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Nucleus

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https://www.readbyqxmd.com/read/28085555/sox9-chromatin-folding-domains-correlate-with-its-real-and-putative-distant-cis-regulatory-elements
#1
Marta Smyk, Kadir Caner Akdemir, Paweł Stankiewicz
Evolutionary conserved transcription factor SOX9, encoded by the dosage sensitive SOX9 gene on chromosome 17q24.3, plays an important role in development of multiple organs, including bones and testes. Heterozygous point mutations and genomic copy-number variant (CNV) deletions involving SOX9 have been reported in patients with campomelic dysplasia (CD), a skeletal malformation syndrome often associated with male-to-female sex reversal. Balanced and unbalanced structural genomic variants with breakpoints mapping up to 1...
January 13, 2017: Nucleus
https://www.readbyqxmd.com/read/28072566/guard-the-guardian-a-crl4-ligase-stands-watch-over-histone-production
#2
Fabienne Lampert, Mia M L Brodersen, Matthias Peter
Histones are evolutionarily conserved proteins that together with DNA constitute eukaryotic chromatin in a defined stoichiometry. Core histones are dynamic scaffolding proteins that undergo a myriad of post-translational modifications, which selectively engage chromosome condensation, replication, transcription and DNA damage repair. Cullin4-RING ubiquitin E3 ligases are known to hold pivotal roles in a wide spectrum of chromatin biology ranging from chromatin remodeling and transcriptional repression, to sensing of cytotoxic DNA lesions...
January 10, 2017: Nucleus
https://www.readbyqxmd.com/read/28071978/nup82-functions-redundantly-with-nup136-in-a-salicylic-acid-dependent-defense-response-of-arabidopsis-thaliana
#3
Kentaro Tamura, Yoichiro Fukao, Noriyuki Hatsugai, Fumiaki Katagiri, Ikuko Hara-Nishimura
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (Nups). NPC mediates macromolecular trafficking between the nucleoplasm and the cytoplasm, but specific roles of individual Nups are poorly understood in higher plants. Here, we show that the novel nucleoporin unique to angiosperm plants (designated as Nup82) functions in a salicylic acid-dependent defense in a redundant manner with Nup136, which is a component of the nuclear basket in the NPC. Arabidopsis thaliana Nup82 had a similar amino acid sequence to the N-terminal half of Nup136 and a Nup82-GFP fusion was localized on the nuclear envelope...
January 10, 2017: Nucleus
https://www.readbyqxmd.com/read/28068183/nucleolar-aggresomes-mediate-release-of-pericentric-heterochromatin-and-nuclear-destruction-of-genotoxically-treated-cancer-cells
#4
Kristine Salmina, Anda Huna, Inna Inashkina, Alexander Belyayev, Jekabs Krigerts, Ladislava Pastova, Alejandro Vazquez-Martin, Jekaterina Erenpreisa
The role of the nucleolus and autophagy in maintenance of nuclear integrity is poorly understood. In addition, the mechanisms of nuclear destruction in cancer cells senesced after conventional chemotherapy are unclear. In an attempt to elucidate these issues, we studied teratocarcinoma PA1 cells treated with Etoposide (ETO), focussing on the nucleolus. Following treatment, most cells enter G2 arrest, display persistent DNA damage and activate p53, senescence, and macroautophagy markers. 2-5 µm sized nucleolar aggresomes (NoA) containing fibrillarin (FIB) and damaged rDNA, colocalised with ubiquitin, pAMPK, and LC3-II emerge, accompanied by heterochromatin fragments, when translocated perinuclearly...
January 9, 2017: Nucleus
https://www.readbyqxmd.com/read/28060565/paraspeckles-as-rhythmic-nuclear-mrna-anchorages-responsible-for-circadian-gene-expression
#5
Manon Torres, Denis Becquet, Marie-Pierre Blanchard, Séverine Guillen, Bénédicte Boyer, Mathias Moreno, Jean-Louis Franc, Anne-Marie François-Bellan
Circadian clocks regulate rhythmic gene expression levels by means of mRNA oscillations that are mainly driven by post-transcriptional regulation. We identified a new post-transcriptional mechanism, which involves nuclear bodies called paraspeckles. Major components of paraspeckles including the long noncoding RNA Neat1, which is the structural component, and its major protein partners, as well as the number of paraspeckles, follow a circadian pattern in pituitary cells. Paraspeckles are known to retain within the nucleus RNAs containing inverted repeats of Alu sequences...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28060558/the-connection-between-brg1-ctcf-and-topoisomerases-at-tad-boundaries
#6
A Rasim Barutcu, Jane B Lian, Janet L Stein, Gary S Stein, Anthony N Imbalzano
The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28060557/control-of-nuclear-organization-by-f-actin-binding-proteins
#7
Karin Pfisterer, Asier Jayo, Maddy Parsons
The regulation of nuclear shape and deformability is a key factor in controlling diverse events from embryonic development to cancer cell metastasis, but the mechanisms governing this process are still unclear. Our recent study demonstrated an unexpected role for the F-actin bundling protein fascin in controlling nuclear plasticity through a direct interaction with Nesprin-2. Nesprin-2 is a component of the LINC complex that is known to couple the F-actin cytoskeleton to the nuclear envelope. We demonstrated that fascin, which is predominantly associated with peripheral F-actin rich filopodia, binds directly to Nesprin-2 at the nuclear envelope in a range of cell types...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28045584/epigenetic-countermarks-in-mitotic-chromosome-condensation
#8
Karel H M van Wely, Carmen Mora Gallardo, Kendra R Vann, Tatiana G Kutateladze
Mitosis in metazoans is characterized by abundant phosphorylation of histone H3 and involves the recruitment of condensin complexes to chromatin. The relationship between the 2 phenomena and their respective contributions to chromosome condensation in vivo remain poorly understood. Recent studies have shown that H3T3 phosphorylation decreases binding of histone readers to methylated H3K4 in vitro and is essential to displace the corresponding proteins from mitotic chromatin in vivo. Together with previous observations, these data provide further evidence for a role of mitotic histone H3 phosphorylation in blocking transcriptional programs or preserving the 'memory' PTMs...
