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Cellular and Molecular Life Sciences :... Aug 2020During embryonic development, one of the two X chromosomes of a mammalian female cell is randomly inactivated by the X chromosome inactivation mechanism, which is mainly... (Review)
Review
During embryonic development, one of the two X chromosomes of a mammalian female cell is randomly inactivated by the X chromosome inactivation mechanism, which is mainly dependent on the regulation of the non-coding RNA X-inactive specific transcript at the X chromosome inactivation center. There are three proteins that are essential for X-inactive specific transcript to function properly: scaffold attachment factor-A, lamin B receptor, and SMRT- and HDAC-associated repressor protein. In addition, the absence of X-inactive specific transcript expression promotes tumor development. During the process of chromosome inactivation, some tumor suppressor genes escape inactivation of the X chromosome and thereby continue to play a role in tumor suppression. A well-functioning tumor suppressor gene on the idle X chromosome in women is one of the reasons they have a lower propensity to develop cancer than men, women thereby benefit from this enhanced tumor suppression. This review will explore the mechanism of X chromosome inactivation, discuss the relationship between X chromosome inactivation and tumorigenesis, and consider the consequent sex differences in cancer.
Topics: Chromosomes, Human, X; Humans; Mutation; Neoplasms; RNA, Long Noncoding; Sex Characteristics; Tumor Suppressor Proteins; X Chromosome Inactivation
PubMed: 32040694
DOI: 10.1007/s00018-020-03469-z -
Microorganisms Sep 2023When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the...
When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active mA and mC DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(mC)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding mA, mC, and mC DNA MTases, respectively, occur in approximately the ratio 4:2:1.
PubMed: 37894082
DOI: 10.3390/microorganisms11102424 -
International Journal of Molecular... Jul 2021Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA...
Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NCoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in reduced methylation of ICR in locus and promoter in mouse embryonic fibroblasts. However, nothing is known about how Kaiso influences DNA methylation at the genome level. Here we show that deficiency of Kaiso led to whole-genome hypermethylation, using Kaiso deficient human renal cancer cell line obtained via CRISPR/CAS9 genome editing. However, Kaiso serves to protect genic regions, enhancers, and regions with a low level of histone modifications from demethylation. We detected hypomethylation of binding sites for Oct4 and Nanog in Kaiso deficient cells. Kaiso immunoprecipitated with de novo DNA methyltransferases DNMT3a/3b, but not with maintenance methyltransferase DNMT1. Thus, Kaiso may attract methyltransferases to surrounding regions and modulate genome methylation in renal cancer cells apart from being methyl DNA binding protein.
Topics: DNA (Cytosine-5-)-Methyltransferases; DNA Methylation; Fibroblasts; Gene Editing; Genomic Imprinting; HEK293 Cells; Humans; Insulin-Like Growth Factor II; Locus Control Region; Promoter Regions, Genetic; RNA, Long Noncoding; Transcription Factors; Tripartite Motif Proteins; Ubiquitin-Protein Ligases; DNA Methyltransferase 3B
PubMed: 34299205
DOI: 10.3390/ijms22147587 -
Nature Communications May 2023Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative RNA splicing in individual cells, it suffers from a low read throughput. Here,...
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, a method that removes most artifact cDNAs and concatenates multiple cDNAs for PacBio circular consensus sequencing (CCS) to achieve high-throughput and high-accuracy single-cell RNA isoform sequencing. HIT-scISOseq can yield >10 million high-accuracy long-reads in a single PacBio Sequel II SMRT Cell 8M. We also report the development of scISA-Tools that demultiplex HIT-scISOseq concatenated reads into single-cell cDNA reads with >99.99% accuracy and specificity. We apply HIT-scISOseq to characterize the transcriptomes of 3375 corneal limbus cells and reveal cell-type-specific isoform expression in them. HIT-scISOseq is a high-throughput, high-accuracy, technically accessible method and it can accelerate the burgeoning field of long-read single-cell transcriptomics.
Topics: RNA; RNA Isoforms; High-Throughput Nucleotide Sequencing; Consensus; Protein Isoforms; Sequence Analysis, DNA; Sequence Analysis, RNA
PubMed: 37149708
DOI: 10.1038/s41467-023-38324-9 -
Nucleic Acids Research Dec 2020Analysis of genomic DNA from pathogenic strains of Burkholderia cenocepacia J2315 and Escherichia coli O104:H4 revealed the presence of two unusual MTase genes. Both are...
