Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner

SUMMARYLinker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we have identified a new function of histone H1 in chromatin structure and transcription using a range of genomic approaches. We show that histone H1-depleted cells accumulate nascent non-coding RNAs on chromatin, suggesting that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accumulated non-coding transcripts have reduced levels of m6A modification and cause replication-transcription conflicts. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism and DNA replication to maintain genome performance.

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Genome-wide errant targeting by Hairy

eLife ◽

10.7554/elife.06394 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 7

Author(s):

Kurtulus Kok ◽

Ahmet Ay ◽

Li M Li ◽

David N Arnosti

Keyword(s):

Gene Expression ◽

Target Genes ◽

Regulatory Elements ◽

Transcriptional Repressors ◽

Biochemical Activity ◽

Specific Effects ◽

Genome Wide ◽

Context Specific ◽

Enhancer Of Split ◽

Drosophila Embryos

Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.

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Cell Context-specific Effects of the β-Tubulin Glycylation Domain on Assembly and Size of Microtubular Organelles

Molecular Biology of the Cell ◽

10.1091/mbc.e04-03-0247 ◽

2004 ◽

Vol 15 (9) ◽

pp. 4136-4147 ◽

Cited By ~ 40

Author(s):

Rupal Thazhath ◽

Maria Jerka-Dziadosz ◽

Jianming Duan ◽

Dorota Wloga ◽

Martin A. Gorovsky ◽

...

Keyword(s):

Posttranslational Modification ◽

Basal Bodies ◽

Cortical Microtubules ◽

Microtubule Associated Proteins ◽

Specific Effects ◽

Associated Proteins ◽

Context Specific ◽

Mutant Cells ◽

Microtubular Organelles ◽

Β Tubulin

Tubulin glycylation is a posttranslational modification found in cells with cilia or flagella. The ciliate Tetrahymena has glycylation on ciliary and cortical microtubules. We showed previously that mutating three glycylation sites on β-tubulin produces immotile 9 + 0 axonemes and inhibits cytokinesis. Here, we use an inducible glycylation domain mutation and epitope tagging to evaluate the potential of glycylation-deficient tubulin for assembly and maintenance of microtubular systems. In axonemes, the major defects, including lack of the central pair, occurred during assembly, and newly made cilia were abnormally short. The glycylation domain also was required for maintenance of the length of already assembled cilia. In contrast to the aberrant assembly of cilia, several types of cortical organelles showed an abnormally high number of microtubules in the same mutant cells. Thus, the consequences of deficiency in tubulin glycylation are organelle type specific and lead to either insufficient assembly (cilia) or excessive assembly (basal bodies and cortical microtubules). We suggest that the diverse functions of the β-tubulin glycylation domain are executed by spatially restricted microtubule-associated proteins.

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H3K27 modifiers regulate lifespan in C. elegans in a context-dependent manner

BMC Biology ◽

10.1186/s12915-021-00984-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Abigail R. R. Guillermo ◽

Karolina Chocian ◽

Gavriil Gavriilidis ◽

Julien Vandamme ◽

Anna Elisabetta Salcini ◽

...

Keyword(s):

Lifespan Extension ◽

Dependent Manner ◽

Loss Of Function ◽

Animal Cells ◽

C Elegans ◽

Specific Effects ◽

Aberrant Gene Expression ◽

Lysine Methyltransferase ◽

Epigenetic Signatures ◽

Aberrant Gene

Abstract Background Evidence of global heterochromatin decay and aberrant gene expression in models of physiological and premature ageing have long supported the “heterochromatin loss theory of ageing”, which proposes that ageing is aetiologically linked to, and accompanied by, a progressive, generalised loss of repressive epigenetic signatures. However, the remarkable plasticity of chromatin conformation suggests that the re-establishment of such marks could potentially revert the transcriptomic architecture of animal cells to a “younger” state, promoting longevity and healthspan. To expand our understanding of the ageing process and its connection to chromatin biology, we screened an RNAi library of chromatin-associated factors for increased longevity phenotypes. Results We identified the lysine demethylases jmjd-3.2 and utx-1, as well as the lysine methyltransferase mes-2 as regulators of both lifespan and healthspan in C. elegans. Strikingly, we found that both overexpression and loss of function of jmjd-3.2 and utx-1 are all associated with enhanced longevity. Furthermore, we showed that the catalytic activity of UTX-1, but not JMJD-3.2, is critical for lifespan extension in the context of overexpression. In attempting to reconcile the improved longevity associated with both loss and gain of function of utx-1, we investigated the alternative lifespan pathways and tissue specificity of longevity outcomes. We demonstrated that lifespan extension caused by loss of utx-1 function is daf-16 dependent, while overexpression effects are partially independent of daf-16. In addition, lifespan extension was observed when utx-1 was knocked down or overexpressed in neurons and intestine, whereas in the epidermis, only knockdown of utx-1 conferred improved longevity. Conclusions We show that the regulation of longevity by chromatin modifiers can be the result of the interaction between distinct factors, such as the level and tissue of expression. Overall, we suggest that the heterochromatin loss model of ageing may be too simplistic an explanation of organismal ageing when molecular and tissue-specific effects are taken into account.