January 3, 2017: Nucleus
https://www.readbyqxmd.com/read/28045568/tissue-specific-nets-alter-genome-organization-and-regulation-even-in-a-heterologous-system
#9
Jose I de Las Heras, Nikolaj Zuleger, Dzmitry G Batrakou, Rafal Czapiewski, Alastair R W Kerr, Eric C Schirmer
Different cell types exhibit distinct patterns of 3D genome organization that correlate with changes in gene expression in tissue and differentiation systems. Several tissue-specific nuclear envelope transmembrane proteins (NETs) have been found to influence the spatial positioning of genes and chromosomes that normally occurs during tissue differentiation. Here we study 3 such NETs: NET29, NET39, and NET47, which are expressed preferentially in fat, muscle and liver, respectively. We found that even when exogenously expressed in a heterologous system they can specify particular genome organization patterns and alter gene expression...
January 3, 2017: Nucleus
https://www.readbyqxmd.com/read/28033038/mgo3-and-gip1-act-synergistically-for-the-maintenance-of-centromeric-cohesion
#10
Morgane Batzenschlager, Anne-Catherine Schmit, Etienne Herzog, Joerg Fuchs, Veit Schubert, Guy Houlné, Marie-Edith Chabouté
The control of genomic maintenance during S phase is crucial in eukaryotes. It involves the establishment of sister chromatid cohesion, ensuring faithful chromosome segregation, as well as proper DNA replication and repair to preserve genetic information. In animals, nuclear periphery proteins - including inner nuclear membrane proteins and nuclear pore-associated components - are key factors which regulate DNA integrity. Corresponding functional homologues are not so well known in plants which may have developed specific mechanisms due to their sessile life...
December 29, 2016: Nucleus
https://www.readbyqxmd.com/read/28032817/the-brca1-ubiquitin-ligase-function-sets-a-new-trend-for-remodelling-in-dna-repair
#11
Ruth M Densham, Joanna R Morris
The protein product of the breast and ovarian cancer gene, BRCA1, is part of an obligate heterodimer with BARD1. Together these RING bearing proteins act as an E3 ubiquitin ligase. Several functions have been attributed to BRCA1 that contribute to genome integrity but which of these, if any, require this enzymatic function was unclear. Here we review recent studies clarifying the role of BRCA1 E3 ubiquitin ligase in DNA repair. Perhaps the most surprising finding is the narrow range of BRCA1 functions this activity relates to...
December 29, 2016: Nucleus
https://www.readbyqxmd.com/read/27813701/uncleprot-universal-nuclear-protein-database-of-barley-the-first-nuclear-protein-database-that-distinguishes-proteins-from-different-phases-of-the-cell-cycle
#12
Nicolas Blavet, Jana Uřinovská, Hana Jeřábková, Ivo Chamrád, Jan Vrána, René Lenobel, Jana Beinhauer, Marek Šebela, Jaroslav Doležel, Beáta Petrovská
Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking...
November 4, 2016: Nucleus
https://www.readbyqxmd.com/read/27797635/shared-mechanisms-in-physiological-and-pathological-nucleoplasmic-reticulum-formation
#13
Marek Mateusz Drozdz, David John Vaux
The mammalian nuclear envelope (NE) can develop complex dynamic membrane-bounded invaginations in response to both physiological and pathological stimuli. Since the formation of these nucleoplasmic reticulum (NR) structures can occur during interphase, without mitotic NE breakdown and reassembly, some other mechanism must drive their development. Here we consider models for deformation of the interphase NE, together with the evidence for their potential roles in NR formation.