Analysis of genomic DNA from pathogenic strains of Burkholderia cenocepacia J2315 and Escherichia coli O104:H4 revealed the presence of two unusual MTase genes. Both are plasmid-borne ORFs, carried by pBCA072 for B. cenocepacia J2315 and pESBL for E. coli O104:H4. Pacific Biosciences SMRT sequencing was used to investigate DNA methyltransferases M.BceJIII and M.EcoGIX, using artificial constructs. Mating properties of engineered pESBL derivatives were also investigated. Both MTases yield promiscuous m6A modification of single strands, in the context SAY (where S = C or G and Y = C or T). Strikingly, this methylation is asymmetric in vivo, detected almost exclusively on one DNA strand, and is incomplete: typically, around 40% of susceptible motifs are modified. Genetic and biochemical studies suggest that enzyme action depends on replication mode: DNA Polymerase I (PolI)-dependent ColE1 and p15A origins support asymmetric modification, while the PolI-independent pSC101 origin does not. An MTase-PolI complex may enable discrimination of PolI-dependent and independent plasmid origins. M.EcoGIX helps to establish pESBL in new hosts by blocking the action of restriction enzymes, in an orientation-dependent fashion. Expression and action appear to occur on the entering single strand in the recipient, early in conjugal transfer, until lagging-strand replication creates the double-stranded form.
Topics: Bacterial Proteins; Burkholderia cenocepacia; DNA Methylation; DNA Polymerase I; DNA Replication; DNA, Single-Stranded; Escherichia coli O104; Escherichia coli Proteins; Genome, Bacterial; Methyltransferases; Plasmids; Ribosomal Proteins
PubMed: 33270887
DOI: 10.1093/nar/gkaa1163 -
FASEB Journal : Official Publication of... Jul 2020Peroxisome proliferator-activated receptor alpha (PPARα, NR1C1) belongs to a large family of ligand-dependent nuclear receptors (NRs). It is one of the best studied NRs... (Review)
Review
Peroxisome proliferator-activated receptor alpha (PPARα, NR1C1) belongs to a large family of ligand-dependent nuclear receptors (NRs). It is one of the best studied NRs which controls the lipid metabolism (mainly fatty acid oxidation) and inflammation, and has been a promising target for treating metabolic disorders such as fatty liver and cardiometabolic diseases. The function of PPARα relies on its interaction with various coregulators upon different stimulating contexts, and, thereby, activates or represses its transcription targets in a gene-selective manner. Understanding the transcription factor and coregulator network underlying the PPARα regulation is prerequisite to decipher its gene- and context-selectivity for designing better therapeutic ligands. In this review, we will summarize current knowledge of PPARα coregulator network, with major focus on a relatively well-studied corepressor complex containing core subunits of nuclear receptor corepressor (NCOR or NCOR1), silencing mediator of retinoic acid and thyroid hormone receptor (SMRT or NCOR2), G-protein suppressor 2 (GPS2), transducin β-like protein 1 (TBL1 or TBL1X), TBL-related 1 (TBLR1 or TBL1XR1), and the catalytic core of histone deacetylase 3 (HDAC3). We will mainly review the molecular events of the complex and sub-complexes in controlling the liver metabolism. We will also discuss the potential perturbation of the subunit expression in human livers during liver metabolic disorder progression which potentially defines the patient disease susceptibility and drug responses.
Topics: Animals; Gene Regulatory Networks; Humans; Liver; Nuclear Receptor Co-Repressor 1; Nuclear Receptor Co-Repressor 2; PPAR alpha
PubMed: 32396271
DOI: 10.1096/fj.202000055RR -
Nature Communications May 2023Placental development relies on coordinated cell fate decisions governed by signalling inputs. However, little is known about how signalling cues are transformed into...
Placental development relies on coordinated cell fate decisions governed by signalling inputs. However, little is known about how signalling cues are transformed into repressive mechanisms triggering lineage-specific transcriptional signatures. Here, we demonstrate that upon inhibition of the Fgf/Erk pathway in mouse trophoblast stem cells (TSCs), the Ets2 repressor factor (Erf) interacts with the Nuclear Receptor Co-Repressor Complex 1 and 2 (NCoR1/2) and recruits it to key trophoblast genes. Genetic ablation of Erf or Tbl1x (a component of the NCoR1/2 complex) abrogates the Erf/NCoR1/2 interaction. This leads to mis-expression of Erf/NCoR1/2 target genes, resulting in a TSC differentiation defect. Mechanistically, Erf regulates expression of these genes by recruiting the NCoR1/2 complex and decommissioning their H3K27ac-dependent enhancers. Our findings uncover how the Fgf/Erf/NCoR1/2 repressive axis governs cell fate and placental development, providing a paradigm for Fgf-mediated transcriptional control.
