scholarly journals Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif

Genetics ◽  
2020 ◽  
Vol 215 (1) ◽  
pp. 75-87 ◽  
Author(s):  
Robin L. Armstrong ◽  
Souradip Das ◽  
Christina A. Hill ◽  
Robert J. Duronio ◽  
Jared T. Nordman
Keyword(s):  
Cell Cycle ◽  
Genome Stability ◽  
Cell Lineage ◽  
Replication Timing ◽  
Cell Types ◽  
Replication Initiation ◽  
Control Factor ◽  
Binding Motif ◽  
Tissue Specific ◽  
Specific Manner

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

scholarly journals Rif1 functions in a tissue-specific manner to control replication timing through its PP1-binding motif

2019 ◽  
Author(s):  
Robin L. Armstrong ◽  
Souradip Das ◽  
Christina A. Hill ◽  
Robert J. Duronio ◽  
Jared T. Nordman
Keyword(s):  
Cell Cycle ◽  
Genome Stability ◽  
Cell Lineage ◽  
Replication Timing ◽  
Cell Types ◽  
Replication Initiation ◽  
Control Factor ◽  
Binding Motif ◽  
Tissue Specific ◽  
Specific Manner

AbstractReplication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early and late replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

scholarly journals Regulation of DNA Replication Licensing and Re-Replication by Cdt1

2021 ◽  
Vol 22 (10) ◽  
pp. 5195
Author(s):  
Hui Zhang
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Dna Replication ◽  
Genome Stability ◽  
E3 Ligase ◽  
S Phase ◽  
Replication Initiation ◽  
Nuclear Antigen ◽  
Repair Synthesis ◽  
Ubiquitin E3 Ligase

In eukaryotic cells, DNA replication licensing is precisely regulated to ensure that the initiation of genomic DNA replication in S phase occurs once and only once for each mitotic cell division. A key regulatory mechanism by which DNA re-replication is suppressed is the S phase-dependent proteolysis of Cdt1, an essential replication protein for licensing DNA replication origins by loading the Mcm2-7 replication helicase for DNA duplication in S phase. Cdt1 degradation is mediated by CRL4Cdt2 ubiquitin E3 ligase, which further requires Cdt1 binding to proliferating cell nuclear antigen (PCNA) through a PIP box domain in Cdt1 during DNA synthesis. Recent studies found that Cdt2, the specific subunit of CRL4Cdt2 ubiquitin E3 ligase that targets Cdt1 for degradation, also contains an evolutionarily conserved PIP box-like domain that mediates the interaction with PCNA. These findings suggest that the initiation and elongation of DNA replication or DNA damage-induced repair synthesis provide a novel mechanism by which Cdt1 and CRL4Cdt2 are both recruited onto the trimeric PCNA clamp encircling the replicating DNA strands to promote the interaction between Cdt1 and CRL4Cdt2. The proximity of PCNA-bound Cdt1 to CRL4Cdt2 facilitates the destruction of Cdt1 in response to DNA damage or after DNA replication initiation to prevent DNA re-replication in the cell cycle. CRL4Cdt2 ubiquitin E3 ligase may also regulate the degradation of other PIP box-containing proteins, such as CDK inhibitor p21 and histone methylase Set8, to regulate DNA replication licensing, cell cycle progression, DNA repair, and genome stability by directly interacting with PCNA during DNA replication and repair synthesis.

scholarly journals KLF4 suppresses transformation of pre-B cells by ABL oncogenes

Blood ◽  
2006 ◽  
Vol 109 (2) ◽  
pp. 747-755 ◽  
Author(s):  
Michael G. Kharas ◽  
Isharat Yusuf ◽  
Vanessa M. Scarfone ◽  
Vincent W. Yang ◽  
Julia A. Segre ◽  
...  
Keyword(s):  
Cell Cycle ◽  
B Cells ◽  
Tumor Suppressor ◽  
B Cell ◽  
Cell Activation ◽  
Cell Transformation ◽  
Cell Lineage ◽  
Cell Types ◽  
B Cell Malignancies

Abstract Genes that are strongly repressed after B-cell activation are candidates for being inactivated, mutated, or repressed in B-cell malignancies. Krüppel-like factor 4 (Klf4), a gene down-regulated in activated murine B cells, is expressed at low levels in several types of human B-cell lineage lymphomas and leukemias. The human KLF4 gene has been identified as a tumor suppressor gene in colon and gastric cancer; in concordance with this, overexpression of KLF4 can suppress proliferation in several epithelial cell types. Here we investigate the effects of KLF4 on pro/pre–B-cell transformation by v-Abl and BCR-ABL, oncogenes that cause leukemia in mice and humans. We show that overexpression of KLF4 induces arrest and apoptosis in the G1 phase of the cell cycle. KLF4-mediated death, but not cell-cycle arrest, can be rescued by Bcl-XL overexpression. Transformed pro/pre-B cells expressing KLF4 display increased expression of p21CIP and decreased expression of c-Myc and cyclin D2. Tetracycline-inducible expression of KLF4 in B-cell progenitors of transgenic mice blocks transformation by BCR-ABL and depletes leukemic pre-B cells in vivo. Collectively, our work identifies KLF4 as a putative tumor suppressor in B-cell malignancies.

