Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation

Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization, and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating HOXA expression during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks. Interestingly, Nup93 and CTCF are associated with the 3' and 5′HOXA genes respectively. Depletions of Nup93 and CTCF antagonistically modulate expression levels of 3′and 5′HOXA genes in undifferentiated NT2/D1 cells. Nup93 also regulates the localization of the HOXA gene locus, which disengages from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. The dynamic association of Nup93 and CTCF with the HOXA locus during differentiation correlates with its spatial positioning and expression. While Nup93 tethers the HOXA locus to the nuclear periphery, CTCF potentially regulates looping of the HOXA gene cluster in a temporal manner. In summary, Nup93 and CTCF complement one another in modulating the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

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Nup93 and CTCF co-modulate spatiotemporal dynamics and function of the HOXA gene cluster during differentiation

10.1101/646224 ◽

2019 ◽

Author(s):

Ajay S. Labade ◽

Adwait Salvi ◽

Krishanpal Karmodiya ◽

Kundan Sengupta

Keyword(s):

Gene Expression ◽

Gene Locus ◽

Nuclear Periphery ◽

Spatiotemporal Dynamics ◽

Differentiated Cells ◽

Undifferentiated Cells ◽

Dynamics And Function ◽

Hoxa Gene Expression ◽

And Function ◽

Hoxa Gene

ABSTRACTNucleoporins regulate nuclear transport. In addition, nucleoporins also modulate chromatin organization and gene expression. Here we investigated the role of nucleoporin Nup93, in regulating HOXA gene expression during differentiation. ChIP-Seq analysis revealed that Nup93 associates with genes involved in development and differentiation. Furthermore, Nup93 occupancy significantly overlaps with CTCF. Interestingly, Nup93 and CTCF show antagonistic roles in regulating 3’ and 5’ end HOXA genes in undifferentiated cells. The HOXA gene locus untethered from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. Remarkably, occupancy of Nup93 and CTCF on HOXA gene locus progressively declined during differentiation but was restored in differentiated cells, consistent with the rerepression and re-localization of the HOXA gene locus with the nuclear periphery upon differentiation. In summary, Nup93 is a key modulator of the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

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First person – Ajay Labade and Adwait Salvi

Journal of Cell Science ◽

10.1242/jcs.259605 ◽

2021 ◽

Vol 134 (23) ◽

Keyword(s):

Genome Organization ◽

Harvard University ◽

Early Career ◽

First Person ◽

3D Genome ◽

Dynamics And Function ◽

And Function ◽

Selection Of ◽

Hoxa Gene

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Ajay Labade and Adwait Salvi are co-first authors on ‘ Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation’, published in JCS. Ajay is a postdoctoral researcher in the lab of Dr Jason Buenrostro at Harvard University, Cambridge, USA, where he develops multimodal genomics technologies for the investigation of functional genome organization. Adwait is a PhD student in the lab of Filippo Rijli at Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, who works on deciphering the role of 3D genome organization in gene regulation during differentiation.

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Regulation Of Normal and Malignant Hoxa Gene Expression Through Higher H3K79 Methylated States

Blood ◽

10.1182/blood.v122.21.2492.2492 ◽

2013 ◽

Vol 122 (21) ◽

pp. 2492-2492 ◽

Cited By ~ 1

Author(s):

Aniruddha J Deshpande ◽

Liying Chen ◽

Amit U. Sinha ◽

Nan Zhu ◽

David Chen ◽

...