October 31, 2016: Nucleus
https://www.readbyqxmd.com/read/27929926/comparing-lamin-proteins-post-translational-relative-stability-using-a-2a-peptide-based-system-reveals-elevated-resistance-of-progerin-to-cellular-degradation
#14
Di Wu, Phillip A Yates, Haoyue Zhang, Kan Cao
Nuclear lamins are the major components of the nuclear lamina at the periphery of the nucleus, supporting the nuclear envelope and participating in many nuclear processes, including DNA replication, transcription and chromatin organization. A group of diseases, the laminopathies, is associated with mutations in lamin genes. One of the most striking cases is Hutchinson-Gilford progeria syndrome (HGPS) which is the consequence of a lamin A dominant negative mutant named progerin. Due to the abnormal presence of a permanent C-terminal farnesyl tail, progerin gradually accumulates on the nuclear membrane, perturbing a diversity of signalings and transcriptional events...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27893319/insight-into-the-machinery-that-oils-chromatin-dynamics
#15
Roni H G Wright, Narcis Fernandez-Fuentes, Baldomero Oliva, Miguel Beato
The packaging of genetic information in form of chromatin within the nucleus provides cells with the ability to store and protect massive amounts of information within a compact space. Storing information within chromatin allows selective access to specific DNA sequences by regulating the various levels of chromatin structure from nucleosomes, to chromatin fibers, loops and topological associating domains (TADs) using mechanisms that are being progressively unravelled. However, a relatively unexplored aspect is the energetic cost of changing the chromatin configuration to gain access to DNA information...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27893298/replication-checkpoint-suppression-and-structure-of-centromeric-dna
#16
Francesco Romeo, Lucia Falbo, Vincenzo Costanzo
Human centromeres contain large amounts of repetitive DNA sequences known as α satellite DNA, which can be difficult to replicate and whose functional role is unclear. Recently, we have characterized protein composition, structural organization and checkpoint response to stalled replication forks of centromeric chromatin reconstituted in Xenopus laevis egg extract. We showed that centromeric DNA has high affinity for SMC2-4 subunits of condensins and for CENP-A, it is enriched for DNA repair factors and suppresses the ATR checkpoint to ensure its efficient replication...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27874316/extra-views-on-structure-and-dynamics-of-dna-loops-on-nucleosomes-studied-with-molecular-simulations
#17
Marco Pasi, Dimitar Angelov, Jan Bednar, Stefan Dimitrov, Richard Lavery
It has been shown experimentally that the action of the RSC chromatin remodeler leads to the formation of an irregular, partially remodeled nucleosome, termed a remosome. The remosome contains an extra 30-40 base pairs of DNA compared to a canonical nucleosome. Large-scale molecular simulations have provided information on the probable structure of remosomes and have explained why they remain stable in the absence of RSC. Here we explain how these simulations were carried out and what the resulting remosome models imply in terms of the mechanism of action of RSC...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27858498/sun1-splice-variants-sun1_888-sun1_785-and-predominant-sun1_916-variably-function-in-directional-cell-migration
#18
Yu Nishioka, Hiromasa Imaizumi, Junko Imada, Jun Katahira, Nariaki Matsuura, Miki Hieda
The LINC complex is a multifunctional protein complex that is involved in various processes at the nuclear envelope, such as nuclear migration, mechanotransduction and chromatin tethering in the meiotic phase. However, it remains unknown how these functions are regulated in different cell contexts. An inner nuclear membrane component of the LINC complex, SUN1, is ubiquitously expressed. The human SUN1 gene produces over 10 variants by alternative splicing. Although functions of SUN1 are relatively well characterized, functional differences among SUN1 splice variants are poorly characterized...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27854160/lamin-b1-mediated-demyelination-linking-lamins-lipids-and-leukodystrophies
#19
Quasar S Padiath
Autosomal Dominant Leukodystrophy (ADLD), a fatal adult onset demyelinating disorder, is the only human disease that has been linked to mutations of the nuclear lamina protein, lamin B1, and is primarily caused by duplications of the LMNB1 gene. Why CNS myelin is specifically targeted and the mechanisms underlying ADLD are unclear. Recent work from our group has demonstrated that over expression of lamin B1 in oligodendrocytes, the myelin producing cells in the CNS, resulted in age dependent epigenetic modifications, transcriptional down-regulation of lipogenic gene expression and significant reductions of myelin-enriched lipids...
November 2016: Nucleus
https://www.readbyqxmd.com/read/27813696/chromatin-changes-in-smarcal1-deficiency-a-hypothesis-for-the-gene-expression-alterations-of-schimke-immuno-osseous-dysplasia
#20
Marie Morimoto, Kunho Choi, Cornelius F Boerkoel, Kyoung Sang Cho
Mutations in SMARCAL1, which encodes a DNA annealing helicase with roles in DNA replication fork restart, DNA repair, and gene expression modulation, cause Schimke immuno-osseous dysplasia (SIOD), an autosomal recessive disease characterized by skeletal dysplasia, renal disease, T-cell immunodeficiency, and arteriosclerosis. The clinical features of SIOD arise from pathological changes in gene expression; however, the underlying mechanism for these gene expression alterations remains unclear. We hypothesized that changes of the epigenome alter gene expression in SIOD...
November 2016: Nucleus
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