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Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner

Scientific Reports ◽

10.1038/s41598-021-89075-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nesreen Hamad ◽

Ryoma Yoneda ◽

Masatomo So ◽

Riki Kurokawa ◽

Takashi Nagata ◽

...

Keyword(s):

Shear Stress ◽

Neurodegenerative Diseases ◽

Suppressive Effect ◽

Dependent Manner ◽

Aggregation State ◽

Fused In Sarcoma ◽

Sequence Dependent ◽

Non Coding Rna ◽

Aggregation Inhibitors ◽

Amorphous Aggregation

AbstractFused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.

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Specific release of membrane-bound annexin II and cortical cytoskeletal elements by sequestration of membrane cholesterol.

Molecular Biology of the Cell ◽

10.1091/mbc.8.3.533 ◽

1997 ◽

Vol 8 (3) ◽

pp. 533-545 ◽

Cited By ~ 159

Author(s):

T Harder ◽

R Kellner ◽

R G Parton ◽

J Gruenberg

Keyword(s):

Actin Cytoskeleton ◽

Cytoskeletal Proteins ◽

Annexin Ii ◽

Dependent Manner ◽

Cortical Actin ◽

Independent Manner ◽

Low Concentrations ◽

Early Endosomes ◽

Associated Proteins ◽

Cytoskeletal Elements

Annexin II is an abundant protein which is present in the cytosol and on the cytoplasmic face of plasma membrane and early endosomes. It is generally believed that this association occurs via Ca(2+)-dependent binding to lipids, a mechanism typical for the annexin protein family. Although previous studies have shown that annexin II is involved in early endosome dynamics and organization, the precise biological role of the protein is unknown. In this study, we found that approximately 50% of the total cellular annexin was associated with membranes in a Ca(2+)-independent manner. This binding was extremely tight, since it resisted high salt and, to some extent, high pH treatments. We found, however, that membrane-associated annexin II could be quantitatively released by low concentrations of the cholesterol-sequestering agents filipin and digitonin. Both treatments released an identical and limited set of proteins but had no effects on other membrane-associated proteins. Among the released proteins, we identified, in addition to annexin II itself, the cortical cytoskeletal proteins alpha-actinin, ezrin and moesin, and membrane-associated actin. Our biochemical and immunological observations indicate that these proteins are part of a complex containing annexin II and that stability of the complex is sensitive to cholesterol sequestering agents. Since annexin II is tightly membrane-associated in a cholesterol-dependent manner, and since it seems to interact physically with elements of the cortical actin cytoskeleton, we propose that the protein serves as interface between membranes containing high amounts of cholesterol and the actin cytoskeleton.

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ERP Evidence for Implicit Priming of Top–Down Control of Attention

Journal of Cognitive Neuroscience ◽

10.1162/jocn_a_00925 ◽

2016 ◽

Vol 28 (5) ◽

pp. 763-772 ◽

Cited By ~ 2

Author(s):

Chris Blais ◽

Emily Hubbard ◽

George R. Mangun

Keyword(s):

Associative Learning ◽

Stroop Effect ◽

Congruency Effect ◽

Simon Task ◽

Electrical Signal ◽

Lower Visual Field ◽

Specific Effects ◽

High Conflict ◽

Contemporary Work ◽

Context Specific

Proportion congruency effects are the observation that the magnitude of the Stroop effect increases as the proportion of congruent trials in a block increases. Contemporary work shows that proportion effects can be specific to a particular context. For example, in a Simon task in which items appearing above fixation are mostly congruent and items appearing below fixation are mostly incongruent, the Simon effect is larger for the items appearing at the top. There is disagreement as to whether these context-specific effects result from simple associative learning or, instead, a type of conflict-mediated associative learning. Here, we address this question in an ERP study using a Simon task in which the proportion congruency effect was context-specific, manipulating the proportion of congruent trials based on location (upper vs. lower visual field). We found significant behavioral proportion congruency effects that varied with the specific contexts. In addition, we observed that the N2 response of the ERPs to the stimuli was larger in amplitude for the high congruent (high conflict) versus low congruent (low conflict) conditions/contexts. Because the N2 is known to be greater in amplitude also for trials where conflict is high and is believed to be an electrical signal related to conflict detection in the medial frontal cortex, this supports the idea that conflict-mediated associative learning is involved in the proportion congruency effect.