scholarly journals Replication timing maintains the global epigenetic state in human cells

2019 ◽  
Author(s):  
Kyle N. Klein ◽  
Peiyao A. Zhao ◽  
Xiaowen Lyu ◽  
Daniel A. Bartlett ◽  
Amar Singh ◽  
...  
Keyword(s):  
Embryonic Stem ◽  
Cancer Cell Line ◽  
Replication Timing ◽  
Cell Types ◽  
Control Factor ◽  
Epigenetic State ◽  
Genome Wide ◽  
A Genome ◽  
A Cell ◽  
Early Replication

AbstractDNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B chromatin compartments, respectively. Early replication is also associated with active histone modifications and transcriptional permissiveness. However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that RT is central to epigenome maintenance and compartmentalization in both human embryonic stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches as previously suspected, lead to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone modification changes coincided with global reorganization of genome compartments, transcription changes and a genome wide strengthening of TAD structures. Inducible degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-regulation, supporting previously speculative models in which the timing of chromatin assembly at the replication fork plays a key role in maintaining the global epigenetic state, which in turn drives genome architecture.

scholarly journals The coordinated localization of mRNA to centrosomes facilitates error-free mitosis

2020 ◽  
Author(s):  
Pearl V. Ryder ◽  
Junnan Fang ◽  
Dorothy A. Lerit
Keyword(s):  
Cell Cycle ◽  
Genome Stability ◽  
Fragile X ◽  
Protein Localization ◽  
Cell Types ◽  
Rna Granules ◽  
Mental Retardation Protein ◽  
Pericentriolar Material ◽  
Cycle Dependent ◽  
Post Transcriptional Regulation

AbstractCentrosomes are microtubule-organizing centers required for error-free mitosis and embryonic development. The microtubule-nucleating activity of centrosomes is conferred by the pericentriolar material (PCM), a composite of numerous proteins subject to cell cycle-dependent oscillations in levels and organization. In diverse cell types, mRNAs localize to centrosomes and may contribute to changes in PCM abundance. Here, we investigate the regulation of mRNA localization to centrosomes in the rapidly cycling Drosophila melanogaster embryo. We find that RNA localization to centrosomes is regulated during the cell cycle and developmentally. We identify a novel role for the fragile-X mental retardation protein (FMRP), which localizes to pericentrosomal RNA granules, in the post-transcriptional regulation of centrosomal RNA. Further, the mis-targeting of a model centrosomal mRNA, centrocortin (cen), is sufficient to alter cognate protein localization to centrosomes and impair spindle morphogenesis and genome stability.

scholarly journals A Novel Rb- and p300-Binding Protein Inhibits Transactivation by MyoD

2000 ◽  
Vol 20 (23) ◽  
pp. 8903-8915 ◽  
Author(s):  
W. Robb MacLellan ◽  
G. Xiao ◽  
M. Abdellatif ◽  
Michael D. Schneider
Keyword(s):  
Cell Cycle ◽  
Skeletal Muscle ◽  
Binding Motif ◽  
Tissue Specific ◽  
Yeast Two Hybrid System ◽  
C Terminus ◽  
Acid Protein ◽  
P300 Binding ◽  
Amino Acid Protein ◽  
Novel Protein

ABSTRACT The retinoblastoma protein (Rb) regulates both the cell cycle and tissue-specific transcription, by modulating the activity of factors that associate with its A-B and C pockets. In skeletal muscle, Rb has been reported to regulate irreversible cell cycle exit and muscle-specific transcription. To identify factors interacting with Rb in muscle cells, we utilized the yeast two-hybrid system, using the A-B and C pockets of Rb as bait. A novel protein we have designated E1A-like inhibitor of differentiation 1 (EID-1), was the predominant Rb-binding clone isolated. It is preferentially expressed in adult cardiac and skeletal muscle and encodes a 187-amino-acid protein, with a classic Rb-binding motif (LXCXE) in its C terminus. Overexpression of EID-1 in skeletal muscle inhibited tissue-specific transcription. Repression of skeletal muscle-restricted genes was mediated by a block to transactivation by MyoD independent of G1 exit and, surprisingly, was potentiated by a mutation that prevents EID-1 binding to Rb. Inhibition of MyoD may be explained by EID-1's ability to bind and inhibit p300's histone acetylase activity, an essential MyoD coactivator. Thus, EID-1 binds both Rb and p300 and is a novel repressor of MyoD function.