Keyword(s):

Gene Expression ◽

Target Genes ◽

Chromatin Accessibility ◽

Epigenetic Changes ◽

Hematopoietic Differentiation ◽

Chip Sequencing ◽

Hoxa Genes ◽

Hoxa Gene Expression ◽

H3k79 Methylation ◽

Hoxa Gene

Abstract The clustered Hoxa genes Hoxa5-Hoxa10 are important for self-renewal and differentiation of hematopoietic stem and progenitor cells. These genes are often aberrant upregulated in human malignancies, one of the most striking examples of which are leukemias with rearrangements of the mixed lineage leukemia (MLL) gene. Since these key posterior Hoxa cluster genes are known to show graded down-regulation upon hematopoietic differentiation, we sought to assess the epigenetic changes associated with this tightly controlled, developmentally critical transcriptional program. We performed ChIP sequencing on lineage negative, Sca-1 + Kit + (LSK) cells where the posterior Hoxa5-10genes are highly expressed compared to granulocyte macrophage progenitors (GMPs) that show markedly lower expression of these transcripts. We observed a dramatic diminution in H3K79 di/tri methylation as cells differentiated from LSKs to GMPs. In contrast, we found minimal changes in H3K79 mono-methylation during the LSK-GMP transition suggesting that high expression of Hoxa genes is maintained through higher H3K79 methylated states in normal hematopoiesis. Strikingly, the removal of H3K79 me2/3 but not me1 was sufficient for repressive epigenetic mechanisms such as polycomb repressive complex 2 (PRC2)- mediated H3K27 tri-methylation to invade the Hoxa locus during the LSK to GMP differentiation. The decrease in H3K79 di/tri methylation upon hematopoietic differentiation may be the result of a graded decrease in expression of the DOT1L co-factor Af10 which we have recently found to regulate the transition from H3K79 mono to dimethylation. Next we wanted to probe whether MLL-leukemias drive Hoxa gene expression through increased conversion of H3K79 methylation from the mono to the di/tri-methylated states. We performed ChIP sequencing for H3K79 me1/2/3 to identify the different states of H3K79 methylation across the epigenetic landscape of MLL-transformed cells. Strikingly we observed that in both murine and human leukemia, there was a dramatic hyper-conversion of H3K79 mono-methylation to di/trimethylation specifically at MLL-AF9 target genes. Af10 deletion in the MLL-AF9 leukemia significantly reduced H3K79me2/3 while retaining - and in some cases even increasing - H3K79 me1 at MLL-target genes. We then assessed chromatin accessibility at the Hoxa locus following nuclease digestion and observed that the diminution of H3K79me2/3 was enough to significantly reduce chromatin accessibility at the Hoxa locus despite the relative retention of H3K79me1. Similar to the LSK-GMP transition, reduction in H3K79 me2/3 but not H3K79me1 was accompanied by a dramatic increase in H3K27me3 in a very specific subset of genes including Hoxa5-10. The genetic and epigenetic changes resulting from Af10 deletion significantly impaired MLL-leukemogenesis and sensitized leukemia cells to DOT1L inhibition. These results suggest that the expression of Hoxa genes in hematopoiesis is controlled through higher H3K79 methylated states, possibly aided by the DOT1L co-factor Af10. The MLL-AF9 fusion seems to hijack this mode of regulation through aberrant hyperconversion of H3K79 methylation to higher methylated states at critical oncogenic targets including the Hoxa genes. These data suggest that targeting the interaction between DOT1L and Af10 is a potential therapeutic strategy since it blunts the conversion of H3K79me1 to higher states of methylation by MLL-fusion proteins and thus significantly impairs MLL-mediated transformation. Disclosures: Armstrong: Epizyme: Consultancy.

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Faculty Opinions recommendation of Dynamics and function of Langerhans cells in vivo: dermal dendritic cells colonize lymph node areas distinct from slower migrating Langerhans cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1015121.342353 ◽

2005 ◽

Author(s):

Andrea Sant

Keyword(s):

Dendritic Cells ◽

Lymph Node ◽

Langerhans Cells ◽

Dynamics And Function ◽

And Function

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Correlating polymer structure, dynamics, and function with atomic force microscopy

Journal of Polymer Science ◽

10.1002/pol.20210321 ◽

2021 ◽

Author(s):

Julia G. Murphy ◽

Jonathan G. Raybin ◽

Steven J. Sibener

Keyword(s):

