Blanca Lago Solis
    •  & Emi Nagoshi
  • Article
    | Open Access

    Gene-regulatory networks are thought to be complex, and yet perturbation of just a few transcription factors (TFs) can have major consequences. Here the authors apply DNA polymer modelling and simulations to predict how 3D genome structure and TF-DNA interactions can give rise to transcriptional regulation operating over broad genomic regions, where small perturbations can have long-reaching effects.

    • C. A. Brackley
    • , N. Gilbert
    •  & D. Marenduzzo
  • Article
    | Open Access

    As corals struggle to survive under climate change, it is crucial to know whether they can withstand increasing seawater temperatures. Using a controlled thermal stress experiment across three divergent coral holobionts, this study examines metatranscriptomic responses to heat stress corresponding to the coral host, photosymbionts and associated microbiota.

    • Viridiana Avila-Magaña
    • , Bishoy Kamel
    •  & Mónica Medina
  • Article
    | Open Access

    The causal relationship between DNA demethylation and gene expression regulation has not yet been fully resolved. Here the authors develop a nuclease-dead Cas9 (dCas9) and gRNA site-specific targeting approach to physically block DNA methylation at specific promoters to cause DNA demethylation in cells and tackle this question.

    • Daniel M. Sapozhnikov
    •  & Moshe Szyf
  • Article
    | Open Access

    Ufmylation is a well-established ubiquitin-like protein modification, but its mechanism is largely unclear. Here, the authors present a crystal structure of the ufmylation-specific E1-E2 complex, revealing differences to the ubiquitination machinery and mechanistic details of the ufmylation process.

    • Manoj Kumar
    • , Prasanth Padala
    •  & Reuven Wiener
  • Article
    | Open Access

    CHARGE syndrome that affects cerebellar development can be caused by haploinsufficiency of the chromatin remodeling enzyme CHD7; however the precise role of CHD7 remains unknown. Here the authors show CHD7 promotes chromatin accessibility and enhancer activity in granule cell precursors and regulates morphogenesis of the cerebellar cortex, where loss of CHD7 triggers cerebellar polymicrogyria.

    • Naveen C. Reddy
    • , Shahriyar P. Majidi
    •  & Harrison W. Gabel
  • Article
    | Open Access

    Single-cell profiling has led to the identification of diverse cell types. Here, the authors generate a harmonized cell atlas of the mouse post-natal spinal cord. They also provide spatial analysis of the distribution of the identified cell types and an open-source cell type classifier.

    • Daniel E. Russ
    • , Ryan B. Patterson Cross
    •  & Ariel J. Levine
  • Article
    | Open Access

    Genetic code expansion strategies are limited to specific codons that can be reassigned to new amino acids. Here the authors show that quadruplet-decoding tRNAs (qtRNAs) can be rapidly discovered and evolved to decode new quadruplet codons, enabling four independent decoding events in a single protein in living cells.

    • Erika A. DeBenedictis
    • , Gavriela D. Carver
    •  & Ahmed H. Badran
  • Article
    | Open Access

    The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.

    • Shalu Jhanwar
    • , Jonas Malkmus
    •  & Rolf Zeller
  • Article
    | Open Access

    A comprehensive analysis of the ocular networks among various tissues is necessary to understand eye physiology in health and disease. Here the authors present a multi-species single-cell transcriptomic atlas consisting of cells of the cornea, iris, ciliary body, neural retina, retinal pigmented epithelium, and choroid.

    • Pradeep Gautam
    • , Kiyofumi Hamashima
    •  & Yuin-Han Loh
  • Article
    | Open Access

    DNA supercoiling can result in underwinding with negative supercoiling or overwinding with positive supercoiling of the DNA double helix. Here the authors reveal insights into the dynamic relationship between DNA supercoiling-induced sequence-dependent disruptions to base pairing, DNA looping, and the shape of the DNA molecule.

    • Jonathan M. Fogg
    • , Allison K. Judge
    •  & Lynn Zechiedrich
  • Article
    | Open Access

    Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.

    • Kanghyun Lee
    • , Thomas Ziegelhoffer
    •  & Elizabeth A. Craig
  • Article
    | Open Access

    While phosphorylation is an essential post-translational modification in eukaryotes only recently the phosphoproteome of prokaryotes has been provided. Here, Schastnaya et al. mutate 52 phosphosites on 23 E. coli enzymes and apply metabolomics to provide evidence for the functional relevance of bacterial phosphorylation events.