Topics: Mice; Animals; Female; Pregnancy; Trophoblasts; Fibroblast Growth Factor 2; Placenta; Cell Differentiation; Gene Expression Regulation; Nuclear Receptor Co-Repressor 1; Nuclear Receptor Co-Repressor 2
PubMed: 37137875
DOI: 10.1038/s41467-023-38101-8 -
Viruses May 2022Papillomaviruses (PV) replicate in undifferentiated keratinocytes at low levels and to high levels in differentiated cells. The restricted replication in... (Review)
Review
Papillomaviruses (PV) replicate in undifferentiated keratinocytes at low levels and to high levels in differentiated cells. The restricted replication in undifferentiated cells is mainly due to the expression of the conserved viral E8^E2 repressor protein, a fusion protein consisting of E8 and the hinge, DNA-binding, and dimerization domain of E2. E8^E2 binds to viral genomes and represses viral transcription and genome replication by recruiting cellular NCoR/SMRT-HDAC3 corepressor complexes. Tissue culture experiments have revealed that E8^E2 modulates long-term maintenance of extrachromosomal genomes, productive replication, and immortalization properties in a virus type-dependent manner. Furthermore, in vivo experiments have indicated that Mus musculus PV1 E8^E2 is required for tumor formation in immune-deficient mice. In summary, E8^E2 is a crucial inhibitor whose levels might determine the outcome of PV infections.
Topics: Animals; DNA-Binding Proteins; Mice; Papillomaviridae; Papillomavirus Infections; Viral Proteins; Virus Replication
PubMed: 35632695
DOI: 10.3390/v14050953 -
PloS One 2022The epigenetics of bacteria, and bacteria with a reduced genome in particular, is of great interest, but is still poorly understood. Mycoplasma gallisepticum, a...
The epigenetics of bacteria, and bacteria with a reduced genome in particular, is of great interest, but is still poorly understood. Mycoplasma gallisepticum, a representative of the class Mollicutes, is an excellent model of a minimal cell because of its reduced genome size, lack of a cell wall, and primitive cell organization. In this study we investigated DNA modifications of the model object Mycoplasma gallisepticum and their roles. We identified DNA modifications and methylation motifs in M. gallisepticum S6 at the genome level using single molecule real time (SMRT) sequencing. Only the ANCNNNNCCT methylation motif was found in the M. gallisepticum S6 genome. The studied bacteria have one functional system for DNA modifications, the Type I restriction-modification (RM) system, MgaS6I. We characterized its activity, affinity, protection and epigenetic functions. We demonstrated the protective effects of this RM system. A common epigenetic signal for bacteria is the m6A modification we found, which can cause changes in DNA-protein interactions and affect the cell phenotype. Native methylation sites are underrepresented in promoter regions and located only near the -35 box of the promoter, which does not have a significant effect on gene expression in mycoplasmas. To study the epigenetics effect of m6A for genome-reduced bacteria, we constructed a series of M. gallisepticum strains expressing EGFP under promoters with the methylation motifs in their different elements. We demonstrated that m6A modifications of the promoter located only in the -10-box affected gene expression and downregulated the expression of the corresponding gene.
Topics: Mycoplasma gallisepticum; DNA, Bacterial; DNA Restriction-Modification Enzymes; Tenericutes; DNA Methylation
PubMed: 36413541
DOI: 10.1371/journal.pone.0277819 -
Frontiers in Immunology 2022Dendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance...
Dendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT (NCoR2) enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4 and CD8 T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic and transcriptomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion represses mTOR-STAT3-IL10 signaling in cDC1 by down-regulating NR4A1. Besides, and were down-regulated in () depleted cDC1, supporting increased production of inflammatory cytokines. Moreover, studies in mice showed, adoptive transfer of SMRT depleted cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8 T-cell frequency, respectively. We also depicted decreased expression in Rheumatoid Arthritis, a Th1/Th17 disease.
Topics: Animals; CD8-Positive T-Lymphocytes; Cytokines; Dendritic Cells; Interleukin-10; Interleukin-12; Interleukin-23; Interleukin-6; Mice; Nuclear Receptor Co-Repressor 1; Nuclear Receptor Co-Repressor 2; STAT3 Transcription Factor; TOR Serine-Threonine Kinases
PubMed: 36238311
DOI: 10.3389/fimmu.2022.910705