Molecular biology articles within Nature Communications

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  • Article
    | Open Access

    AUXIN RESPONSE FACTORS (ARFs) are a family of plant-specific transcriptional factors involved in auxin signaling. Here, the authors adapt DAP-seq technology to show the binding landscape of 14 maize ARFs and reveal class-specific binding properties and transcriptional coordination by ARFs from different classes.

    • Mary Galli
    • , Arjun Khakhar
    •  & Andrea Gallavotti

  • Article
    | Open Access

    Small interfering (siRNAs) can be toxic to cancer cells. Here the authors investigate the toxicity of microRNA in cancer cells by performing a siRNA screen that tests the miRNA activities of an extensive list of miRNAs with different 6mer seed sequences.

    • Quan Q. Gao
    • , William E. Putzbach
    •  & Marcus E. Peter

  • Article
    | Open Access

    Divergent transcription from promoters and enhancers occurs in many species, but it is unclear if it is a general feature of all eukaryotic cis regulatory elements. Here the authors define cis regulatory elements in worms, flies, and human; and identify several differences in regulatory architecture among metazoans.

    • Mahmoud M. Ibrahim
    • , Aslihan Karabacak
    •  & Uwe Ohler

  • Article
    | Open Access

    Microorganisms must regulate allocation of resources in nutrient-limited conditions. Here, the authors combine Ribo-seq, RNA-seq and TSS-seq to study resource allocation in the acetogen C. ljungdahlii, and show that dynamic regulation of translational efficiency of metabolic pathways is critical.

    • Mahmoud M. Al-Bassam
    • , Ji-Nu Kim
    •  & Karsten Zengler

  • Article
    | Open Access

    Functional peptides can be encoded by short open reading frames in non-coding RNA. Here, the authors identify a 87aa peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) that can reduce glioblastoma proliferation via interaction with PAF1 which sequentially inhibits the transcriptional elongation of some oncogenes.

    • Maolei Zhang
    • , Kun Zhao
    •  & Nu Zhang

  • Article
    | Open Access

    Bacterial chemoreceptors form clusters, preferably at  the cell poles. Here, Koler et al. show that polar and lateral clusters exhibit distinct long-term positional dynamics   and that polar bias may be due to differences in mobility of receptor complexes between the polar and lateral cell regions.

    • Moriah Koler
    • , Eliran Peretz
    •  & Ady Vaknin

  • Article
    | Open Access

    Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG and discuss mechanistic implications.

    • Kazuki Kato
    • , Hiroshi Nishimasu
    •  & Osamu Nureki

  • Article
    | Open Access

    TDP-43 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitinated inclusions (FTD-TDP). Here, the authors identify the transcriptional elongation factor Ell as a strong modifier of TDP-43-mediated neurodegeneration through the Ell transcriptional elongation complexes LEC and SEC.

    • Chia-Yu Chung
    • , Amit Berson
    •  & Nancy M. Bonini

  • Article
    | Open Access

    The transcription factor DAF-16/FOXO is a downstream effector of insulin/insulin-like growth factor signaling and plays an important role in stress resistance and longevity. Here, the authors show that DAF-16/FOXO can form a complex with HLH-30/TFEB to synergistically regulate transcription of target genes in response to certain stress stimuli.

    • Xin-Xuan Lin
    • , Ilke Sen
    •  & Christian G. Riedel

  • Article
    | Open Access

    Self-renewal and pluripotency of human embryonic stem cells (hESCs) depends upon the function of the transcription factor OCT4. Here, the authors identified proteins associated with the OCT4 enhancer, notably ZNF207 that maintains both pluripotency and differentiation towards ectoderm through isoform switching.

    • Fang Fang
    • , Ninuo Xia
    •  & Renee A. Reijo Pera

  • Article
    | Open Access

    Protein NEDDylation increases upon proteotoxic stress but the function of this response remains to be elucidated. Here, the authors show that NEDDylation contributes to the cellular defence against proteotoxicity by promoting nuclear protein aggregation and protecting the ubiquitin proteasome system.

    • Chantal M. Maghames
    • , Sofia Lobato-Gil
    •  & Dimitris P. Xirodimas

  • Article
    | Open Access

    The autophagic receptor p62 recognizes arginylated (Nt-R) substrates through its ZZ domain (p62ZZ). Here the authors identify a p62 auto regulatory mechanism and provide structural insights into the selective recognition of Nt-R by p62ZZ and further show that Nt-R binding stimulates p62 oligomerization and macroautophagy.

