autophagy_rnaseq.bib

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@article{Singh2009a,
abstract = {The intracellular storage and utilization of lipids are critical to maintain cellular energy homeostasis. During nutrient deprivation, cellular lipids stored as triglycerides in lipid droplets are hydrolysed into fatty acids for energy. A second cellular response to starvation is the induction of autophagy, which delivers intracellular proteins and organelles sequestered in double-membrane vesicles (autophagosomes) to lysosomes for degradation and use as an energy source. Lipolysis and autophagy share similarities in regulation and function but are not known to be interrelated. Here we show a previously unknown function for autophagy in regulating intracellular lipid stores (macrolipophagy). Lipid droplets and autophagic components associated during nutrient deprivation, and inhibition of autophagy in cultured hepatocytes and mouse liver increased triglyceride storage in lipid droplets. This study identifies a critical function for autophagy in lipid metabolism that could have important implications for human diseases with lipid over-accumulation such as those that comprise the metabolic syndrome.},
author = {Singh, Rajat and Kaushik, Susmita and Wang, Yongjun and Xiang, Youqing and Novak, Inna and Komatsu, Masaaki and Tanaka, Keiji and Cuervo, Ana Maria and Czaja, Mark J.},
doi = {10.1038/nature07976},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Singh et al. - 2009 - Autophagy regulates lipid metabolism.pdf:pdf},
isbn = {doi:10.1038/nature07976},
issn = {0028-0836},
journal = {Nature},
month = {apr},
number = {7242},
pages = {1131--1135},
pmid = {19339967},
publisher = {NIH Public Access},
title = {{Autophagy regulates lipid metabolism}},
url = {http://www.nature.com/doifinder/10.1038/nature07976},
volume = {458},
year = {2009}
}
@article{Ashburner2000,
abstract = {Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.},
archivePrefix = {arXiv},
arxivId = {10614036},
author = {Ashburner, Michael and Ball, Catherine A. and Blake, Judith A. and Botstein, David and Butler, Heather and Cherry, J. Michael and Davis, Allan P. and Dolinski, Kara and Dwight, Selina S. and Eppig, Janan T. and Harris, Midori A. and Hill, David P. and Issel-Tarver, Laurie and Kasarskis, Andrew and Lewis, Suzanna and Matese, John C. and Richardson, Joel E. and Ringwald, Martin and Rubin, Gerald M. and Sherlock, Gavin},
doi = {10.1038/75556},
eprint = {10614036},
isbn = {1061-4036 (Print)$\backslash$r1061-4036 (Linking)},
issn = {1061-4036},
journal = {Nature Genetics},
month = {may},
number = {1},
pages = {25--29},
pmid = {10802651},
publisher = {Nature Publishing Group},
title = {{Gene Ontology: tool for the unification of biology}},
url = {http://www.nature.com/doifinder/10.1038/75556},
volume = {25},
year = {2000}
}
@article{Roberts2009,
abstract = {AIMS/HYPOTHESIS:Previous studies have shown relationships between fatty acid ratios in adipose tissue triacylglycerol (TG), adipocyte size and measures of insulin sensitivity. We hypothesised that variations in adipose tissue de novo lipogenesis (DNL) in relation to adiposity might explain some of these observations.$\backslash$n$\backslash$nMETHODS:In a cross-sectional study, subcutaneous abdominal adipose tissue biopsies from 59 people were examined in relation to fasting and post-glucose insulin sensitivity. Adipocyte size, TG fatty acid composition and mRNA expression of lipogenic genes were determined.$\backslash$n$\backslash$nRESULTS:We found strong positive relationships between adipose tissue TG content of the fatty acids myristic acid (14:0) and stearic acid (18:0) with insulin sensitivity (HOMA model) (p {\textless} 0.01 for each), and inverse relationships with adipocyte size (p {\textless} 0.01, p {\textless} 0.05, respectively). Variation in 18:0 content was the determinant of the adipose tissue TG 18:1 n-9/18:0 ratio, which correlated negatively with insulin sensitivity (p {\textless} 0.01), as observed previously. Adipose tissue 18:0 content correlated positively with the mRNA expression of lipogenic genes (e.g. FASN, p {\textless} 0.01). Lipogenic gene expression (a composite measure derived from principal components analysis) was inversely correlated with adipocyte cell size (p {\textless} 0.001). There was no relationship between dietary saturated fatty acid intake and adipose tissue 18:0 content.