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https://www.readbyqxmd.com/read/28615474/regulation-of-expression-of-human-rna-polymerase-ii-transcribed-snrna-genes
#1
REVIEW
Joana Guiro, Shona Murphy
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3' end formation of the transcripts...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28615473/forkhead-box-transcription-factor-l2-activates-fcp3c-to-regulate-insect-chorion-formation
#2
Yu-Xuan Ye, Peng-Lu Pan, Ji-Yu Xu, Zhang-Fei Shen, Dong Kang, Jia-Bao Lu, Qing-Lin Hu, Hai-Jian Huang, Yi-Han Lou, Nai-Ming Zhou, Chuan-Xi Zhang
Most animals are oviparous. However, the genes regulating egg shell formation remain not very clear. In this study, we found that Nilaparvata lugens Forkhead box transcription factor L2 (NlFoxL2) directly activated follicle cell protein 3C (NlFcp3C) to regulate chorion formation. NlFoxL2 and NlFcp3C had a similar expression pattern, both highly expressed in the follicular cells of female adults. Knockdown of NlFoxL2 or NlFcp3C also resulted in the same phenotypes: obesity and female infertility. RNA interference (RNAi) results suggested that NlFcp3C is a downstream gene of NlFoxL2 Furthermore, transient expression showed that NlFoxL2 could directly activate the NlFcp3C promoter...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28615472/neuronal-circadian-clock-protein-oscillations-are-similar-in-behaviourally-rhythmic-forager-honeybees-and-in-arrhythmic-nurses
#3
T Fuchikawa, K Beer, C Linke-Winnebeck, R Ben-David, A Kotowoy, V W K Tsang, G R Warman, E C Winnebeck, C Helfrich-Förster, G Bloch
Internal clocks driving rhythms of about a day (circadian) are ubiquitous in animals, allowing them to anticipate environmental changes. Genetic or environmental disturbances to circadian clocks or the rhythms they produce are commonly associated with illness, compromised performance or reduced survival. Nevertheless, some animals including Arctic mammals, open sea fish and social insects such as honeybees are active around-the-clock with no apparent ill effects. The mechanisms allowing this remarkable natural plasticity are unknown...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28592509/comparative-functional-genomic-screens-of-three-yeast-deletion-collections-reveal-unexpected-effects-of-genotype-in-response-to-diverse-stress
#4
Erica Acton, Amy Huei-Yi Lee, Pei Jun Zhao, Stephane Flibotte, Mauricio Neira, Sunita Sinha, Jennifer Chiang, Patrick Flaherty, Corey Nislow, Guri Giaever
The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, 'prototrophic' versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PBprot) or by backcrossing (Backcrossed, BCprot) to a wild-type strain...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28566301/understanding-rna-modifications-the-promises-and-technological-bottlenecks-of-the-epitranscriptome
#5
REVIEW
Matthias Schaefer, Utkarsh Kapoor, Michael F Jantsch
The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the 'epitranscriptome'...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28566300/sphingolipids-membrane-microdomains-in-brain-development-function-and-neurological-diseases
#6
REVIEW
Anne S B Olsen, Nils J Færgeman
Sphingolipids are highly enriched in the nervous system where they are pivotal constituents of the plasma membranes and are important for proper brain development and functions. Sphingolipids are not merely structural elements, but are also recognized as regulators of cellular events by their ability to form microdomains in the plasma membrane. The significance of such compartmentalization spans broadly from being involved in differentiation of neurons and synaptic transmission to neuronal-glial interactions and myelin stability...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28539385/phosphatase-ublcp1-controls-proteasome-assembly
#7
Shuangwu Sun, Sisi Liu, Zhengmao Zhang, Wang Zeng, Chuang Sun, Tao Tao, Xia Lin, Xin-Hua Feng
Ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1), an FCP/SCP phosphatase family member, was identified as the first proteasome phosphatase. UBLCP1 binds to proteasome subunit Rpn1 and dephosphorylates the proteasome in vitro However, it is still unclear which proteasome subunit(s) are the bona fide substrate(s) of UBLCP1 and the precise mechanism for proteasome regulation remains elusive. Here, we show that UBLCP1 selectively binds to the 19S regulatory particle (RP) through its interaction with Rpn1, but not the 20S core particle (CP) or the 26S proteasome holoenzyme...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28515224/activin-a-regulates-activation-of-mouse-neutrophils-by-smad3-signalling
#8
Yan Qi, Jingyan Ge, Chunhui Ma, Na Wu, Xueling Cui, Zhonghui Liu
Activin A, a member of the transforming growth factor beta superfamily, acts as a pro-inflammatory factor in acute phase response, and influences the pathological progress of neutrophil-mediated disease. However, whether activin A can exert an effect on the activities of neutrophils remains unclear. In this study, we found that the release of activin A was enhanced from neutrophils of mouse when stimulated with lipopolysaccharide. Furthermore, neutrophils were not only the source of activin A but also the target cells in response to activin A, in which canonical activin signalling components existed, and levels of ACTRIIA, SMAD3 and p-SMAD3 proteins were elevated in activin A-treated neutrophils...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28490658/reviewers-in-2016
#9
EDITORIAL
David M Glover
No abstract text is available yet for this article.