    • Yi Zhang
    • , Su Ran Mun
    •  & Tatiana G. Kutateladze

  • Article
    | Open Access

    Termination of RNA polymerase II (RNAPII) transcription is an essential step of gene expression. Here the authors provide evidence that in fission yeast termination of ncRNA genes occurs by a cleavage-dependent mechanism involving recruitment of mRNA 3′ end processing factors and requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases.

    • Marc Larochelle
    • , Marc-Antoine Robert
    •  & François Bachand

  • Article
    | Open Access

    Inteins can act as post-translational environmental sensors in vivo. Here the authors characterize two inteins present in the Mycobacterium smegmatis replicative helicase DnaB that display distinct splicing behaviors and are differentially sensitive to inhibition by biological stressors and propose that splicing inhibition could modulate DnaB levels to protect the cell against replication stress.

    • Danielle S. Kelley
    • , Christopher W. Lennon
    •  & Marlene Belfort

  • Article
    | Open Access

    It was previously suggested that formation of RNA secondary structure tends to bring the 5′ and 3′ ends of RNA into close proximity. Here the authors use experimental and computational approaches to show that mRNAs and lncRNAs have an intrinsic propensity to fold into structures in which the 5′ end and 3′ end are ≤7 nm apart irrespective of length.

    • Wan-Jung C. Lai
    • , Mohammad Kayedkhordeh
    •  & Dmitri N. Ermolenko

  • Article
    | Open Access

    Paternal contributions to epigenetic inheritance via nucleosomes are poorly understood, as sperm in many organisms replace the majority of nucleosomes with protamines. Here the authors provide evidence that Caenorhabditis elegans sperm retain histone packaging of the genome and provide a histone-based epigenetic memory that is important for germ cell development in offspring.

    • Tomoko M. Tabuchi
    • , Andreas Rechtsteiner
    •  & Susan Strome

  • Article
    | Open Access

    Primordial Germ Cell-Like Cells (PGCLCs) are an in vitro model for primordial germ cell development. Here, the authors couple a novel compound reporter with CRISPR screening to identify key genes for exit from pluripotency and acquisition of PGCLC fate; specifically identifying Nr5a2 and Zfp296.

    • Jamie A. Hackett
    • , Yun Huang
    •  & M. Azim Surani

  • Article
    | Open Access

    The HIV Tat protein recruits a host elongation factor from the cellular 7SK complex to the viral TAR RNA to ensure transcriptional elongation. Here, Pham et al. solve the structures of both 7SK and TAR RNAs in complex with Tat’s RNA binding domain and gain mechanistic insights into the process.

    • Vincent V. Pham
    • , Carolina Salguero
    •  & Victoria M. D’Souza

  • Article
    | Open Access

    T-acute lymphoblastic leukemia is an aggressive cancer. Here the authors provide insights into the functional role of SHQ1, an H/ACA snoRNP assembly factor involved in snRNA pseudouridylation, in T-lymphoblastic leukemia cell survival through regulating the maturation of MYC mRNA.

    • Hexiu Su
    • , Juncheng Hu
    •  & Hudan Liu

  • Article
    | Open Access

    Chr3q26 rearrangements cause overexpression of EVI1 and associate with myeloid neoplasms, but the mechanism behind this association is unclear. Here, using a novel mouse model they show that EVI1 causes premalignant myeloid expansion with suppression of other lineages through upregulation of Spi1/PU.1.

    • Edward Ayoub
    • , Michael P. Wilson
    •  & Archibald S. Perkins

  • Article
    | Open Access

    Incorporation of mismatched nucleotides during DNA replication or repair can lead to mutagenesis. Here the authors reveal that DNA ligase can ligate NHEJ intermediates following incorporation of 8-oxodGTP or dGTP opposite T by DNA Polymerase mu (Pol mu) in vitro, which suggests that Pol mu could cause promutagenic mismatches during DSB repair.

    • Melike Çağlayan
    •  & Samuel H. Wilson

  • Article
    | Open Access

    The role of the genome structure in the establishment of the embryonic and trophoblast lineages is still not well understood. Here the authors perform promoter capture Hi-C in mouse trophoblast and embryonic stem cells and find divergent networks of repressive and active chromatin interactions between the two lineages.

    • Stefan Schoenfelder
    • , Borbala Mifsud
    •  & Miguel R. Branco

  • Article
    | Open Access

    Homologous recombination ensures genome integrity during meiotic recombination. Here the authors reveal that factors SWS1 and SWSAP1 are critical for meiotic homologues recombination, particularly in promoting assembly of RAD51 and DMC1 on early recombination intermediates.

    • Carla M. Abreu
    • , Rohit Prakash
    •  & Maria Jasin

  • Article
    | Open Access

    Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a non-Hodgkin-type B cell lymphoma. Here, the authors identify two risk loci for WM/LPL in a two-stage GWAS involving a family-oversampling approach and provide evidence for a functional role of the non-coding SNP rs116446171.

