Poly ADP-ribosylation of SET8 leads to aberrant H4K20me1 domains in mammalian cells

In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised and it undergoes degradation via ubiquitylation pathway. Knockdown of PARP1 shifted the relative dynamic equilibrium of H4K20me2 to H4k20me3 in cells. Overexpression or knockdown of PARP1 led to aberrant H4K20me1 domains genome-wide, impacting Wnt signaling pathways genes and transcription factor binding site enrichment. Therefore, SET8 mediated chromatin remodeling and gene expression in mammalian cells are influenced by poly ADP-ribosylation by PARP1.

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Gcn5-mediated acetylation at MBF-regulated promoters induces the G1/S transcriptional wave

Nucleic Acids Research ◽

10.1093/nar/gkz561 ◽

2019 ◽

Vol 47 (16) ◽

pp. 8439-8451 ◽

Cited By ~ 1

Author(s):

Alberto González-Medina ◽

Elena Hidalgo ◽

José Ayté

Keyword(s):

Cell Cycle ◽

Molecular Mechanisms ◽

Histone H3 ◽

Dependent Manner ◽

Saga Complex ◽

Lysine Residues ◽

Physical Barriers ◽

A Cell ◽

Cycle Dependent ◽

Regulated Promoters

Abstract In fission yeast, MBF-dependent transcription is inactivated at the end of S phase through a negative feedback loop that involves the co-repressors, Yox1 and Nrm1. Although this repression system is well known, the molecular mechanisms involved in MBF activation remain largely unknown. Compacted chromatin constitutes a barrier to activators accessing promoters. Here, we show that chromatin regulation plays a key role in activating MBF-dependent transcription. Gcn5, a part of the SAGA complex, binds to MBF-regulated promoters through the MBF co-activator Rep2 in a cell cycle-dependent manner and in a reverse correlation to the binding of the MBF co-repressors, Nrm1 or Yox1. We propose that the co-repressors function as physical barriers to SAGA recruitment onto MBF promoters. We also show that Gcn5 acetylates specific lysine residues on histone H3 in a cell cycle-regulated manner. Furthermore, either in a gcn5 mutant or in a strain in which histone H3 is kept in an unacetylated form, MBF-dependent transcription is downregulated. In summary, Gcn5 is required for the full activation and correct timing of MBF-regulated gene transcription.

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Genome-Wide Analysis of the Relationship between Transcriptional Regulation by Rpd3p and the Histone H3 and H4 Amino Termini in Budding Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.24.20.8823-8833.2004 ◽

2004 ◽

Vol 24 (20) ◽

pp. 8823-8833 ◽

Cited By ~ 35

Author(s):

Nevin Sabet ◽

Sam Volo ◽

Cailin Yu ◽

James P. Madigan ◽

Randall H. Morse

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Histone H3 ◽

Global Gene Expression ◽

Amino Terminus ◽

Histone H4 ◽

Histone Tails ◽

Genome Wide ◽

Lysine Residues ◽

The Relationship

ABSTRACT The histone amino termini have emerged as key targets for a variety of modifying enzymes that function as transcriptional coactivators and corepressors. However, an important question that has remained largely unexplored is the extent to which specific histone amino termini are required for the activating and repressive functions of these enzymes, Here we address this issue by focusing on the prototypical histone deacetylase, Rpd3p, in the budding yeast Saccharomyces cerevisiae. We show that targeting Rpd3p to a reporter gene in this yeast can partially repress transcription when either the histone H3 or the histone H4 amino terminus is deleted, indicating that the “tails” are individually dispensable for repression by Rpd3p. In contrast, we find that the effect of rpd3 gene disruption on global gene expression is considerably reduced in either a histone H3Δ1-28 (H3 lacking the amino-terminal 28 amino acids) or a histone H4(K5,8,12,16Q) (H4 with lysine residues 5, 8, 12, and 16 changed to glutamine residues) background compared to the wild-type background, indicating a requirement for one or both of these histone tails in Rpd3p-mediated regulation for many genes. These results suggest that acetylation of either the H3 or the H4 amino terminus could suffice to allow the activation of such genes. We also examine the relationship between H3 tails and H4 tails in global gene expression and find substantial overlap among the gene sets regulated by these histone tails. We also show that the effects on genome-wide expression of deleting the H3 or H4 amino terminus are similar but not identical to the effects of mutating the lysine residues in these same regions. These results indicate that the gene regulatory potential of the H3 and H4 amino termini is substantially but not entirely contained in these modifiable lysine residues.