$\backslash$n$\backslash$nCONCLUSIONS/INTERPRETATION:Our data suggest a physiological mechanism whereby DNL is downregulated as adipocytes expand. Taken together with other data, they also suggest that hepatic and adipose tissue DNL are not regulated in parallel. We also confirm a strong relationship between small adipocytes and insulin sensitivity, which is independent of BMI.},
author = {Roberts, R. and Hodson, L. and Dennis, A. L. and Neville, M. J. and Humphreys, S. M. and Harnden, K. E. and Micklem, K. J. and Frayn, K. N.},
doi = {10.1007/s00125-009-1300-4},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Roberts et al. - 2009 - Markers of de novo lipogenesis in adipose tissue Associations with small adipocytes and insulin sensitivity in h.pdf:pdf},
isbn = {0012-186X},
issn = {0012186X},
journal = {Diabetologia},
keywords = {Adipocytes,De novo lipogenesis,Dietary fatty acids,Insulin sensitivity,Saturated fatty acids,Stearic acid,Stearoyl-CoA desaturase,Triacylglycerol},
month = {may},
number = {5},
pages = {882--890},
pmid = {19252892},
publisher = {Springer-Verlag},
title = {{Markers of de novo lipogenesis in adipose tissue: Associations with small adipocytes and insulin sensitivity in humans}},
url = {http://link.springer.com/10.1007/s00125-009-1300-4},
volume = {52},
year = {2009}
}
@article{Kim2015,
abstract = {HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.},
archivePrefix = {arXiv},
arxivId = {15334406},
author = {Kim, Daehwan and Langmead, Ben and Salzberg, Steven L},
doi = {10.1038/nmeth.3317},
eprint = {15334406},
isbn = {1548-7091},
issn = {1548-7091},
journal = {Nature Methods},
month = {apr},
number = {4},
pages = {357--360},
pmid = {25751142},
publisher = {Nature Publishing Group},
title = {{HISAT: a fast spliced aligner with low memory requirements}},
url = {http://www.nature.com/doifinder/10.1038/nmeth.3317},
volume = {12},
year = {2015}
}
@article{Martinez-Vicente2010,
abstract = {Continuous turnover of intracellular components by autophagy is necessary to preserve cellular homeostasis in all tissues. Alterations in macroautophagy, the main process responsible for bulk autophagic degradation, have been proposed to contribute to pathogenesis in Huntington's disease (HD), a genetic neurodegenerative disorder caused by an expanded polyglutamine tract in the huntingtin protein. However, the precise mechanism behind macroautophagy malfunction in HD is poorly understood. In this work, using cellular and mouse models of HD and cells from humans with HD, we have identified a primary defect in the ability of autophagic vacuoles to recognize cytosolic cargo in HD cells. Autophagic vacuoles form at normal or even enhanced rates in HD cells and are adequately eliminated by lysosomes, but they fail to efficiently trap cytosolic cargo in their lumen. We propose that inefficient engulfment of cytosolic components by autophagosomes is responsible for their slower turnover, functional decay and accumulation inside HD cells.},
author = {Martinez-Vicente, Marta and Talloczy, Zsolt and Wong, Esther and Tang, Guomei and Koga, Hiroshi and Kaushik, Susmita and de Vries, Rosa and Arias, Esperanza and Harris, Spike and Sulzer, David and Cuervo, Ana Maria},
doi = {10.1038/nn.2528},
isbn = {1546-1726 (Electronic)$\backslash$n1097-6256 (Linking)},
issn = {1097-6256},
journal = {Nature Neuroscience},
month = {may},
number = {5},
pages = {567--576},
pmid = {20383138},
title = {{Cargo recognition failure is responsible for inefficient autophagy in Huntington's disease}},
url = {http://www.nature.com/doifinder/10.1038/nn.2528},
volume = {13},
year = {2010}
}
@article{Green1974,