    • Mary L. McMaster
    • , Sonja I. Berndt
    •  & Neil E. Caporaso

  • Article
    | Open Access

    During stress conditions bacterial ribosomes dimerize and form inactive but stable hibernating 100S particles, a process that is facilitated by the hibernation-promoting factor (HPF). Here the authors analyze 100S dimer formation as a function of HPF protein concentration and present the Thermus thermophilus 100S ribosome cryo-EM structure.

    • Rasmus Kock Flygaard
    • , Niels Boegholm
    •  & Lasse B. Jenner

  • Article
    | Open Access

    Transcription-coupled homologous recombination (TC-HR) is activated by reactive oxygen species-induced DNA damage to maintain transcribed genome stability. The authors demonstrate that R loops are induced by ROS at the transcribed genome, triggering a CSB-RAD52- dependent but BRCA1/2-independent RAD51 loading for repair.

    • Yaqun Teng
    • , Tribhuwan Yadav
    •  & Li Lan

  • Article
    | Open Access

    Five validation pillars have been proposed to verify the specificity of research antibodies. Here the authors screen 6,000 antibodies from the Human Protein Atlas with these methods to provide an antibody validation resource for providers and users.

    • Fredrik Edfors
    • , Andreas Hober
    •  & Mathias Uhlen

  • Article
    | Open Access

    The β-barrel assembly machinery (BAM) catalyzes β-barrel protein insertion into the outer membrane of E.coli. Here authors employ high-sensitivity solid-state NMR to reveal how the lipid environment and formation of the BamA-BamCDE complex affect BamA structure and dynamics with regards to the lateral gate and the β-barrel associated domains.

    • Cecilia Pinto
    • , Deni Mance
    •  & Marc Baldus

  • Article
    | Open Access

    Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.

    • Diako Ebrahimi
    • , Christopher M. Richards
    •  & Reuben S. Harris

  • Article
    | Open Access

    It remains unclear how microbial sensing during early-life colonization results in immune homeostasis rather than acute inflammation. Here the authors show that zebrafish larvae colonization suppresses intestinal MyD88, accounting for a considerable proportion of microbiota-induced alterations in immune setpoint.

    • Bjørn E. V. Koch
    • , Shuxin Yang
    •  & Herman P. Spaink

  • Article
    | Open Access

    Mitosis poses a challenge for transcriptional programs, as it is thought that several proteins lose binding on condensed chromosomes. Here, the authors analyze the chromatin-bound proteome through the cell cycle, revealing retention of most transcription factors and preservation of the regulatory landscape.

    • Paul Adrian Ginno
    • , Lukas Burger
    •  & Dirk Schübeler

  • Article
    | Open Access

    It has previously been established that DNA end resection in yeast and in humans is under CDK control. Here the authors explain how phosphorylation regulates the capacity of Sae2 — the yeast orthologue of human CtIP — to promote DNA end resection.

    • Elda Cannavo
    • , Dominic Johnson
    •  & Petr Cejka

  • Article
    | Open Access

    Around 10% of high-grade serous ovarian carcinomas (HGSOC) harbor BRCA1 promoter methylation, but it is uncertain how it predicts response to PARP inhibition. Here, the authors show that homozygous BRCA1 methylation predicts response to rucaparib while heterozygous methylation of BRCA1 predicts resistance in HGSOC.

    • Olga Kondrashova
    • , Monique Topp
    •  & Clare L. Scott

  • Article
    | Open Access

    USP24 has previously been reported to be involved in cancer progression. Here, the authors demonstrate that USP24 stabilizes p300 and β-TrCP to increase the levels of NF-κB and histone-3 acetylation, and decrease DNMT1 and IκB levels which promotes IL-6 expression in M2 macrophages and lung cancer cells.

    • Yi-Chang Wang
    • , Yu-Syuan Wu
    •  & Jan-Jong Hung

  • Article
    | Open Access

    DNA damage induces checkpoints to ensure that damage is not transferred to the next generation, but the molecular pathways responsible for checkpoint recovery are not clear. Here the authors show that the nutrient sensor mTORC1 is a determinant for G2/M checkpoint recovery through regulation of cyclin B1 and PLK1 expression.

    • Hui-Ju Hsieh
    • , Wei Zhang
    •  & Guang Peng

  • Article
    | Open Access

    Incomplete splicing of HTT results in the production of the highly pathogenic exon 1 HTT protein. Here the authors identify the necessary intronic regions and the underlying mechanisms that contribute to this process.

    • Andreas Neueder
    • , Anaelle A. Dumas
    •  & Gillian P. Bates

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