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The Gene Expression and Enzyme Activity of Plant 3-Deoxy-D-Manno-2-Octulosonic Acid-8-Phosphate Synthase Are Preferentially Associated with Cell Division in a Cell Cycle-Dependent Manner

PLANT PHYSIOLOGY ◽

10.1104/pp.103.026872 ◽

2003 ◽

Vol 133 (1) ◽

pp. 348-360 ◽

Cited By ~ 20

Author(s):

Frédéric Delmas ◽

Johann Petit ◽

Jérôme Joubès ◽

Martial Séveno ◽

Thomas Paccalet ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Enzyme Activity ◽

Cell Division ◽

Dependent Manner ◽

A Cell ◽

Cycle Dependent ◽

Phosphate Synthase

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Codon bias determines sorting of ion channel protein

10.1101/2020.03.17.994780 ◽

2020 ◽

Author(s):

Marina Kithil ◽

Anja Jeannine Engel ◽

Markus Langhans ◽

Oliver Rauh ◽

Matea Cartolano ◽

...

Keyword(s):

Mammalian Cells ◽

Secretory Pathway ◽

Model Systems ◽

Dependent Manner ◽

Intracellular Proteins ◽

Polypeptide Folding ◽

A Cell ◽

Identical Amino Acid Sequence ◽

Cycle Dependent ◽

The Impact

AbstractThe choice of codons can influence local translation kinetics during protein synthesis. The question of whether the modulation of polypeptide folding and binding to chaperons influences sorting of nascent membrane proteins remains unclear. Here, we use two similar K+ channels as model systems to examine the impact of codon choice on protein sorting. By monitoring transient expression of GFP tagged proteins in mammalian cells we find that targeting of one channel to the secretory pathway is insensitive to codon optimization. In contrast, sorting of the second channel to the mitochondria is very sensitive to codon choice. The protein with an identical amino acid sequence is sorted in a codon and cell cycle dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves together with a cell-state depending decoding mechanism as a secondary code for sorting intracellular proteins.

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Investigating the Central Dogma of Molecular Biology in the Context of Nuclear Architecture and Cell Cycle

10.1101/810499 ◽

2019 ◽

Author(s):

Shivnarayan Dhuppar ◽

Aprotim Mazumder

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Single Molecule ◽

Mammalian Cells ◽

Nuclear Architecture ◽

Nuclear Lamina ◽

Gene Copy ◽

A Cell ◽

Cycle Dependent

AbstractNuclear architecture is the organization of the genome within a cell nucleus with respect to different nuclear landmarks such as nuclear lamina, matrix or nucleoli. Lately it has emerged as a major regulator of gene expression in mammalian cells. The studies connecting nuclear architecture with gene expression are largely population-averaged and do not report on the heterogeneity in genome organization or in gene expression within a population. In this report we present a method for combining 3D DNA Fluorescence in situ Hybridization (FISH) with single molecule RNA FISH (smFISH) and immunofluorescence to study nuclear architecture-dependent gene regulation on a cell-by-cell basis. We further combine it with an imaging-based cell cycle staging to correlate nuclear architecture with gene expression across the cell cycle. We present this in the context of Cyclin A2 (CCNA2) gene for its known cell cycle-dependent expression. We show that, across the cell cycle, the expression of a CCNA2 gene copy is stochastic and depends neither on its sub-nuclear position—which usually lies close to nuclear lamina—nor on the expression from the other copies.

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Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics

10.1101/2020.04.27.064691 ◽

2020 ◽

Author(s):

Pierre-Olivier Estève ◽

Udayakumar S. Vishnu ◽

Hang Gyeong Chin ◽

Sriharsa Pradhan

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Histone Deacetylases ◽

Mammalian Cells ◽

Chromatin Accessibility ◽

Cell Type Specificity ◽

Myc Oncogene ◽

Genome Wide ◽

A Cell ◽

Accessible Chromatin

AbstractChromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S and G2/M) - specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with down regulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.

