scholarly journals Rhythmic chromatin interactions with lamin B1 reflect stochasticity in variable lamina-associated domains during the circadian cycle

2019 ◽  
Author(s):  
Annaël Brunet ◽  
Frida Forsberg ◽  
Philippe Collas
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Nuclear Lamina ◽  
Circadian Cycle ◽  
Chromatin Dynamics ◽  
Nuclear Lamins ◽  
Lamin B1 ◽  
Chromatin Interactions ◽  
Periodic Gene ◽  
Periodic Gene Expression

AbstractMany mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications and chromosomal interactions. Here, we report periodic interactions of chromatin with nuclear lamins, suggesting rhythmic associations with the nuclear lamina. Entrainment of the circadian clock is accompanied in mouse liver by a gain of lamin B1-chromatin interactions, followed by oscillations in these interactions at hundreds of lamina-associated domains (LADs). A subset of these oscillations exhibit distinct 12, 18, 24 or 30-h periodicity in our dataset, and affect one or both LAD borders or entire stand-alone LADs. However, most LADs are conserved during the circadian cycle, and periodic LADs are seldom occurrences rather than dominant features of variable LADs. Periodic LADs display oscillation asynchrony between 5’ and 3’ LAD borders, and are uncoupled from periodic gene expression within or in vicinity of these LADs. Accordingly, periodic genes, including central clock-control genes, are often located megabases away from LADs, suggesting residence in a transcriptionally permissive environment throughout the circadian cycle. Autonomous oscillatory associations of the genome with nuclear lamins provide new evidence for rhythmic spatial chromatin configurations. Nevertheless, our data suggest that periodic LADs reflect stochasticity in lamin-chromatin interactions underlying chromatin dynamics in the liver during the circadian cycle. They also argue that periodic gene expression is by and large not regulated by rhythmic chromatin associations with the nuclear lamina.

scholarly journals Oscillatory Phosphorylation of Yeast Fus3 MAP Kinase Controls Periodic Gene Expression and Morphogenesis

2008 ◽  
Vol 18 (23) ◽  
pp. 1897
Author(s):  
Zoe Hilioti ◽  
Walid Sabbagh ◽  
Saurabh Paliwal ◽  
Adriel Bergmann ◽  
Marcus D. Goncalves ◽  
...  
Keyword(s):  
Gene Expression ◽  
Map Kinase ◽  
Periodic Gene ◽  
Periodic Gene Expression

scholarly journals Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control

2012 ◽  
Vol 23 (16) ◽  
pp. 3079-3093 ◽  
Author(s):  
Gavin D. Grant ◽  
Joshua Gamsby ◽  
Viktor Martyanov ◽  
Lionel Brooks ◽  
Lacy K. George ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Binding ◽  
Luciferase Activity ◽  
Binding Motif ◽  
Sequencing Analysis ◽  
Peak Expression ◽  
Periodic Gene ◽  
Regulated Gene Expression ◽  
Periodic Gene Expression

We developed a system to monitor periodic luciferase activity from cell cycle–regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle–regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle regulators, FOXJ3 and FOXK1. Knockdown of FOXJ3 and FOXK1 eliminated cell cycle–dependent oscillations and resulted in decreased cell proliferation rates. Analysis of genes regulated by FOXJ3 and FOXK1 showed that FOXJ3 may regulate a network of zinc finger proteins and that FOXK1 binds to the promoter and regulates DHFR, TYMS, GSDMD, and the E2F binding partner TFDP1. Chromatin immunoprecipitation followed by high-throughput sequencing analysis identified 4329 genomic loci bound by FOXK1, 83% of which contained a FOXK1-binding motif. We verified that a subset of these loci are activated by wild-type FOXK1 but not by a FOXK1 (H355A) DNA-binding mutant.

scholarly journals Oscillatory Phosphorylation of Yeast Fus3 MAP Kinase Controls Periodic Gene Expression and Morphogenesis

2008 ◽  
Vol 18 (21) ◽  
pp. 1700-1706 ◽  
Author(s):  
Zoe Hilioti ◽  
Walid Sabbagh ◽  
Saurabh Paliwal ◽  
Adriel Bergmann ◽  
Marcus D. Goncalves ◽  
...  
Keyword(s):  
Gene Expression ◽  
Map Kinase ◽  
Periodic Gene ◽  
Periodic Gene Expression

scholarly journals CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps

2019 ◽  
Author(s):  
Tom Aharon Hait ◽  
Ran Elkon ◽  
Ron Shamir
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Cell Types ◽  
Specific Gene ◽  
Cell Type ◽  
Chromatin Interactions ◽  
Cell Type Specific ◽  
Novel Method ◽  
Validation Scheme

AbstractSpatiotemporal gene expression patterns are governed to a large extent by enhancer elements, typically located distally from their target genes. Identification of enhancer-promoter (EP) links that are specific and functional in individual cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS, a new statistical inference method that utilizes multiple replicates per cell type to infer cell type-specific EP links. Computationally predicted EP links are usually benchmarked against experimentally determined chromatin interactions measured by ChIA-PET and promoter-capture HiC techniques. We expand this validation scheme by using also loops that overlap in their anchor sites. In analyzing 1,366 samples from ENCODE, Roadmap epigenomics and FANTOM5, CT-FOCS inferred highly cell type-specific EP links more accurately than state-of-the-art methods. We illustrate how our inferred EP links drive cell type-specific gene expression and regulation.

scholarly journals Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

2020 ◽  
Author(s):  
Lei Chang ◽  
Mengfan Li ◽  
Shipeng Shao ◽  
Chen Li ◽  
Shanshan Ai ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Three Dimensional ◽  
Higher Order ◽  
Order Structure ◽  
Chromatin Dynamics ◽  
Lamin B1 ◽  
Chromatin Architecture ◽  
Chromatin Interactions ◽  
Molecular Machinery

Abstract The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.

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