Cytokinin promotes catalase and ascorbate peroxidase activities and preserves the chloroplast integrity during dark-senescence

Increased oxidative stress displayed during dark-senescence of wheat leaves (Triticum aestivum L.) is caused not only by the increased levels of radicals but also by a toss of antioxidant capacity. Mature leaves were incubated in 6-benzylaminopurine (BAP 10(-4) M) or water (control) during 6d in the dark. The senescence-delaying effect of BAP was associated with the retention of the chtoroplast structure, 60% of the initial content of chLorophyll (Chl) and 77% of the initial content of protein. BAP reduced the degradation of the light-harvesting chLorophyll a/b binding protein (LHCP-2), and the large (LSU) and small subunits (SSU) of Rubisco. Our results indicated that the presence of the NADPH:protochLorophyllide oxidoreductase (POR, EC.1.6.99.1) was not promoted by the cytokinin, leading to the conclusion that BAP maintains the level of Chl, preventing its degradation, rather than inducing Chl biosynthesis. The internal structure of chLoroplasts was maintained in BAP-treated leaves for up to 6 d, with well-organized grana thylakoids and small plastoglobul

Allele-specific control of replication timing and genome organization during development

DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus × castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq), and chromatin accessibility (ATAC-seq). We also present HARP, a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/6, 129/sv, and CAST/Ei), parental configurations, and gender revealed significant RT asynchrony between alleles across ∼12% of the autosomal genome linked to subspecies genomes but not to parental origin, growth conditions, or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not as strongly with SNP density, gene expression, imprinting, or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types, including extraembryonic endoderm stem (XEN) cells, four male and female primary mouse embryonic fibroblasts (MEFs), and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs were largely lost in all differentiated cell types, accompanied by novel sites of allelic asynchrony at a considerably smaller proportion of the genome, suggesting that genome organization of homologs converges to similar folding patterns during cell fate commitment

DNA replication timing alterations identify common markers between distinct progeroid diseases

International audienc

Cellular senescence induces replication stress with almost no affect on DNA replication timing

<p>Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence (RS), or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear.</p> <p>Here, we studied the DNA replication program during senescence progression in proliferative and pre-senescent cells from donors of various ages by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing (TRT).</p> <p>We demonstrate that, progression into RS leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in RT of the <i>CREB5</i> gene in all pre-senescent cells, RT was globally unaffected by replication stress during entry into either oncogene-induced or RS. Consequently, we conclude that RT alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that RT is largely resistant to replication stress.</p

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the&nbsp;necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function

Sanger sequencing data to verify mouse Dppa locus deletion

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM.Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27.PMID: 30595451</ul

Sanger sequencing data to verify mouse Rex1 locus deletion

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM.Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27.PMID: 30595451</ul

An integrative ENCODE resource for cancer genomics

ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis

Paisaje Cultural Urbano e Identitad Territorial

Linguaggio contemporaneo e preesistenze: dialogo in un mondo globalizzato Il tema del rapporto con l’antico trova una giusta dimensione operativa quando, superando la sfera delle ideologie e quella delle opposte ragioni della memoria e dello sviluppo, indirizza positivamente l’azione progettuale ora per differenza ora per empatia, a seconda delle circostanze, ma crea sempre una forte tensione tra le ragioni dell’esistente e le necessità del nuovo. Intervenire nell’antico e per l’antico significa, pertanto, riprogettare il nostro modo di relazionarci con il passato, rinegoziandone identità e valori alla luce del nostro presente. Da questa angolazione il patrimonio non è solo lo spazio della memoria o quello della storia, ma diviene lo spazio del desiderio che trae alimento dal mito dell’araba fenice: esso, come principio evolutivo, rappresenta l’inizio di un incessante ricominciamento e l'occasione per una mediazione tra globale e locale