Molecular biology

  • Article
    | Open Access

    Nucleosomes form arrays with even spacing between them in virtually all eukaryotes; however, their biogenesis is incompletely understood. Here the authors show that nucleosome density and DNA sequence along with the Ino80 chromatin remodeling complex play a role in nucleosome array formation in yeast and that the transcriptional machinery disrupts evenly-spaced nucleosomes.

    • Ashish Kumar Singh
    • , Tamás Schauer
    •  & Felix Mueller-Planitz
  • Article
    | Open Access

    During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.

    • Dafne Ibarra-Morales
    • , Michael Rauer
    •  & Nicola Iovino
  • Article
    | Open Access

    Polycomb Repressive Complex 2, an important regulator of embryonic development, exists in two configurations, PRC2.1 and PRC2.2. Here the authors dissect the functional contributions of these two PRC2 subunits and observed complex-specific alterations in the cell state of pluripotent and early differentiating cells.

    • Chet H. Loh
    • , Siebe van Genesen
    •  & Gert Jan C. Veenstra
  • Article
    | Open Access

    Ty3 retrotransposon integrates with an exquisite specificity upstream of RNA Polymerase III-transcribed genes, such as transfer RNAs. Here the authors resolve a cryo-EM structure of an active Ty3 intasome in complex with a TFIIIB-bound tRNA promoter, shedding light into the molecular determinants of harmless retrotransposition.

    • Guillermo Abascal-Palacios
    • , Laura Jochem
    •  & Alessandro Vannini
  • Article
    | Open Access

    Cilia are microtubule-based organelles containing proteins transported from the cell body. Here, the authors show that the multicilia of mouse ependymal cells contain ribosomal components, tubulin mRNA,18 S rRNA and nascent tubulin peptides, suggesting local translation in the ciliary compartment.

    • Kai Hao
    • , Yawen Chen
    •  & Xueliang Zhu
  • Article
    | Open Access

    The differentiation of naive T cells to immune suppressing induced regulatory T (iTreg) cells requires TGF-beta-1 and downregulation of mTORC1 activity, which inhibits mRNA translation. Here the authors show that iTreg cell differentiation uses an alternate mRNA translation mechanism involving translation factors DAP5 and eIF3d.

    • Viviana Volta
    • , Sandra Pérez-Baos
    •  & Robert J. Schneider
  • Article
    | Open Access

    Revealing mechanisms of complex protein machines requires simultaneous exploration of multiple structural coordinates. Here the authors report two-colour fluorescence microscopy combined with photoinduced electron transfer probes to simultaneously detect two structural coordinates in single protein molecules.

    • Jonathan Schubert
    • , Andrea Schulze
    •  & Hannes Neuweiler
  • Article
    | Open Access

    Relapsed/refractory multiple myeloma (RRMM) is characterized by a remarkable heterogeneity and high drug resistance. Here, the authors analyse RRMM samples by single-cell RNA-sequencing, revealing molecular features associated with high-risk chromosomal 1q-gain and changes in the tumor microenvironment.

    • Stephan M. Tirier
    • , Jan-Philipp Mallm
    •  & Karsten Rippe
  • Article
    | Open Access

    The molecular origins of epialleles remain unknown. Here, the authors show that a positive feedback loop between H3K9me2 and CMT2/3 is a major contributing factor to the origins of spontaneous epialleles and that heterochromatin is a quantitative trait associated with spontaneous epiallele formation.

    • Yinwen Zhang
    • , Hosung Jang
    •  & Robert J. Schmitz
  • Article
    | Open Access

    Microbial DNA glycosylases associated with the biosynthesis of DNA-damaging antibiotics have evolved self-resistance for their cognate natural products. Here, the authors provide evidence that cellular self-resistance is enabled by reduced affinity of the glycosylases for the excision products of the corresponding DNA lesions.

    • Elwood A. Mullins
    • , Jonathan Dorival
    •  & Brandt F. Eichman
  • Article
    | Open Access

    Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage with an aggressive subtype caused by translocations involving PAX3- /PAX7-FOXO1 chimeric transcription factors. Here the authors show that the BRG1-containing BAF complex is overexpressed and acts largely independently of the PAX3-FOXO1 chimera on chromatin to result in a myogenic differentiation blockade in this malignancy.

    • Dominik Laubscher
    • , Berkley E. Gryder
    •  & Javed Khan
  • Article
    | Open Access

    The RNA genome of the Hepatitis C Virus binds to the liver-specific miR122. Here the authors report the crystal structure of the Ago2:miR122:HCV complex showing that the viral RNA’s structural element traps the Ago2:miR-122 complex on the 5’ end of the viral genome to protect it from degradation.