abstract = {When cells of the established preadipose line 3T3-L1 enter a resting state, they accumulate triglyceride and convert to adipose cells. The adipose conversion is brought about by a large increase in the rate of triglyceride synthesis, as measured by the incorporation rate of labeled palmitate, acetate, and glucose. In a resting 3T3 subline which does not undergo the adipose conversion, the rate of triglyceride synthesis from these precursors is very low, and similar to that of growing 3T3-L1 cells, before their adipose conversion begins. If 3T3-L1 cells incorporate bromodeoxyuridine during growth, triglyceride synthesis does not increase when the cells reach a stationary state, and triglycerides do not accumulate. As would be expected from their known actions on tissue adipose cells, lipogenic and lipolytic hormones and drugs affect the rate of synthesis and accumulation of triglyceride by 3T3-L1 cells, but in contrast to bromodeoxyuridine, these modulating agents do not seem to affect the proportion of cells which undergoes the adipose conversion. Insulin markedly increases the rate of synthesis and accumulation of triglyceride by fatty 3T3-L1 cells, and produces a related increase in cell protein content. Of 20 randomly selected clones isolated from the original 3T3 stock, 19 are able to convert to adipose cells. The probability of such a conversion varies greatly among the different clones, in most cases being much lower than for 3T3-L1; but once the conversion takes place, the adipose cells produced from all of the 19 clones appear similar. The adipose conversion would seem to depend on an on-off switch, which is on with a different probability in different clones. This probability is quasistably inherited by the clonal progeny. ?? 1975.},
author = {Green, Howard and Kehinde, Olaniyi},
doi = {10.1016/0092-8674(75)90087-2},
isbn = {0092-8674 (Print)$\backslash$n0092-8674 (Linking)},
issn = {00928674},
journal = {Cell},
month = {oct},
number = {1},
pages = {19--27},
pmid = {4426090},
title = {{An established preadipose cell line and its differentiation in culture II. Factors affecting the adipose conversion}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0092867474901160},
volume = {5},
year = {1975}
}
@article{Singh2009,
abstract = {The relative balance between the quantity of white and brown adipose tissue can profoundly affect lipid stor- age and whole-body energy homeostasis. However, the mechanisms regulating the formation, expansion, and interconversion of these 2 distinct types of fat remain unknown. Recently, the lysosomal degradative pathway of macroautophagy has been identified as a regulator of cellular differentiation, suggesting that autophagy may modulate this process in adipocytes. The function of autophagy in adipose differentiation was therefore examined in the current study by genetic inhibition of the critical macroautophagy gene autophagy-related 7 (Atg7). Knockdown of Atg7 in 3T3-L1 preadipocytes inhibited lipid accumulation and decreased protein lev- els of adipocyte differentiation factors. Knockdown of Atg5 or pharmacological inhibition of autophagy or lysosome function also had similar effects. An adipocyte-specific mouse knockout of Atg7 generated lean mice with decreased white adipose mass and enhanced insulin sensitivity. White adipose tissue in knockout mice had increased features of brown adipocytes, which, along with an increase in normal brown adipose tissue, led to an elevated rate of fatty acid, $\beta$-oxidation, and a lean body mass. Autophagy therefore functions to regulate body lipid accumulation by controlling adipocyte differentiation and determining the balance between white and brown fat. Introduction},
author = {Singh, Rajat and Xiang, Youqing and Wang, Yongjun and Baikati, Kiran and Cuervo, Ana Maria and Luu, Yen K. and Tang, Yan and Pessin, Jeffrey E. and Schwartz, Gary J. and Czaja, Mark J.},
doi = {10.1172/JCI39228},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Singh et al. - 2009 - Autophagy regulates adipose mass and differentiation in mice.pdf:pdf},
isbn = {0021-9738},
issn = {00219738},
journal = {Journal of Clinical Investigation},
month = {nov},
number = {11},
pages = {3329--3339},
pmid = {19855132},
publisher = {American Society for Clinical Investigation},