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Roscovitine, a specific inhibitor of cyclin-dependent protein kinases, reversibly inhibits chromatin condensation during in vitro maturation of porcine oocytes

Zygote ◽

10.1017/s0967199401001356 ◽

2001 ◽

Vol 9 (4) ◽

pp. 309-316 ◽

Cited By ~ 21

Author(s):

Carsten Krischek ◽

Burkhard Meinecke

Keyword(s):

Map Kinase ◽

Protein Kinases ◽

Chromatin Condensation ◽

Specific Inhibitor ◽

Histone H1 ◽

Dependent Manner ◽

Free Medium ◽

Concentration Dependent Manner ◽

Dependent Protein

In the present study the effects of roscovitine on the in vitro nuclear maturation of porcine oocytes were investigated. Roscovitine, a specific inhibitor of cyclin-dependent protein kinases, prevented chromatin condensation in a concentration-dependent manner. This inhibition was reversible and was accompanied by non-activation of p34cdc2/histone H1 kinase. It also decreased enzyme activity of MAP kinase, suggesting a correlation between histone H1 kinase activation and the onset of chromatin condensation. The addition of roscovitine (50 μM) to extracts of metaphase II oocytes revealed that the MAP kinase activity was not directly affected by roscovitine, which indicates a possible link between histone H1 and MAP kinase. Chromatin condensation occurred between 20 and 28 h of culture of cumulus-oocyte complexes (COCs) in inhibitor-free medium (germinal vesicle stage I, GV1: 74.6% and 13.7%, respectively). Nearly the same proportion of chromatin condensation was detected in COCs incubated initially in inhibitor-free medium for 20-28 h and subsequently in roscovitine-supplemented medium (50 μM) for a further 2-10 h (GV I: 76.2% and 18.8%, respectively). This observation indicates that roscovitine prevents chromatin condensation even after an initial inhibitor-free cultivation for 20 h. Extending this initial incubation period to ≥22 h led to an activation of histone H1 and MAP kinase and increasing proportions of oocytes exhibiting chromatin condensation in the presence of roscovitine. It is concluded that histone H1 kinase is involved in the induction of chromatin condensation during in vitro maturation of porcine oocytes.

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Phosphorylation of linker histones by DNA-dependent protein kinase is required for DNA ligase IV-dependent ligation in the presence of histone H1

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0401179102 ◽

2005 ◽

Vol 102 (6) ◽

pp. 1877-1882 ◽

Cited By ~ 36

Author(s):

B. Kysela ◽

M. Chovanec ◽

P. A. Jeggo

Keyword(s):

Protein Kinase ◽

Histone H1 ◽

Dna Ligase ◽

Dependent Protein Kinase ◽

Linker Histones ◽

Dna Ligase Iv ◽

Ligase Iv ◽

Dependent Protein

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Association between Hsp90 and the ClC-2 chloride channel upregulates channel function

AJP Cell Physiology ◽

10.1152/ajpcell.00209.2005 ◽

2006 ◽

Vol 290 (1) ◽

pp. C45-C56 ◽

Cited By ~ 35

Author(s):

Alexandre Hinzpeter ◽

Joanna Lipecka ◽

Franck Brouillard ◽

Maryvonne Baudoin-Legros ◽

Michal Dadlez ◽

...

Keyword(s):

Chloride Channel ◽

Fluid Transport ◽

Cell Swelling ◽

Dependent Manner ◽

Patch Clamp Technique ◽

Mass Spectrometry Identification ◽

Voltage Dependent ◽

Channel Expression ◽

Associated Proteins ◽

Cellular Stresses

The voltage-dependent ClC-2 chloride channel has been implicated in a variety of physiological functions, including fluid transport across specific epithelia. ClC-2 is activated by hyperpolarization, weakly acidic external pH, intracellular Cl−, and cell swelling. To add more insight into the mechanisms involved in ClC-2 regulation, we searched for associated proteins that may influence ClC-2 activity. With the use of immunoprecipitation of ClC-2 from human embryonic kidney-293 cells stably expressing the channel, followed by electrophoretic separation of coimmunoprecipitated proteins and mass spectrometry identification, Hsp70 and Hsp90 were unmasked as possible ClC-2 interacting partners. Association of Hsp90 with ClC-2 was confirmed in mouse brain. Inhibition of Hsp90 by two specific inhibitors, geldanamycin or radicicol, did not affect total amounts of ClC-2 but did reduce plasma membrane channel abundance. Functional experiments using the whole cell configuration of the patch-clamp technique showed that inhibition of Hsp90 reduced ClC-2 current amplitude and impaired the intracellular Cl− concentration [Cl−]-dependent rightward shift of the fractional conductance. Geldanamycin and radicicol increased both the slow and fast activation time constants in a chloride-dependent manner. Heat shock treatment had the opposite effect. These results indicate that association of Hsp90 with ClC-2 results in greater channel activity due to increased cell surface channel expression, facilitation of channel opening, and enhanced channel sensitivity to intracellular [Cl−]. This association may have important pathophysiological consequences, enabling increased ClC-2 activity in response to cellular stresses such as elevated temperature, ischemia, or oxidative reagents.

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