May 2017: Open Biology
https://www.readbyqxmd.com/read/28490657/targeting-endogenous-proteins-for-degradation-through-the-affinity-directed-protein-missile-system
#10
Luke J Fulcher, Luke D Hutchinson, Thomas J Macartney, Craig Turnbull, Gopal P Sapkota
Targeted proteolysis of endogenous proteins is desirable as a research toolkit and in therapeutics. CRISPR/Cas9-mediated gene knockouts are irreversible and often not feasible for many genes. Similarly, RNA interference approaches necessitate prolonged treatments, can lead to incomplete knockdowns and are often associated with off-target effects. Targeted proteolysis can overcome these limitations. In this report, we describe an affinity-directed protein missile (AdPROM) system that harbours the von Hippel-Lindau (VHL) protein, the substrate receptor of the Cullin2 (CUL2) E3 ligase complex, tethered to polypeptide binders that selectively bind and recruit endogenous target proteins to the CUL2-E3 ligase complex for ubiquitination and proteasomal degradation...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28469008/the-early-response-during-the-interaction-of-fungal-phytopathogen-and-host-plant
#11
REVIEW
Yilin Shen, Na Liu, Chuang Li, Xin Wang, Xiaomeng Xu, Wan Chen, Guozhen Xing, Wenming Zheng
Plants can be infected by a variety of pathogens, most of which can cause severe economic losses. The plants resist the invasion of pathogens via the innate or acquired immune system for surviving biotic stress. The associations between plants and pathogens are sophisticated beyond imaging and the interactions between them can occur at a very early stage after their touching each other. A number of researchers in the past decade have shown that many biochemical events appeared even as early as 5 min after their touching for plant disease resistance response...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28469007/golgi-anti-apoptotic-protein-a-tale-of-camels-calcium-channels-and-cancer
#12
REVIEW
Guia Carrara, Maddy Parsons, Nuno Saraiva, Geoffrey L Smith
Golgi anti-apoptotic protein (GAAP), also known as transmembrane Bax inhibitor-1 motif-containing 4 (TMBIM4) or Lifeguard 4 (Lfg4), shares remarkable amino acid conservation with orthologues throughout eukaryotes, prokaryotes and some orthopoxviruses, suggesting a highly conserved function. GAAPs regulate Ca(2+) levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store-operated Ca(2+) entry, are essential for the viability of human cells, and affect orthopoxvirus virulence...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28469006/shaping-development-by-stochasticity-and-dynamics-in-gene-regulation
#13
REVIEW
Peng Dong, Zhe Liu
Animal development is orchestrated by spatio-temporal gene expression programmes that drive precise lineage commitment, proliferation and migration events at the single-cell level, collectively leading to large-scale morphological change and functional specification in the whole organism. Efforts over decades have uncovered two 'seemingly contradictory' mechanisms in gene regulation governing these intricate processes: (i) stochasticity at individual gene regulatory steps in single cells and (ii) highly coordinated gene expression dynamics in the embryo...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28446711/chemical-roots-of-biological-evolution-the-origins-of-life-as-a-process-of-development-of-autonomous-functional-systems
#14
REVIEW
Kepa Ruiz-Mirazo, Carlos Briones, Andrés de la Escosura
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446710/linear-ubiquitin-chains-enzymes-mechanisms-and-biology
#15
REVIEW
Katrin Rittinger, Fumiyo Ikeda
Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446709/control-of-mitochondrial-biogenesis-and-function-by-the-ubiquitin-proteasome-system
#16
REVIEW
Piotr Bragoszewski, Michal Turek, Agnieszka Chacinska
Mitochondria are pivotal organelles in eukaryotic cells. The complex proteome of mitochondria comprises proteins that are encoded by nuclear and mitochondrial genomes. The biogenesis of mitochondrial proteins requires their transport in an unfolded state with a high risk of misfolding. The mislocalization of mitochondrial proteins is deleterious to the cell. The electron transport chain in mitochondria is a source of reactive oxygen species that damage proteins. Mitochondrial dysfunction is linked to many pathological conditions and, together with the loss of cellular protein homeostasis (proteostasis), are hallmarks of ageing and ageing-related degeneration diseases...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446708/structural-and-functional-analysis-of-oceanobacillus-iheyensis-macrodomain-reveals-a-network-of-waters-involved-in-substrate-binding-and-catalysis
#17
Rubén Zapata-Pérez, Fernando Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Jordi Juanhuix, Álvaro Sánchez-Ferrer
Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446707/deterministic-versus-stochastic-model-of-reprogramming-new-evidence-from-cellular-barcoding-technique
#18
Anastasia M Yunusova, Veniamin S Fishman, Gennady V Vasiliev, Nariman R Battulin
Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446706/a-sister-of-nanog-regulates-genes-expressed-in-pre-implantation-human-development
#19
Thomas L Dunwell, Peter W H Holland
The NANOG homeobox gene plays a pivotal role in self-renewal and maintenance of pluripotency in human, mouse and other vertebrate embryonic stem cells, and in pluripotent cells of the blastocyst inner cell mass. There is a poorly studied and atypical homeobox locus close to the Nanog gene in some mammals which could conceivably be a cryptic paralogue of NANOG, even though the loci share only 20% homeodomain identity. Here we argue that this gene, NANOGNB (NANOG Neighbour), is an extremely divergent duplicate of NANOG that underwent radical sequence change in the mammalian lineage...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446705/diverse-integrin-adhesion-stoichiometries-caused-by-varied-actomyosin-activity
#20
Natalia A Bulgakova, Jutta Wellmann, Nicholas H Brown
Cells in an organism are subjected to numerous sources of external and internal forces, and are able to sense and respond to these forces. Integrin-mediated adhesion links the extracellular matrix outside cells to the cytoskeleton inside, and participates in sensing, transmitting and responding to forces. While integrin adhesion rapidly adapts to changes in forces in isolated migrating cells, it is not known whether similar or more complex responses occur within intact, developing tissues. Here, we studied changes in integrin adhesion composition upon different contractility conditions in Drosophila embryonic muscles...
April 2017: Open Biology
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