    • Luca F. R. Gebert
    • , Mansun Law
    •  & Ian J. MacRae
  • Article
    | Open Access

    The bat sarbecovirus RaTG13 is a close relative of SARS-CoV-2, but its spike protein doesn’t efficiently bind human ACE2. Here, the authors show that exchange of spike residue 403 between RaTG13 and SARS-CoV-2 spike proteins affects binding to human ACE2 and entry of pseudotyped viruses.

    • Fabian Zech
    • , Daniel Schniertshauer
    •  & Frank Kirchhoff
  • Article
    | Open Access

    Plant light harvesting complex (LHC)‐like proteins protect the photosynthetic machinery from excess light. Here the authors show that plant LHC‐like dimers are stabilized by associated pigments and can quench chlorophyll fluorescence via direct energy transfer from chlorophyll to zeaxanthin.

    • Petra Skotnicová
    • , Hristina Staleva-Musto
    •  & Roman Sobotka
  • Article
    | Open Access

    Engineering biosynthetic assembly lines is a powerful path to new natural products but is challenging with current methods. Here the authors use CRISPR-Cas9 to exchange subdomains within NRPS to alter substrate selectivity.

    • Wei Li Thong
    • , Yingxin Zhang
    •  & Jason Micklefield
  • Article
    | Open Access

    Imbalance and loss of cell types is a hallmark in many diseases. Still, quantifying compositional changes in scRNAseq data remains challenging. Here the authors present scCODA, a Bayesian model to assess cell type compositions in scRNA-seq data.

    • M. Büttner
    • , J. Ostner
    •  & B. Schubert
  • Article
    | Open Access

    Forward genetic approaches such as CRISPR screens are powerful ways to identify essential genes and those that influence host-pathogen interactions. Here the authors design a bioinformatics portal for sgRNA design and a recombination-mediated cassette system for delivery into mosquito cell lines.

    • Raghuvir Viswanatha
    • , Enzo Mameli
    •  & Norbert Perrimon
  • Article
    | Open Access

    Dynamic changes in chromatin landscape affect CD8+ T cell phenotype and function in chronic infections and cancer. Here the authors show that targeting the histone demethylase LSD1 increases the persistence of progenitor exhausted CD8+ T cells, improving response to immune checkpoint blockade in preclinical cancer models.

    • Yi Liu
    • , Brian Debo
    •  & Yang Shi
  • Article
    | Open Access

    Processing bodies are phase separated compartments enriched in translationally repressed mRNAs. Here, Smith et al. show that, in sensory neurons, eukaryotic elongation factor 2 kinase (eEF2K) plays key roles in the regulation of processing body abundance and the formation of translationally inactive ribosomes.

    • Patrick R. Smith
    • , Sarah Loerch
    •  & Zachary T. Campbell
  • Article
    | Open Access

    Many interactions between viral and host proteins are mediated by short peptide motifs. Here, using a phage-based viral peptide library, the authors identify 269 peptide-based interactions for 18 coronaviruses, including an interaction between SARS-CoV-2 N and G3BP1/2 that affects stress granules.

    • Thomas Kruse
    • , Caroline Benz
    •  & Ylva Ivarsson
  • Article
    | Open Access

    The coverage and throughput of data-independent acquisition (DIA)-based phosphoproteomics is limited by its dependence on experimental spectral libraries. Here the authors develop a DIA workflow based on in silico spectral libraries generated by a novel deep neural network to expand phosphoproteome coverage.

    • Ronghui Lou
    • , Weizhen Liu
    •  & Wenqing Shui
  • Article
    | Open Access

    SPOP functions as a tumour suppressor in prostate cancer but how the protein is regulated is unclear. Here, the authors identify G3BP1 as a competitive inhibitor of SPOP and show that G3BP1-SPOP axis activates androgen signalling to drive tumorigenesis.

    • Chandrani Mukhopadhyay
    • , Chenyi Yang
    •  & Pengbo Zhou
  • Article
    | Open Access

    Several proteomic approaches allow the analysis of covalent protein SUMOylation, but it remains challenging to systematically study the consequences of a substrate being modified. Here, the authors combine proximity biotinylation and protein-fragment complementation to identify SUMO-dependent protein interactors.

