bims-nutges 2021-08-15 papers

Issue of 2021–08–15
four papers selected by
Kanwal Tariq, Stockholm University

Mol Cell. 2021 Aug 05. pii: S1097-2765(21)00579-7. [Epub ahead of print]

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

Célia Jeronimo, Andrew Angel, Vu Q Nguyen, Jee Min Kim, Christian Poitras, Elie Lambert, Pierre Collin, Jane Mellor, Carl Wu, François Robert.

The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

Keywords: Chd1; FACT; Pob3; RNA polymerase II; Spt16; chromatin remodeling; histone chaperone; mathematical modeling; nucleosome unwrapping; single-molecule tracking

DOI: https://doi.org/10.1016/j.molcel.2021.07.010

Sci Adv. 2021 Aug;pii: eabf3641. [Epub ahead of print]7(33):

Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization.

Nicholas A W Bell, Philip J Haynes, Katharina Brunner, Taiana Maia de Oliveira, Maria M Flocco, Bart W Hoogenboom, Justin E Molloy.

Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme that plays important roles in DNA repair, chromatin organization and transcription regulation. Although binding and activation of PARP1 by DNA damage sites has been extensively studied, little is known about how PARP1 binds to long stretches of undamaged DNA and how it could shape chromatin architecture. Here, using single-molecule techniques, we show that PARP1 binds and condenses undamaged, kilobase-length DNA subject to sub-piconewton mechanical forces. Stepwise decondensation at high force and DNA braiding experiments show that the condensation activity is due to the stabilization of DNA loops by PARP1. PARP inhibitors do not affect the level of condensation of undamaged DNA but act to block condensation reversal for damaged DNA in the presence of NAD+ Our findings suggest a mechanism for PARP1 in the organization of chromatin structure.

DOI: https://doi.org/10.1126/sciadv.abf3641

Plant J. 2021 Aug 14.

Nuclear organization in crucifer genomes: nucleolus-associated telomere clustering is not a universal interphase configuration in Brassicaceae.

Wenbo Shan, Michaela Kubová, Terezie Mandáková, Martin A Lysak.

Arabidopsis thaliana (arabidopsis) has become a major plant research model where interphase nuclear organization exhibits unique features, including nucleolus-associated telomere clustering. The chromocenter (CC)-loop model, or rosette-like configuration, describes intranuclear chromatin organization in arabidopsis as megabase-long loops anchored in, and emanating from, peripherally positioned chromocenters, and those containing telomeres associate with the nucleolus. To investigate whether the CC-loop organization is universal across the mustard family (crucifers), the nuclear distributions of centromeres, telomeres and nucleoli were analyzed by fluorescence in situ hybridization in seven diploid species (2n = 10 - 16) representing major crucifer clades with an up to 26-fold variation in genome size (160 Mb - 4 260 Mb). Nucleolus-associated telomere clustering was confirmed in arabidopsis (157 Mb) and was newly identified as the major nuclear phenotype in other species with a small genome (215 - 381 Mb). In large-genome species (2 611 - 4 264 Mb), centromeres and telomeres adopted either a Rabl-like configuration or dispersed distribution in the nuclear interior; telomeres only rarely associated with the nucleolus. In Arabis cypria (381 Mb) and Bunias orientalis (2 611 Mb), tissue-specific patterns deviating from the major nuclear phenotypes were observed in anther and stem tissues, respectively. The rosette-like configuration, including nucleolus-associated telomere clustering in small-genome species from different infrafamiliar clades, suggests that genomic properties rather than phylogenetic position, determine the interphase nuclear organization. Our data suggest that nuclear genome size, average chromosome size and degree of longitudinal chromosome compartmentalization affect interphase chromosome organization in crucifer genomes.

Keywords: Arabidopsis; Cruciferae; Rabl; centromere; chromocenter-loop model; interphase; nucleolus; pre-meiosis; rosette-like organization; telomere

DOI: https://doi.org/10.1111/tpj.15459

Front Mol Biosci. 2021 ;8 644133

Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.

Benjamin R Gilbert, Zane R Thornburg, Vinson Lam, Fatema-Zahra M Rashid, John I Glass, Elizabeth Villa, Remus T Dame, Zaida Luthey-Schulten.

JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A's genome and physical size are approximately one-tenth those of the model bacterial organism Escherichia coli's, and the corresponding reduction in complexity and scale provides a unique opportunity for whole-cell modeling. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network and a kinetic model of genetic information processing. In addition to that information, whole-cell, spatially-resolved kinetic models require cellular architecture, including spatial distributions of ribosomes and the circular chromosome's configuration. We reconstruct cellular architectures of Syn3A cells at the single-cell level directly from cryo-electron tomograms, including the ribosome distributions. We present a method of generating self-avoiding circular chromosome configurations in a lattice model with a resolution of 11.8 bp per monomer on a 4 nm cubic lattice. Realizations of the chromosome configurations are constrained by the ribosomes and geometry reconstructed from the tomograms and include DNA loops suggested by experimental chromosome conformation capture (3C) maps. Using ensembles of simulated chromosome configurations we predict chromosome contact maps for Syn3A cells at resolutions of 250 bp and greater and compare them to the experimental maps. Additionally, the spatial distributions of ribosomes and the DNA-crowding resulting from the individual chromosome configurations can be used to identify macromolecular structures formed from ribosomes and DNA, such as polysomes and expressomes.

Keywords: JCVI-syn3A; bacterial minimal cell; chromosome conformation capture (3C) maps; chromosome modeling; computational modeling; cryo-electron tomography; ribosome distribution; whole-cell models

DOI: https://doi.org/10.3389/fmolb.2021.644133