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Regulation of the expression and activity of Unr in mammalian cells

Biochemical Society Transactions ◽

10.1042/bst20150165 ◽

2015 ◽

Vol 43 (6) ◽

pp. 1241-1246 ◽

Cited By ~ 15

Author(s):

Emma C. Anderson ◽

Pól Ó Catnaigh

Keyword(s):

Mammalian Cells ◽

Alternative Polyadenylation ◽

Dependent Manner ◽

Factor X ◽

Mammalian Development ◽

Ras Gene ◽

Polypyrimidine Tract Binding Protein ◽

A Cell ◽

Internal Initiation ◽

Cycle Dependent

Unr (upstream of N-ras) is a post-transcriptional regulator of gene expression, essential for mammalian development and mutated in many human cancers. The expression of unr is itself regulated at many levels; transcription of unr, which also affects expression of the downstream N-ras gene, is tissue and developmental stage-dependent and is repressed by c-Myc and Max (Myc associated factor X). Alternative splicing gives rise to six transcript variants, which include three different 5′-UTRs. The transcripts are further diversified by the use of three alternative polyadenylation signals, which governs whether AU-rich instability elements are present in the 3′-UTR or not. Translation of at least some unr transcripts can occur by internal initiation and is regulated in a cell-cycle-dependent manner; binding of PTB (polypyrimidine tract-binding protein) and Unr to the 5′-UTR inhibits translation, but these are displaced by heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNPC1/C2) during mitosis to stimulate translation. Finally, Unr is post-translationally modified by phosphorylation and lysine acetylation, although it is not yet known how these modifications affect Unr activity.

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Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65

The Journal of Cell Biology ◽

10.1083/jcb.201811038 ◽

2019 ◽

Vol 218 (3) ◽

pp. 820-838 ◽

Cited By ~ 6

Author(s):

Colin E. Delaney ◽

Stephen P. Methot ◽

Micol Guidi ◽

Iskra Katic ◽

Susan M. Gasser ◽

...

Keyword(s):

Gene Expression ◽

Mass Spectrometry ◽

Cell Cycle ◽

Stress Resistance ◽

Transcriptional Repression ◽

Dependent Manner ◽

A Cell ◽

H3k9 Dimethylation ◽

Cycle Dependent ◽

Unstructured Protein

The segregation of the genome into accessible euchromatin and histone H3K9-methylated heterochromatin helps silence repetitive elements and tissue-specific genes. In Caenorhabditis elegans, MET-2, the homologue of mammalian SETDB1, catalyzes H3K9me1 and me2, yet like SETDB1, its regulation is enigmatic. Contrary to the cytosolic enrichment of overexpressed MET-2, we show that endogenous MET-2 is nuclear throughout development, forming perinuclear foci in a cell cycle–dependent manner. Mass spectrometry identified two cofactors that bind MET-2: LIN-65, a highly unstructured protein, and ARLE-14, a conserved GTPase effector. All three factors colocalize in heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9 dimethylation, dispersion of heterochromatic foci, and derepression of MET-2 targets. Mutation of met-2 or lin-65 also disrupts the perinuclear anchoring of genomic heterochromatin. Loss of LIN-65, like that of MET-2, compromises temperature stress resistance and germline integrity, which are both linked to promiscuous repeat transcription and gene expression.

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Codon Bias Can Determine Sorting of a Potassium Channel Protein

Cells ◽

10.3390/cells10051128 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1128

Author(s):

Anja J. Engel ◽

Marina Kithil ◽

Markus Langhans ◽

Oliver Rauh ◽

Matea Cartolano ◽

...

Keyword(s):

Mammalian Cells ◽

Codon Bias ◽

Secretory Pathway ◽

Model Systems ◽

Dependent Manner ◽

Intracellular Membrane ◽

Synonymous Codons ◽

State Dependent ◽

A Cell ◽

Cycle Dependent

Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K+ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves, together with a cell-state-dependent decoding mechanism, as a secondary code for sorting intracellular membrane proteins.

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