    • Evgeniya Schastnaya
    • , Zrinka Raguz Nakic
    •  & Uwe Sauer
  • Article
    | Open Access

    Anaplastic large cell lymphoma (ALCL) is an aggressive T-cell lymphoma often with poor prognosis. To identify genes defining ALCL cell state and dependencies, the authors here characterize ALCL-specific super-enhancers and describe the BATF3/IL-2R−module as a therapeutic opportunity for ALCL.

    • Huan-Chang Liang
    • , Mariantonia Costanza
    •  & Olaf Merkel
  • Article
    | Open Access

    Retinoblastoma is the most frequent intraocular paediatric malignancy whose molecular basis remains poorly understood. Here, the authors perform multi-omic analysis and identify two subtypes; one in a cone differentiated state and one more aggressive showing cone dedifferentiation and expressing neuronal markers.

    • Jing Liu
    • , Daniela Ottaviani
    •  & François Radvanyi
  • Article
    | Open Access

    In Saccharomyces cerevisiae, unchecked proliferation of Ty1 retrotransposons is controlled by the process of copy number control (CNC), which requires the p22/p18 protein, translated from an internal transcript within the Ty1 GAG gene. Here, the authors present the 2.8 Å crystal structure of a minimal p18 from Ty1-Gag that is able to restrict Ty1 transposition and identify two dimer interfaces in p18, whose roles were probed by mutagenesis both in vitro and in vivo. As p22/p18 contains only one of two conserved domains required for retroelement Gag assembly, they propose that p22/p18-Gag interactions block the Ty1 virus-like particle assembly pathway, resulting in defective particles incapable of supporting retrotransposition.

    • Matthew A. Cottee
    • , Sean L. Beckwith
    •  & Ian A. Taylor
  • Article
    | Open Access

    KLF4, OCT4, SOX2 and MYC cooperate to reorganize chromatin during somatic cell reprogramming. Here the authors show that KLF4 forms a liquid-like biomolecular condensate that recruits OCT4 and SOX2, and that condensation of the isolated KLF4 DNA binding domain with DNA is enhanced by CpG methylation

    • Rajesh Sharma
    • , Kyoung-Jae Choi
    •  & Josephine C. Ferreon
  • Article
    | Open Access

    The mechanisms that allow cancer cells to survive with monosomies are poorly understood. Here the authors analyse p53-deficient monosomic cell lines using transcriptomics and proteomics, and find that impaired ribosome biogenesis and p53 downregulation are associated with sustained monosomies.

    • Narendra Kumar Chunduri
    • , Paul Menges
    •  & Zuzana Storchova
  • Article
    | Open Access

    Replicative hexameric helicases are fundamental components of replisomes. Here the authors resolve a cryo-EM structure of the E1 helicase from papillomavirus bound to a DNA replication fork, providing insights into the mechanism of DNA unwinding by these hexameric enzymes.

    • Abid Javed
    • , Balazs Major
    •  & Elena V. Orlova
  • Article
    | Open Access

    m6Am is a modification of the 5′ end of mRNAs catalyzed by PCIF1. Here, Zhang et al. show that HIV infection induces a decrease in m6Am of cellular mRNAs through Vpr-mediated PCIF1 ubiquitination and degradation, resulting in increased HIV replication through regulation of host transcription factors.

    • Qiong Zhang
    • , Yuqi Kang
    •  & Tariq M. Rana
  • Article
    | Open Access

    A strategy to control HIV-1 infection is to stably repress HIV-1 and induce “deep latency”. Here the authors show that a recombinant anti-HIV-1-1 protein can be packaged as mRNA into exosomes and delivered systemically to repress HIV-1-1 within the context of virus infected mice and achieve long term silencing of HIV-1-1 expression.

    • Surya Shrivastava
    • , Roslyn M. Ray
    •  & Kevin V. Morris
  • Article
    | Open Access

    Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation for the absence of such tRNA densities in related herpesviruses.

    • Yun-Tao Liu
    • , David Strugatsky
    •  & Z. Hong Zhou
  • Article
    | Open Access

    Transcription in archaea is known to be regulated through the recruitment of RNA polymerase to promoters. Here, the authors show that the archaeon Saccharolobus solfataricus regulates transcription globally through a rate-limiting promoter-proximal elongation step.

    • Fabian Blombach
    • , Thomas Fouqueau
    •  & Finn Werner