title = {{Autophagy regulates adipose mass and differentiation in mice}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19855132 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2769174},
volume = {119},
year = {2009}
}
@article{Love2014,
abstract = {In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at 
                  http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
                  
                .},
author = {Love, Michael I and Huber, Wolfgang and Anders, Simon},
doi = {10.1186/s13059-014-0550-8},
isbn = {1465-6906},
issn = {1474-760X},
journal = {Genome Biology},
number = {12},
pages = {550},
pmid = {25516281},
title = {{Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}},
url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8},
volume = {15},
year = {2014}
}
@article{Dong2011,
abstract = {Autophagy is a lysosomal pathway by which intracellular organelles and proteins are degraded to supply the cell with energy and to maintain cellular homeostasis. Recently, lipid droplets (LDs) have been identified as a substrate for macroautophagy. In addition to the classic pathway of lipid metabolism by cytosolic lipases, LDs are sequestered in autophagosomes that fuse with lysosomes for the breakdown of LD components by lysosomal enzymes. The ability of autophagy to respond to changes in nutrient supply allows the cell to alter LD metabolism to meet the cell's energy demands. Pathophysiological changes in autophagic function can alter cellular lipid metabolism and promote disease states. Autophagy therefore represents a new cellular target for abnormalities in lipid metabolism and accumulation. {\textcopyright} 2011 Elsevier Ltd.},
author = {Dong, Hanqing and Czaja, Mark J.},
doi = {10.1016/j.tem.2011.02.003},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Dong, Czaja - 2011 - Regulation of lipid droplets by autophagy.pdf:pdf},
isbn = {1879-3061 (Electronic)$\backslash$r1043-2760 (Linking)},
issn = {10432760},
journal = {Trends in Endocrinology and Metabolism},
number = {6},
pages = {234--240},
pmid = {21419642},
publisher = {Elsevier Ltd},
title = {{Regulation of lipid droplets by autophagy}},
url = {http://dx.doi.org/10.1016/j.tem.2011.02.003},
volume = {22},
year = {2011}
}
@article{AlAdhami2015,
abstract = {Genomic imprinting is an epigenetic mechanism that restrains the expression of ∼ 100 eutherian genes in a parent-of-origin-specific manner. The reason for this selective targeting of genes with seemingly disparate molecular functions is unclear. In the present work, we show that imprinted genes are coexpressed in a network that is regulated at the transition from proliferation to quiescence and differentiation during fibroblast cell cycle withdrawal, adipogenesis in vitro, and muscle regeneration in vivo. Imprinted gene regulation is not linked to alteration of DNA methylation or to perturbation of monoallelic, parent-of-origin-dependent expression. Overexpression and knockdown of imprinted gene expression alters the sensitivity of preadipocytes to contact inhibition and adipogenic differentiation. In silico and in cellulo experiments showed that the imprinted gene network includes biallelically expressed, nonimprinted genes. These control the extracellular matrix composition, cell adhesion, cell junction, and extracellular matrix-activated and growth factor-activated signaling. These observations show that imprinted genes share a common biological process that may account for their seemingly diverse roles in embryonic development, obesity, diabetes, muscle physiology, and neoplasm.},
author = {{Al Adhami}, Hala and Evano, Brendan and {Le Digarcher}, Anne and Gueydan, Charlotte and Dubois, Emeric and Parrinello, Hugues and Dantec, Christelle and Bouschet, Tristan and Varrault, Annie and Journot, Laurent},
doi = {10.1101/gr.175919.114},
isbn = {1088-9051},
issn = {15495469},
journal = {Genome Research},
month = {mar},
number = {3},
pages = {353--367},
pmid = {25614607},
title = {{A systems-level approach to parental genomic imprinting: The imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25614607 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4352888 http://genome.cshlp.org/lookup/doi/10.1101/gr.175919.114},
