AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

AbstractAside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.

Download Full-text

Acute condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae

10.1101/195487 ◽

2017 ◽

Cited By ~ 2

Author(s):

Matthew Robert Paul ◽

Tovah Elise Markowitz ◽

Andreas Hochwagen ◽

Sevinç Ercan

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Genome Organization ◽

Large Scale ◽

Global Gene Expression ◽

Higher Order ◽

Gene Clustering ◽

Global Changes ◽

Chromatin Compaction ◽

And Function

AbstractCondensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation leads to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program of S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.Significance StatementGene expression occurs in the context of higher-order chromatin organization, which helps compact the genome within the spatial constraints of the nucleus. To what extent higher-order chromatin compaction affects gene expression remains unknown. Here, we show that gene expression and genome compaction can be uncoupled in the single-celled model eukaryote Saccharomyces cerevisiae. Inactivation of the conserved condensin complex, which also organizes the human genome, leads to broad genome decompaction in this organism. Unexpectedly, this reorganization has no immediate effect on the transcriptome. These findings indicate that the global gene expression program is robust to large-scale changes in genome architecture in yeast, shedding important new light on the evolution and function of genome organization in gene regulation.

Download Full-text

Role of lamins in 3D genome organization and global gene expression

Nucleus ◽

10.1080/19491034.2019.1578601 ◽

2019 ◽

Vol 10 (1) ◽

pp. 33-41 ◽

Cited By ~ 3

Author(s):

Youngjo Kim ◽

Xiaobin Zheng ◽

Yixian Zheng

Keyword(s):

Gene Expression ◽

Genome Organization ◽

Global Gene Expression ◽

3D Genome

Download Full-text

Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response

10.1101/2020.01.24.917823 ◽

2020 ◽

Author(s):

Ariadna Picart-Picolo ◽

Stefan Grob ◽

Nathalie Picault ◽

Michal Franek ◽

Thierry halter ◽

...

Keyword(s):

Gene Expression ◽

Genomic Instability ◽

Ribosomal Rna ◽

Plant Pathogen ◽

Genome Organization ◽

Global Gene Expression ◽

Rrna Gene ◽

3D Genome ◽

Gene Copies ◽

Pathogen Response

ABSTRACTAmong the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA line). Compared to the wild-type Col-0, the 20rDNA line shows several signs of genomic instability, such as variations in 3D genome organization, spontaneous double-strand breaks accumulation, transcriptomic changes, and higher DNA methylation level. Strikingly, using genomic and microscopic approaches, we identified seven large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. As a consequence, more than 600 genes were duplicated, often associated with an increase in their expression level. Among them, we found several upregulated genes involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and we discuss their potential implications on plant genome evolution.

Download Full-text

Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽

10.1534/genetics.119.302978 ◽

2020 ◽

Vol 214 (3) ◽

pp. 651-667 ◽

Cited By ~ 2

Author(s):

Marco Di Stefano ◽

Francesca Di Giovanni ◽

Vasilisa Pozharskaia ◽

Mercè Gomar-Alba ◽

Davide Baù ◽

...

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Nuclear Organization ◽

Nuclear Periphery ◽

Three Dimensional ◽

Global Gene Expression ◽

3D Genome ◽

Expression Of Genes ◽

Genome Wide ◽

Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

Download Full-text

Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains

Genes ◽

10.3390/genes10030196 ◽

2019 ◽

Vol 10 (3) ◽

pp. 196 ◽

Cited By ~ 6

Author(s):

Phoebe Oldach ◽

Conrad A. Nieduszynski

Keyword(s):

Dna Replication ◽

Genome Organization ◽

Mammalian Cells ◽

Replication Timing ◽

S Phase ◽

Genome Architecture ◽

3D Genome ◽

Synchronized Cells ◽

Dna Replication Timing ◽

Phase Entry

3D genome organization is strongly predictive of DNA replication timing in mammalian cells. This work tested the extent to which loop-based genome architecture acts as a regulatory unit of replication timing by using an auxin-inducible system for acute cohesin ablation. Cohesin ablation in a population of cells in asynchronous culture was shown not to disrupt patterns of replication timing as assayed by replication sequencing (RepliSeq) or BrdU-focus microscopy. Furthermore, cohesin ablation prior to S phase entry in synchronized cells was similarly shown to not impact replication timing patterns. These results suggest that cohesin-mediated genome architecture is not required for the execution of replication timing patterns in S phase, nor for the establishment of replication timing domains in G1.