Atomic Force Microscopy ◽

Polymer Structure ◽

Force Microscopy ◽

Structure Dynamics ◽

Atomic Force ◽

Dynamics And Function ◽

And Function

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Exploring the microbiome in health and disease

Toxicology Research and Application ◽

10.1177/2397847317741884 ◽

2017 ◽

Vol 1 ◽

pp. 239784731774188 ◽

Cited By ~ 5

Author(s):

Elena Scotti ◽

Stéphanie Boué ◽

Giuseppe Lo Sasso ◽

Filippo Zanetti ◽

Vincenzo Belcastro ◽

...

Keyword(s):

Human Health ◽

Metabolic Diseases ◽

Skin Diseases ◽

Human Microbiome ◽

Chronic Obstructive ◽

Microbial Composition ◽

Obstructive Pulmonary Disease ◽

New Findings ◽

Dynamics And Function ◽

And Function

The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.

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Critical requirement of SOS1 RAS-GEF function for mitochondrial dynamics, metabolism, and redox homeostasis

Oncogene ◽

10.1038/s41388-021-01886-3 ◽

2021 ◽

Author(s):

Rósula García-Navas ◽

Pilar Liceras-Boillos ◽

Carmela Gómez ◽

Fernando C. Baltanás ◽

Nuria Calzada ◽

...

Keyword(s):

Mitochondrial Dynamics ◽

Redox Homeostasis ◽

Atp Production ◽

Oxidative Energy Metabolism ◽

Ras Activation ◽

Mitochondrial Defects ◽

Critical Requirement ◽

Dynamics And Function ◽

And Function ◽

And Control

AbstractSOS1 ablation causes specific defective phenotypes in MEFs including increased levels of intracellular ROS. We showed that the mitochondria-targeted antioxidant MitoTEMPO restores normal endogenous ROS levels, suggesting predominant involvement of mitochondria in generation of this defective SOS1-dependent phenotype. The absence of SOS1 caused specific alterations of mitochondrial shape, mass, and dynamics accompanied by higher percentage of dysfunctional mitochondria and lower rates of electron transport in comparison to WT or SOS2-KO counterparts. SOS1-deficient MEFs also exhibited specific alterations of respiratory complexes and their assembly into mitochondrial supercomplexes and consistently reduced rates of respiration, glycolysis, and ATP production, together with distinctive patterns of substrate preference for oxidative energy metabolism and dependence on glucose for survival. RASless cells showed defective respiratory/metabolic phenotypes reminiscent of those of SOS1-deficient MEFs, suggesting that the mitochondrial defects of these cells are mechanistically linked to the absence of SOS1-GEF activity on cellular RAS targets. Our observations provide a direct mechanistic link between SOS1 and control of cellular oxidative stress and suggest that SOS1-mediated RAS activation is required for correct mitochondrial dynamics and function.

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Dynamics and function of compact nucleosome arrays

Nature Structural & Molecular Biology ◽

10.1038/nsmb.1650 ◽

2009 ◽

Vol 16 (9) ◽

pp. 938-944 ◽

Cited By ~ 88

Author(s):

Michael G Poirier ◽

Eugene Oh ◽

Hannah S Tims ◽

Jonathan Widom

Keyword(s):

Dynamics And Function ◽

And Function ◽

Nucleosome Arrays

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Dynamics and mechanism of ultrafast water–protein interactions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1602916113 ◽

2016 ◽

Vol 113 (30) ◽

pp. 8424-8429 ◽

Cited By ~ 77

Author(s):

Yangzhong Qin ◽

Lijuan Wang ◽

Dongping Zhong

Keyword(s):

Protein Interactions ◽

Hydration Shell ◽

Water Dynamics ◽

Side Chain ◽

Water Molecules ◽

Ultrafast Dynamics ◽

Hydration Water ◽

Water Side ◽

Dynamics And Function ◽

And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

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