volume = {25},
year = {2015}
}
@article{Narendra2008,
abstract = {Loss-of-function mutations in Park2, the gene coding for the ubiquitin ligase Parkin, are a significant cause of early onset Parkinson's disease. Although the role of Parkin in neuron maintenance is unknown, recent work has linked Parkin to the regulation of mitochondria. Its loss is associated with swollen mitochondria and muscle degeneration in Drosophila melanogaster, as well as mitochondrial dysfunction and increased susceptibility to mitochondrial toxins in other species. Here, we show that Parkin is selectively recruited to dysfunctional mitochondria with low membrane potential in mammalian cells. After recruitment, Parkin mediates the engulfment of mitochondria by autophagosomes and the selective elimination of impaired mitochondria. These results show that Parkin promotes autophagy of damaged mitochondria and implicate a failure to eliminate dysfunctional mitochondria in the pathogenesis of Parkinson's disease.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Narendra, Derek and Tanaka, Atsushi and Suen, Der Fen and Youle, Richard J.},
doi = {10.1083/jcb.200809125},
eprint = {arXiv:1011.1669v3},
isbn = {0021-9525},
issn = {00219525},
journal = {Journal of Cell Biology},
month = {dec},
number = {5},
pages = {795--803},
pmid = {19029340},
title = {{Parkin is recruited selectively to impaired mitochondria and promotes their autophagy}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19029340 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2592826 http://www.jcb.org/lookup/doi/10.1083/jcb.200809125},
volume = {183},
year = {2008}
}
@article{Duteil2014,
abstract = {Exposure to environmental cues such as cold or nutritional imbalance requires white adipose tissue (WAT) to adapt its metabolism to ensure survival. Metabolic plasticity is prominently exemplified by the enhancement of mitochondrial biogenesis in WAT in response to cold exposure or $\beta$3-adrenergic stimulation. Here we show that these stimuli increase the levels of lysine-specific demethylase 1 (LSD1) in WAT of mice and that elevated LSD1 levels induce mitochondrial activity. Genome-wide binding and transcriptome analyses demonstrate that LSD1 directly stimulates the expression of genes involved in oxidative phosphorylation (OXPHOS) in cooperation with nuclear respiratory factor 1 (Nrf1). In transgenic (Tg) mice, increased levels of LSD1 promote in a cell-autonomous manner the formation of islets of metabolically active brown-like adipocytes in WAT. Notably, Tg mice show limited weight gain when fed a high-fat diet. Taken together, our data establish LSD1 as a key regulator of OXPHOS and metabolic adaptation in WAT.},
author = {Duteil, Delphine and Metzger, Eric and Willmann, Dominica and Karagianni, Panagiota and Friedrichs, Nicolaus and Greschik, Holger and G{\"{u}}nther, Thomas and Buettner, Reinhard and Talianidis, Iannis and Metzger, Daniel and Sch{\"{u}}le, Roland},
doi = {10.1038/ncomms5093},
issn = {2041-1723},
journal = {Nature communications},
month = {jun},
number = {May},
pages = {4093},
pmid = {24912735},
title = {{LSD1 promotes oxidative metabolism of white adipose tissue.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24912735},
volume = {5},
year = {2014}
}
@article{Khaminets2015,
abstract = {The endoplasmic reticulum (ER) is the largest intracellular endomembrane system, enabling protein and lipid synthesis, ion homeostasis, quality control of newly synthesized proteins and organelle communication. Constant ER turnover and modulation is needed to meet different cellular requirements and autophagy has an important role in this process. However, its underlying regulatory mechanisms remain unexplained. Here we show that members of the FAM134 reticulon protein family are ER-resident receptors that bind to autophagy modifiers LC3 and GABARAP, and facilitate ER degradation by autophagy ('ER-phagy'). Downregulation of FAM134B protein in human cells causes an expansion of the ER, while FAM134B overexpression results in ER fragmentation and lysosomal degradation. Mutant FAM134B proteins that cause sensory neuropathy in humans are unable to act as ER-phagy receptors. Consistently, disruption of Fam134b in mice causes expansion of the ER, inhibits ER turnover, sensitizes cells to stress-induced apoptotic cell death and leads to degeneration of sensory neurons. Therefore, selective ER-phagy via FAM134 proteins is indispensable for mammalian cell homeostasis and controls ER morphology and turnover in mice and humans.},