scholarly journals Epstein-Barr Virus Episome Stability Is Coupled to a Delay in Replication Timing

2008 ◽  
Vol 83 (5) ◽  
pp. 2154-2162 ◽  
Author(s):  
Jing Zhou ◽  
Andrew R. Snyder ◽  
Paul M. Lieberman
Keyword(s):  
Histone Deacetylases ◽  
Genome Stability ◽  
Epstein Barr Virus ◽  
Replication Timing ◽  
Replication Initiation ◽  
Stable Complex ◽  
Telomere Repeat ◽  
Temporal Regulation ◽  
Barr Virus ◽  
Epstein Barr

ABSTRACT The temporal regulation of DNA replication is thought to be important for chromosome organization and genome stability. We show here that Epstein-Barr virus (EBV) genomes replicate in mid- to late S phase and that agents that accelerate replication timing of EBV reduce viral genome stability. Hydroxyurea (HU) treatment, which is known to eliminate EBV episomes, shifted EBV replication to earlier times in the cell cycle. HU treatment correlated with hyperacetylation of histone H3 and loss of telomere repeat factor 2 (TRF2) binding at the EBV origin of plasmid replication (OriP). Deletion of TRF2 binding sites within OriP or short hairpin RNA depletion of TRF2 advanced the replication timing of OriP-containing plasmids. Inhibitors of class I histone deacetylases (HDACs) increased histone acetylation at OriP, advanced the replication timing of EBV, and reduced EBV genome copy number. We also show that HDAC1 and -2 form a stable complex with TRF2 at OriP and that HU treatment inhibits HDAC activity. We propose that the TRF2-HDAC complex enhances EBV episome stability by providing a checkpoint that delays replication initiation at OriP.

scholarly journals Expression of the Id Family Helix-Loop-Helix Regulators During Growth and Development in the Hematopoietic System

Blood ◽  
1997 ◽  
Vol 89 (9) ◽  
pp. 3155-3165 ◽  
Author(s):  
Cathleen L. Cooper ◽  
Gerard Brady ◽  
Fillio Bilia ◽  
Norman N. Iscove ◽  
Peter J. Quesenberry
Keyword(s):  
Cell Lineage ◽  
Cell Types ◽  
Specific Cell ◽  
Proliferative Capacity ◽  
Limited Extent ◽  
Hematopoietic Stem ◽  
Hematopoietic Development ◽  
Helix Loop Helix ◽  
Specific Manner ◽  
Two Factors

Abstract To better understand the molecular mechanism(s) by which growth and differentiation of the primitive hematopoietic stem cell is initiated, as well as the means by which the maturing cell can commit to development along a specific cell lineage, we elected to study the Id family of helix-loop-helix (HLH) transcriptional regulators. Some members of the HLH family are expressed in a stage-specific manner during hematopoietic development and can regulate the ability of immature hematopoietic cells to terminally differentiate. None of the four Id family genes were detected in the most primitive progenitors. Id-1 was widely expressed in proliferating bi- and unipotential progenitors, but its expression was downregulated in cells of increasing maturity; conversely, Id-2 and, to a limited extent, Id-3 gene expression increased as cells matured and lost proliferative capacity. Id-2 expression ran counter to that of Id-1 not only during maturation, but during periods of cell growth and arrest as well. This is quite distinct from the nonhematopoietic tissues, in which these two factors are coordinately expressed and suggests that Id-1 and Id-2 might be regulating very different events during hematopoiesis than they regulate in other cell types.

scholarly journals Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program

2021 ◽  
Author(s):  
Madison Caballero ◽  
Tiffany Ge ◽  
Ana Rita Rebelo ◽  
Seungmae Seo ◽  
Sean Kim ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cellular Proliferation ◽  
Genetic Diseases ◽  
Replication Timing ◽  
Cell Types ◽  
Replication Initiation ◽  
Timing Variability ◽  
Gene Knockouts ◽  
Dna Replication Timing ◽  
Mutant Cells

AbstractCellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. MCM10 mutant cells demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in MCM10-mutant cells was predominantly comprised of replication initiation defects. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel modulator of DNA replication timing.

scholarly journals A mouse tissue atlas of small non-coding RNA

2018 ◽  
Author(s):  
Alina Isakova ◽  
Tobias Fehlmann ◽  
Andreas Keller ◽  
Stephen R. Quake
Keyword(s):  
Distribution Patterns ◽  
Cell Types ◽  
Vital Role ◽  
The Body ◽  
Mouse Tissue ◽  
List Type ◽  
Tissue Specific ◽  
Small Ncrnas ◽  
Mouse Tissues ◽  
Specific Manner

SUMMARYSmall non-coding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that ~ 30% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of eleven profiled tissues we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS-An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues-Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention-miRNA expression is sex specific in healthy tissues-Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain

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