    • Orhi Barroso-Gomila
    • , Fredrik Trulsson
    •  & James D. Sutherland
  • Article
    | Open Access

    Understanding which patients will respond to FOLFIRINOX therapy is important for clinical outcome. Here, the authors show that the MIR1307 is increased pancreatic cancer cell lines and inhibition of the microRNA sensitises cells to treatment.’ stratifying patients to achieve the best clinical outcome. Here, the authors show that the MIR1307 is increased in a subgroup of human pancreatic cancers and inhibition of the microRNA in in vitro and in vivo models of pancreatic cancer sensitises cells to treatment.

    • Pietro Carotenuto
    • , Francesco Amato
    •  & Chiara Braconi
  • Article
    | Open Access

    BRCA1 dysfunction sensitizes cancer cells to PARP inhibitors (PARPi) but the underlying mechanism is unclear. Here, the authors identify RNF19A as a determinant of PARPi sensitivity, showing that RNF19A ubiquitinates BARD1, negatively regulates the BRCA1-BARD1 complex, and inhibits homologous recombination.

    • Qian Zhu
    • , Jinzhou Huang
    •  & Zhenkun Lou
  • Article
    | Open Access

    scRNASeq data is revolutionizing our understanding of biological systems, but is still expensive to generate. Here, the authors present a statistical framework that facilitates informed multi-sample experimental design to reduce unnecessary costs and maximize the utility of the generated data.

    • Katharina T. Schmid
    • , Barbara Höllbacher
    •  & Matthias Heinig
  • Article
    | Open Access

    Development of Cas12a for human therapeutics and diagnostics may significantly benefit from, or even require, chemical modification of its guide RNA. Here the authors show that the noncanonical 5′ pseudoknot structure of the AsCas12a crRNA guide can be heavily modified and still retain very high editing activity in cells and trans cleavage activity in vitro.

    • Eman A. Ageely
    • , Ramadevi Chilamkurthy
    •  & Keith T. Gagnon
  • Article
    | Open Access

    Start codon selection is commonly thought to occur through the unidirectional scanning of the mRNA by the 40 S ribosome. Here the authors provide evidence that the pre-initiation complex can backslide on the mRNA to initiate translation at upstream AUG codons.

    • Yifei Gu
    • , Yuanhui Mao
    •  & Shu-Bing Qian
  • Article
    | Open Access

    Germinal centre (GC) responses may require RNA binding proteins (RBP) for post-transcriptional gene regulation. Here the authors show the RBP HuR supports GCs by promoting Myc and Myc-dependent transcription to enhance antigen-specific GC B cell selection and production of high affinity antibodies.

    • Ines C. Osma-Garcia
    • , Dunja Capitan-Sobrino
    •  & Manuel D. Diaz-Muñoz
  • Article
    | Open Access

    Classical non-homologous end-joining (cNHEJ) is the dominant pathway used by human cells to repair DNA double-strand breaks (DSBs) and maintain genome stability. Here the authors show that PARP1-driven chromatin expansion allows the recruitment of ZNF384, which in turn recruits Ku70/Ku80 to facilitate cNHEJ.

    • Jenny Kaur Singh
    • , Rebecca Smith
    •  & Haico van Attikum
  • Article
    | Open Access

    The tumor suppressor BRCA2 protects stalled DNA replication forks from unrestrained degradation; however the mechanism whereby unprotected stalled forks are preserved and restarted has remained elusive. Here the authors show that the WRN helicase promotes stalled fork recovery and limits fork hyper-degradation in the absence of BRCA2 protection.

    • Arindam Datta
    • , Kajal Biswas
    •  & Robert M. Brosh Jr
  • Article
    | Open Access

    In viruses, multi-subunit ring-ATPases are involved in genome packaging. Here, using single-molecule techniques, the authors determine that the active bacteriophage T4 DNA packaging motor is a pentamer and show that the motor can tolerate inactive subunits, suggesting that strict coordination between the subunits is not crucial.

    • Li Dai
    • , Digvijay Singh
    •  & Venigalla B. Rao
  • Article
    | Open Access

    To characterize molecular changes during cell type transitions, the authors develop a method to simultaneously measure protein expression and thermal stability changes. They apply this approach to study differences between human pluripotent stem cells, their progenies, parental and allogeneic cells.

    • Pierre Sabatier
    • , Christian M. Beusch
    •  & Roman A. Zubarev
  • Article
    | Open Access

    The cereal endosperm is a major determinant of seed size and shape. Here the authors show that a lncRNA, MISSEN, is expressed from the maternally derived allele in rice seeds and regulates a helicase family protein to support efficient nuclear division, distribution and cellularization in the endosperm.

    • Yan-Fei Zhou
    • , Yu-Chan Zhang
    •  & Yue-Qin Chen