Download Full-text

Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

Genes ◽

10.3390/genes10121049 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1049 ◽

Cited By ~ 4

Author(s):

Annick Lesne ◽

Marie-Odile Baudement ◽

Cosette Rebouissou ◽

Thierry Forné

Keyword(s):

Gene Expression ◽

Self Assembly ◽

Genome Organization ◽

Physical Nature ◽

Mammalian Genome ◽

Nuclear Bodies ◽

Control Of Gene Expression ◽

Chromatin Interactions ◽

Nuclear Structures ◽

Genomic Regions

The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active/inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase-separated nuclear bodies possibly contributes to mammalian genome organization and gene expression.

Download Full-text

The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated bysyrAandnodD3

Journal of Bacteriology ◽

10.1128/jb.02626-14 ◽

2015 ◽

Vol 197 (10) ◽

pp. 1792-1806 ◽

Cited By ~ 18

Author(s):

Melanie J. Barnett ◽

Sharon R. Long

Keyword(s):

Gene Expression ◽

Sinorhizobium Meliloti ◽

Developmental Process ◽

Global Gene Expression ◽

Subsequent Increase ◽

Altered Expression ◽

Content Type ◽

Regulatory Circuit ◽

Regulatory Circuits ◽

Exogenous Compounds

ABSTRACTInSinorhizobium meliloti, three NodD transcriptional regulators activate bacterial nodulation (nod) gene expression. NodD1 and NodD2 require plant compounds to activatenodgenes. The NodD3 protein does not require exogenous compounds to activatenodgene expression; instead, another transcriptional regulator, SyrM, activatesnodD3expression. In addition, NodD3 can activatesyrMexpression. SyrM also activates expression of another gene,syrA, which when overexpressed causes a dramatic increase in exopolysaccharide production. In a previous study, we identified more than 200 genes with altered expression in a strain overexpressingnodD3. In this work, we define the transcriptomes of strains overexpressingsyrMorsyrA. ThesyrM,nodD3, andsyrAoverexpression transcriptomes share similar gene expression changes; analyses imply thatnodD3andsyrAare the only targets directly activated by SyrM. We propose that most of the gene expression changes observed whennodD3is overexpressed are due to NodD3 activation ofsyrMexpression, which in turn stimulates SyrM activation ofsyrAexpression. The subsequent increase in SyrA abundance results in broad changes in gene expression, most likely mediated by the ChvI-ExoS-ExoR regulatory circuit.IMPORTANCESymbioses with bacteria are prevalent across the animal and plant kingdoms. Our system of study, the rhizobium-legume symbiosis (Sinorhizobium melilotiandMedicagospp.), involves specific host-microbe signaling, differentiation in both partners, and metabolic exchange of bacterial fixed nitrogen for host photosynthate. During this complex developmental process, both bacteria and plants undergo profound changes in gene expression. TheS. melilotiSyrM-NodD3-SyrA and ChvI-ExoS-ExoR regulatory circuits affect gene expression and are important for optimal symbiosis. In this study, we defined the transcriptomes ofS. melilotioverexpressing SyrM or SyrA. In addition to identifying new targets of the SyrM-NodD3-SyrA regulatory circuit, our work further suggests how it is linked to the ChvI-ExoS-ExoR regulatory circuit.