author = {Khaminets, Aliaksandr and Heinrich, Theresa and Mari, Muriel and Grumati, Paolo and Huebner, Antje K. and Akutsu, Masato and Liebmann, Lutz and Stolz, Alexandra and Nietzsche, Sandor and Koch, Nicole and Mauthe, Mario and Katona, Istvan and Qualmann, Britta and Weis, Joachim and Reggiori, Fulvio and Kurth, Ingo and H{\"{u}}bner, Christian A. and Dikic, Ivan},
doi = {10.1038/nature14498},
isbn = {1476-4687 (Electronic) 0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
month = {jun},
number = {7556},
pages = {354--358},
pmid = {26040720},
title = {{Regulation of endoplasmic reticulum turnover by selective autophagy}},
url = {http://www.nature.com/doifinder/10.1038/nature14498},
volume = {522},
year = {2015}
}
@article{Reyes2013,
abstract = {Alternative usage of exons provides genomes with plasticity to produce different transcripts from the same gene, modulating the function, localization, and life cycle of gene products. It affects most human genes. For a limited number of cases, alternative functions and tissue-specific roles are known. However, recent high-throughput sequencing studies have suggested that much alternative isoform usage across tissues is nonconserved, raising the question of the extent of its functional importance. We address this question in a genome-wide manner by analyzing the transcriptomes of five tissues for six primate species, focusing on exons that are 1:1 orthologous in all six species. Our results support a model in which differential usage of exons has two major modes: First, most of the exons show only weak differences, which are dominated by interspecies variability and may reflect neutral drift and noisy splicing. These cases dominate the genome-wide view and explain why conservation appears to be so limited. Second, however, a sizeable minority of exons show strong differences between tissues, which are mostly conserved. We identified a core set of 3,800 exons from 1,643 genes that show conservation of strongly tissue-dependent usage patterns from human at least to macaque. This set is enriched for exons encoding protein-disordered regions and untranslated regions. Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms.},
author = {Reyes, A. and Anders, S. and Weatheritt, R. J. and Gibson, T. J. and Steinmetz, L. M. and Huber, W.},
doi = {10.1073/pnas.1307202110},
isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {38},
pages = {15377--15382},
pmid = {24003148},
title = {{Drift and conservation of differential exon usage across tissues in primate species}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1307202110},
volume = {110},
year = {2013}
}
@manual{Carlson2017,
abstract = {R package version 3.0.0},
annote = {R package version 3.4.1},
author = {Carlson, M},
title = {{org.Mm.eg.db: Genome wide annotation for Mouse}},
year = {2016}
}
@article{Cochrane2008,
abstract = {The Ensembl Trace Archive (http://trace.ensembl.org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth in data volume and diversity. Selected major developments of 2007 are presented briefly, along with data submission and retrieval information. In the face of increasing requirements for nucleotide trace, sequence and annotation data archiving, data capture priority decisions have been taken at the European Nucleotide Archive. Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured.},
