bims-nucpor 2022-11-06 papers

Issue of 2022‒11‒06
three papers selected by
Sara Mingu
Johannes Gutenberg University

Methods Mol Biol. 2023 ;2551 95-109

Analysis of Tau/Nucleoporin Interactions by Surface Plasmon Resonance Spectroscopy.

Lisa Diez, Larisa E Kapinos, Roderick Y H Lim, Susanne Wegmann.

Tau, a soluble and predominantly neuronal protein, is best known for its microtubule (MT)-binding function in the cytosol, where it decisively contributes to stability as well as modulation of MT dynamics. In Alzheimer's disease and other tauopathies, Tau is altered into forming intracellular neurofibrillary tangles; additionally, also a mislocalization from the cytosol to the nucleus has been observed where interactions of Tau with the nucleus become possible. Using surface plasmon resonance (SPR), it was recently shown that Tau can directly interact with certain nucleoporins (e.g., Nup98), components of the nuclear pore complex (NPC). The NPC constitutes large regulated pores in the nuclear envelope that facilitate the bidirectional exchange of proteins, nucleic acids, and other biomolecules between the inner section of the nucleus and the cytosol, the nucleocytoplasmic transport. The mechanism of Tau/Nup interactions is as yet unknown, and a systematic interaction analysis of Tau with different Nups can be of high value to decipher the molecular binding mechanism of Tau to Nups. SPR is a useful tool to analyze binding affinities and kinetic parameters in a label-free environment. While one interaction partner is immobilized on a sensor chip, the second is supplied within a constant flow of buffer. Binding of mobile molecules to immobilized ones changes the refractive index of the medium close to the sensor surface with the signal being proportional to the bound mass. In this chapter, we describe the application of the SPR technique for the investigation of Tau binding to nucleoporins.

Keywords: Biacore; MAPT; Nuclear pore complex (NPC); Nup98; Surface plasmon resonance (SPR); Tau

DOI: https://doi.org/10.1007/978-1-0716-2597-2_8

Cell Rep. 2022 Nov 01. pii: S2211-1247(22)01437-1. [Epub ahead of print]41(5): 111576

Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization.

Xiaoyu Zhu, Chuangye Qi, Ruoyu Wang, Joo-Hyung Lee, Jiaofang Shao, Lanxin Bei, Feng Xiong, Phuoc T Nguyen, Guojie Li, Joanna Krakowiak, Su-Pin Koh, Lukas M Simon, Leng Han, Travis I Moore, Wenbo Li.

The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.

Keywords: 3D genome organization; CP: Molecular biology; Cut&Run, PRO-seq; Hi-C; HiChIP; dCas9 tethering; enhancers; nuclear pore complex; nucleoporins; transcription

DOI: https://doi.org/10.1016/j.celrep.2022.111576

Ann Neurol. 2022 Nov 05.

Recessive NUP54 variants underlie early-onset dystonia with striatal lesions.

Infantile striatonigral degeneration is caused by a homozygous variant of the nuclear-pore complex (NPC) gene NUP62, involved in nucleo-cytoplasmic trafficking. By querying sequencing-datasets of patients with dystonia and/or Leigh(-like) syndromes, we identified three unrelated individuals with biallelic variants in NUP54. All variants clustered in the C-terminal protein region that interacts with NUP62. Associated phenotypes were similar to those of NUP62-related disease, including early-onset dystonia with dysphagia, choreoathetosis, and T2-hyperintense lesions in striatum. In-silico and protein-biochemical studies gave further evidence for the argument that the variants were pathogenic. We expand the spectrum of NPC component-associated dystonic conditions with localized basal-ganglia abnormalities. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/ana.26544