Download Full-text

Mammary gland morphological and gene expression changes underlying pregnancy protection of breast cancer tumorigenesis

Physiological Genomics ◽

10.1152/physiolgenomics.00056.2011 ◽

2012 ◽

Vol 44 (1) ◽

pp. 76-88 ◽

Cited By ~ 11

Author(s):

Yogi Misra ◽

Pamela A. Bentley ◽

Jeffrey P. Bond ◽

Scott Tighe ◽

Timothy Hunter ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Mammary Gland ◽

Global Gene Expression ◽

Full Term ◽

Mammary Tissue ◽

Protective Mechanism ◽

Global Changes ◽

Term Pregnancy ◽

Short Term Treatment

A full-term pregnancy early in life reduces lifetime risk of developing breast cancer, and the effect can be mimicked in rodents by full-term pregnancy or short-term treatment with exogenous estrogen and progesterone. To gain insight into the protective mechanism, 15 3-mo-old postpubertal virgin Lewis rats were randomly assigned to three groups: control (C), pregnancy (P), or hormone (H). The P group animals underwent a full-term pregnancy, and H group animals were implanted subcutaneously with silastic capsules filled with ethynyl estradiol and megesterol acetate for 21 days. C and P animals were implanted with sham capsules. On day 21 capsules were removed, which was followed by a 49-day involution period, euthanasia, and mammary tissue collection. Global gene expression was measured using Rat Genome 230.2 Arrays. Histological analysis revealed that P and H treatments induced sustained morphological changes in the mammary gland with significantly increased percentages of mammary parenchyma and stromal tissues and higher ratio of stroma to parenchyma. Transcriptome analysis showed that P and H treatments induced sustained global changes in gene expression in the mammary gland. Analysis of commonly up- and downregulated genes in P and H relative to C treatment showed increased expression of three matrix metallopeptidases (Mmp3, 8, and 12), more differentiated mammary phenotype, enhanced innate and adaptive immunity, and reduced cell proliferation and angiogenic signatures. The sustained morphological and global gene expression changes in mammary tissue after pregnancy and hormone treatment may function together to provide the protective effect against breast cancer.

Download Full-text

Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain

Physiological Genomics ◽

10.1152/physiolgenomics.00076.2004 ◽

2004 ◽

Vol 18 (3) ◽

pp. 331-339 ◽

Cited By ~ 18

Author(s):

Dan Zhou ◽

Jin Xue ◽

Orit Gavrialov ◽

Gabriel G. Haddad

Keyword(s):

Gene Expression ◽

Mouse Brain ◽

Global Gene Expression ◽

Brain Regions ◽

Inhibitory Effect ◽

Null Mouse ◽

Null Mutation ◽

Null Mutant ◽

Altered Expression ◽

Null Mutant Mice

Na+/H+ exchanger 1 (NHE1) is well known to function as a major regulator of intracellular pH (pHi). It is activated by low pHi and exchanges extracellular Na+ for intracellular H+ to maintain cellular homeostasis. Despite the fact that we now have evidence suggesting other roles for NHE1, there has been no comprehensive study investigating its role as a signaling molecule. Toward this aim, we used in this study NHE1 null mutant mice and cDNA microarrays to investigate the effects of NHE1 on global gene expression in various regions of the brain, e.g., cortex, hippocampus, brain stem-diencephalon, and cerebellum. We found that a total of 35 to 79 genes were up- or downregulated in each brain region, with the majority being downregulated. The effect of NHE1 null mutation on gene expression is region specific, and only 11 genes were changed in all brain regions studied. Further analysis of the cis-regulatory regions of downregulated genes revealed that transcription suppressors, BCL6 and E4BP4, were probable candidates that mediated the inhibitory effect of NHE1 null mutation. One of the genes, MCT-13, was not only downregulated in the NHE1 null mutant brain but also in tissue cultures treated with an NHE1 inhibitor. We conclude that 1) a relatively small number of genes were altered in the NHE1 null mouse brain; 2) the effects of NHE1 null mutation on gene expression are region specific; and 3) several genes implicated in neurodegeneration have altered expression, potentially offering a molecular explanation for the phenotype of the NHE1 null mouse.

Download Full-text