Spatial organization of transcribed eukaryotic genes
Sophie Ling-chia Wei,A.Yu. Zaika +1 more
TLDR
For example, the authors showed that long highly expressed genes form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs, similar to lampbrush loops and polytene puffs.Abstract:
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription. read more
Citations
More filters
Journal ArticleDOI
Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics
TL;DR: In this article , the authors introduce an approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell, which highlights the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing minor roles for cross-links and topological effects.
Journal ArticleDOI
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription
Kathleen S. M. Reed,Eric S. Davis,Marielle L Bond,Alan Cabrera,Eliza Thulson,Ivana Y Quiroga,Shannon Cassel,Kamisha T. Woolery,Isaac B. Hilton,Hyejung Won,Michael I. Love,Douglas H. Phanstiel +11 more
TL;DR: In this paper , the authors mapped each feature in a genome-wide fashion across eight narrowly spaced time points of macrophage activation to infer potential causal relationships between 3D chromatin structure, enhancers and gene transcription, and found that genes connected by loops exhibit stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone.
Posted ContentDOI
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription
TL;DR: In this article , the authors mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation to infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription.
Posted ContentDOI
True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin
Márton Gelléri,Shih-Ya Chen,Aleksander Szczurek,Barbara Hübner,Michael Sterr,Jan Neumann,Ole Kröger,Filip Sadlo,Jorg Imhoff,Yolanda Markaki,Michael J. Hendzel,Marion Cremer,Thomas Cremer,Hilmar Strickfaden,Christoph Cremer +14 more
TL;DR: This work presents maps of nuclear landscapes with true-to-scale DNA-densities, ranging from <5 Mbp/µm3 to >300 Mbp/, and microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription and replication into nuclei of living cells demonstrated their localization and movements within the ANC and exclusion from the INC.
Posted ContentDOI
Regulation of chromatin microphase separation by adsorbed protein complexes
TL;DR: Genetic modifications affecting the binding strength of chromatin-binding protein complexes may modulate the solvent quality experienced by chromatin and regulate the physical organization of the genome.
References
More filters
Journal ArticleDOI
Capturing Chromosome Conformation
TL;DR: Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.
Journal ArticleDOI
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphège P. Nora,Bryan R. Lajoie,Edda G. Schulz,Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Ikuhiro Okamoto,Ikuhiro Okamoto,Ikuhiro Okamoto,Nicolas Servant,Nicolas Servant,Nicolas Servant,Tristan Piolot,Tristan Piolot,Tristan Piolot,Nynke L. van Berkum,Johannes Meisig,John W. Sedat,Joost Gribnau,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Nils Blüthgen,Job Dekker,Edith Heard,Edith Heard,Edith Heard +26 more
TL;DR: In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, this study sets the stage for the full genetic dissection of the mouse X-inactivation centre.
Journal ArticleDOI
Spheroid Chromatin Units (ν Bodies)
Ada L. Olins,Donald E. Olins +1 more
TL;DR: Linear arrays of spherical chromatin particles about 70 angstroms in diameter have been observed in preparations of isolated eukaryotic nuclei swollen in water, centrifuged onto carbon films, and positively or negatively stained.
Journal ArticleDOI
A guide to super-resolution fluorescence microscopy
TL;DR: These new super-resolution technologies are either based on tailored illumination, nonlinear fluorophore responses, or the precise localization of single molecules and have created unprecedented new possibilities to investigate the structure and function of cells.
Journal ArticleDOI
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Maxim Imakaev,Geoffrey Fudenberg,Rachel Patton McCord,Natalia Naumova,Anton Goloborodko,Bryan R. Lajoie,Job Dekker,Leonid A. Mirny,Leonid A. Mirny +8 more
TL;DR: In this article, the authors present a pipeline that integrates a strategy for mapping of sequencing reads and a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities.