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https://www.readbyqxmd.com/read/29348408/nipbl-haploinsufficiency-reveals-a-constellation-of-transcriptome-disruptions-in-the-pluripotent-and-cardiac-states
#1
Jason A Mills, Pamela S Herrera, Maninder Kaur, Lanfranco Leo, Deborah McEldrew, Jesus A Tintos-Hernandez, Ramakrishnan Rajagopalan, Alyssa Gagne, Zhe Zhang, Xilma R Ortiz-Gonzalez, Ian D Krantz
Cornelia de Lange syndrome (CdLS) is a complex disorder with multiple structural and developmental defects caused by mutations in structural and regulatory proteins involved in the cohesin complex. NIPBL, a cohesin regulatory protein, has been identified as a critical protein responsible for the orchestration of transcriptomic regulatory networks necessary for embryonic development. Mutations in NIPBL are responsible for the majority of cases of CdLS. Through RNA-sequencing of human induced pluripotent stem cells and in vitro-derived cardiomyocytes, we identified hundreds of mRNAs, pseudogenes, and non-coding RNAs with altered expression in NIPBL+/- patient-derived cells...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29346962/osmotic-mechanism-of-the-loop-extrusion-process
#2
Tetsuya Yamamoto, Helmut Schiessel
The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29343761/a-high-throughput-approach-for-the-generation-of-orthogonally-interacting-protein-pairs
#3
Justin Lawrie, Xi Song, Wei Niu, Jiantao Guo
In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature's strategy to construct pre-defined three-dimensional protein architectures, highly specific protein-protein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29341686/nonequilibrium-chromosome-looping-via-molecular-slip-links
#4
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook, D Marenduzzo
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29337080/smc1%C3%AE-substitutes-for-many-meiotic-functions-of-smc1%C3%AE-but-cannot-protect-telomeres-from-damage
#5
Uddipta Biswas, Michelle Stevense, Rolf Jessberger
The cohesin complex is built upon the SMC1/SMC3 heterodimer, and mammalian meiocytes feature two variants of SMC1 named SMC1α and SMC1β. It is unclear why these two SMC1 variants have evolved. To determine unique versus redundant functions of SMC1β, we asked which of the known functions of SMC1β can be fulfilled by SMC1α. Smc1α was expressed under control of the Smc1β promoter in either wild-type or SMC1β-deficient mice. No effect was seen in the former. However, several major phenotypes of SMC1β-deficient spermatocytes were rescued by SMC1α...
January 10, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29335463/sub-kb-hi-c-in-d-melanogaster-reveals-conserved-characteristics-of-tads-between-insect-and-mammalian-cells
#6
Qi Wang, Qiu Sun, Daniel M Czajkowsky, Zhifeng Shao
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29329249/scaffolding-for-repair-understanding-molecular-functions-of-the-smc5-6-complex
#7
REVIEW
Mariana Diaz, Ales Pecinka
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex...
January 12, 2018: Genes
https://www.readbyqxmd.com/read/29326119/association-of-mutations-with-morphologic-dysplasia-in-de-novo-acute-myeloid-leukemia-without-2016-who-classification-defined-cytogenetic-abnormalities
#8
Olga K Weinberg, Christopher J Gibson, Traci M Blonquist, Donna Neuberg, Olga Pozdnyakova, Frank Kuo, Benjamin L Ebert, Robert P Hasserjian
Despite improvements in our understanding of the molecular basis of acute myeloid leukemia, the association between genetic mutations with morphologic dysplasia remains unclear. In this study, we evaluated and scored dysplasia in bone marrow specimens from 168 patients with de novo acute myeloid leukemia; none of these patients had 2016 WHO Classification-defined cytogenetic abnormalities. We then performed targeted sequencing of diagnostic bone marrow aspirates for recurrent mutations associated with myeloid malignancies...
January 11, 2018: Haematologica
https://www.readbyqxmd.com/read/29322283/rational-design-of-engineered-microbial-cell-surface-multi-enzyme-co-display-system-for-sustainable-nadh-regeneration-from-low-cost-biomass
#9
Lei Han, Bo Liang, Jianxia Song
As an important cofactor, NADH is essential for most redox reactions and biofuel cells. However, supply of exogenous NADH is challenged, due to the low production efficiency and high cost of NADH regeneration system, as well as low stability of NADH. Here, we constructed a novel cell surface multi-enzyme co-display system with ratio- and space-controllable manner as exogenous NADH regeneration system for the sustainable NADH production from low-cost biomass. Dockerin-fused glucoamylase (GA) and glucose dehydrogenase (GDH) were expressed and assembled on the engineered bacterial surfaces, which displayed protein scaffolds with various combinations of different cohesins...
January 10, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29316705/translocation-breakpoints-preferentially-occur-in-euchromatin-and-acrocentric-chromosomes
#10
Cheng-Yu Lin, Ankit Shukla, John P Grady, J Lynn Fink, Eloise Dray, Pascal H G Duijf
Chromosomal translocations drive the development of many hematological and some solid cancers. Several factors have been identified to explain the non-random occurrence of translocation breakpoints in the genome. These include chromatin density, gene density and CCCTC-binding factor (CTCF)/cohesin binding site density. However, such factors are at least partially interdependent. Using 13,844 and 1563 karyotypes from human blood and solid cancers, respectively, our multiple regression analysis only identified chromatin density as the primary statistically significant predictor...
January 8, 2018: Cancers
https://www.readbyqxmd.com/read/29313530/histone-h3-lysine-4-monomethylation-modulates-long-range-chromatin-interactions-at-enhancers
#11
Jian Yan, Shi-An A Chen, Andrea Local, Tristin Liu, Yunjiang Qiu, Kristel M Dorighi, Sebastian Preissl, Chloe M Rivera, Chaochen Wang, Zhen Ye, Kai Ge, Ming Hu, Joanna Wysocka, Bing Ren
Long-range chromatin interactions between enhancers and promoters are essential for transcription of many developmentally controlled genes in mammals and other metazoans. Currently, the exact mechanisms that connect distal enhancers to their specific target promoters remain to be fully elucidated. Here, we show that the enhancer-specific histone H3 lysine 4 monomethylation (H3K4me1) and the histone methyltransferases MLL3 and MLL4 (MLL3/4) play an active role in this process. We demonstrate that in differentiating mouse embryonic stem cells, MLL3/4-dependent deposition of H3K4me1 at enhancers correlates with increased levels of chromatin interactions, whereas loss of this histone modification leads to reduced levels of chromatin interactions and defects in gene activation during differentiation...
January 9, 2018: Cell Research
https://www.readbyqxmd.com/read/29300120/extrusion-without-a-motor-a-new-take-on-the-loop-extrusion-model-of-genome-organization
#12
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook, D Marenduzzo
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion...
January 4, 2018: Nucleus
https://www.readbyqxmd.com/read/29279609/molecular-characterization-of-hdac8-deletions-in-individuals-with-atypical-cornelia-de-lange-syndrome
#13
Maria Helgeson, Jennifer Keller-Ramey, Amy Knight Johnson, Jennifer A Lee, Daniel B Magner, Brett Deml, Jacea Deml, Ying-Ying Hu, Zejuan Li, Kirsten Donato, Soma Das, Rachel Laframboise, Sandra Tremblay, Ian Krantz, Sarah Noon, George Hoganson, Jennifer Burton, Christian P Schaaf, Daniela Del Gaudio
Cornelia de Lange syndrome (CdLS) is a rare neurodevelopmental syndrome for which mutations in five causative genes that encode (SMC1A, SMC3, RAD21) or regulate (NIPBL, HDAC8) the cohesin complex, account for ~70% of cases. Herein we report on four female Subjects who were found to carry novel intragenic deletions in HDAC8. In one case, the deletion was found in mosaic state and it was determined to be present in ~38% of blood lymphocytes and in nearly all cells of a buccal sample. All deletions, for which parental blood samples were available, were shown to have arisen de novo...
December 26, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29278534/cohesin-mutations-in-myeloid-malignancies-made-simple
#14
Aaron D Viny, Ross L Levine
PURPOSE OF REVIEW: Recurrent loss of function mutations within genes of the cohesin complex have been identified in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). STAG2 is the most commonly mutated cohesin member in AML as well as solid tumors. STAG2 is recurrently, mutated in Ewing's Sarcoma, bladder cancer, and glioblastoma, and is one of only ten genes known to be recurrently mutated in over four distinct tissue types of human cancer RECENT FINDINGS: The cohesin complex, a multiprotein ring, is canonically known to align and stabilize replicated chromosomes prior to cell division...
December 22, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/29275429/intein-mediated-assembly-of-tunable-scaffoldins-for-facile-synthesis-of-designer-cellulosomes
#15
Zhenlin Han, Wei Wen Su
In this study, extended artificial scaffoldins possessing multiple cohesin modules were created in vivo by employing split-intein-mediated protein ligation. Artificial scaffoldins having one Clostridium thermocellum cohesin (Coht), one carbohydrate binding module (CBM) from Clostridium cellulolyticum scaffolding protein CipC, and one to five cohesins (Cohc) derived from CipC, were assembled. These scaffoldins were used to assemble cellulosomal enzyme complexes for investigating the interplay among endoglucanase, exoglucanase, and scaffoldin-borne CBM, on the hydrolysis of a model microcrystalline cellulose substrate, Avicel...
December 23, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29262328/association-with-aurora-a-controls-n-myc-dependent-promoter-escape-and-pause-release-of-rna-polymerase-ii-during-the-cell-cycle
#16
Gabriele Büchel, Anne Carstensen, Ka-Yan Mak, Isabelle Roeschert, Eoin Leen, Olga Sumara, Julia Hofstetter, Steffi Herold, Jacqueline Kalb, Apoorva Baluapuri, Evon Poon, Colin Kwok, Louis Chesler, Hans Michael Maric, David S Rickman, Elmar Wolf, Richard Bayliss, Susanne Walz, Martin Eilers
MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (Pol II). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A, and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of Pol II promoters and intergenic regions. TFIIIC promotes association of RAD21 with N-MYC target sites and is required for N-MYC-dependent promoter escape and pause release of Pol II...
December 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/29261648/regulation-of-the-cohesin-loading-factor-nipbl-role-of-the-lncrna-nipbl-as1-and-identification-of-a-distal-enhancer-element
#17
Jessica Zuin, Valentina Casa, Jelena Pozojevic, Petros Kolovos, Mirjam C G N van den Hout, Wilfred F J van Ijcken, Ilaria Parenti, Diana Braunholz, Yorann Baron, Erwan Watrin, Frank J Kaiser, Kerstin S Wendt
Cohesin is crucial for genome stability, cell division, transcription and chromatin organization. Its functions critically depend on NIPBL, the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome (CdLS). Other mutations are described in the cohesin subunits SMC1A, RAD21, SMC3 and the HDAC8 protein. In 25-30% of CdLS cases no mutation in the known CdLS genes is detected. Until now, functional elements in the noncoding genome were not characterized in the molecular etiology of CdLS and therefore are excluded from mutation screening, although the impact of such mutations has now been recognized for a wide range of diseases...
December 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29258269/a-topology-centric-view-on-mitotic-chromosome-architecture
#18
REVIEW
Ewa Piskadlo, Raquel A Oliveira
Mitotic chromosomes are long-known structures, but their internal organization and the exact process by which they are assembled are still a great mystery in biology. Topoisomerase II is crucial for various aspects of mitotic chromosome organization. The unique ability of this enzyme to untangle topologically intertwined DNA molecules (catenations) is of utmost importance for the resolution of sister chromatid intertwines. Although still controversial, topoisomerase II has also been proposed to directly contribute to chromosome compaction, possibly by promoting chromosome self-entanglements...
December 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29244163/regulation-of-chromosome-segregation-in-oocytes-and-the-cellular-basis-for-female-meiotic-errors
#19
Jessica Greaney, Zhe Wei, Hayden Homer
BACKGROUND: Meiotic chromosome segregation in human oocytes is notoriously error-prone, especially with ageing. Such errors markedly reduce the reproductive chances of increasing numbers of women embarking on pregnancy later in life. However, understanding the basis for these errors is hampered by limited access to human oocytes. OBJECTIVE AND RATIONALE: Important new discoveries have arisen from molecular analyses of human female recombination and aneuploidy along with high-resolution analyses of human oocyte maturation and mouse models...
December 13, 2017: Human Reproduction Update
https://www.readbyqxmd.com/read/29237741/liberating-cohesin-from-cohesion
#20
REVIEW
Kerry Bloom
Cohesin was identified through its major role in holding sister chromatids together. We are learning through analysis of cohesin and other members of the protein family (SMC [structural maintenance of chromosomes]) and their regulators that these ring complexes contribute to chromosome organization and dynamics throughout the cell cycle. We need to consider not only how ring complexes are regulated but how they interact with their fluctuating chromatin substrate.
November 1, 2017: Genes & Development
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