author = {Cochrane, Guy and Akhtar, Ruth and Aldebert, Philippe and Althorpe, Nicola and Baldwin, Alastair and Bates, Kirsty and Bhattacharyya, Sumit and Bonfield, James and Bower, Lawrence and Browne, Paul and Castro, Matias and Cox, Tony and Demiralp, Fehmi and Eberhardt, Ruth and Faruque, Nadeem and Hoad, Gemma and Jang, Mikyung and Kulikova, Tamara and Labarga, Alberto and Leinonen, Rasko and Leonard, Steven and Lin, Quan and Lopez, Rodrigo and Lorenc, Dariusz and Mcwilliam, Hamish and Mukherjee, Gaurab and Nardone, Francesco and Plaister, Sheila and Robinson, Stephen and Sobhany, Siamak and Vaughan, Robert and Wu, Dan and Zhu, Weimin and Apweiler, Rolf and Hubbard, Tim and Birney, Ewan},
doi = {10.1093/nar/gkm1018},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Cochrane et al. - 2008 - Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Research},
month = {jan},
number = {SUPPL. 1},
pages = {D5--12},
pmid = {18039715},
publisher = {Oxford University Press},
title = {{Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18039715 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2238915},
volume = {36},
year = {2008}
}
@article{Leinonen2011,
abstract = {The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the SRA. The SRA was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA, detail our support for sequencing platforms and provide recommended data submission levels and formats. We also briefly outline our response to the challenge of data growth.},
author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin},
doi = {10.1093/nar/gkq1019},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Leinonen et al. - 2011 - The sequence read archive.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Research},
month = {jan},
number = {SUPPL. 1},
pages = {D19--21},
pmid = {21062823},
publisher = {Oxford University Press},
title = {{The sequence read archive}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21062823 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3013647},
volume = {39},
year = {2011}
}
@manual{Meyer2017,
annote = {R package version 1.6-8},
author = {Meyer, David and Dimitriadou, Evgenia and Hornik, Kurt and Weingessel, Andreas and Leisch, Friedrich and Chang, Chih-Chung and Lin, Chih-Chen},
title = {{e1071: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. https://cran.r-project.org/web/packages/e1071}},
url = {https://cran.r-project.org/package=e1071},
year = {2016}
}
@article{Ritchie2015,
abstract = {limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.},
author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.},
doi = {10.1093/nar/gkv007},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Ritchie et al. - 2015 - Limma powers differential expression analyses for RNA-sequencing and microarray studies.pdf:pdf},
isbn = {0305-1048},
issn = {13624962},
journal = {Nucleic acids research},
number = {7},
pages = {e47},
pmid = {25605792},
title = {{limma powers differential expression analyses for RNA-sequencing and microarray studies}},
volume = {43},
year = {2015}
}
@article{Vives-Bauza2010,
abstract = {Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1) and PARK2/Parkin mutations cause autosomal recessive forms of Parkinson{\&}apos;s disease. Upon a loss of mitochondrial membrane potential (Delta psi(m)) in human cells, cytosolic Parkin has been reported to be recruited to mitochondria, which is followed by a stimulation of mitochondrial autophagy. Here, we show that the relocation of Parkin to mitochondria induced by a collapse of Delta psi(m) relies on PINK1 expression and that overexpression of WT but not of mutated PINK1 causes Parkin translocation to mitochondria, even in cells with normal Delta psi(m). We also show that once at the mitochondria, Parkin is in close proximity to PINK1, but we find no evidence that Parkin catalyzes PINK1 ubiquitination or that PINK1 phosphorylates Parkin. However, co-overexpression of Parkin and PINK1 collapses the normal tubular mitochondrial network into mitochondrial aggregates and/or large perinuclear clusters, many of which are surrounded by autophagic vacuoles. Our results suggest that Parkin, together with PINK1, modulates mitochondrial trafficking, especially to the perinuclear region, a subcellular area associated with autophagy. Thus by impairing this process, mutations in either Parkin or PINK1 may alter mitochondrial turnover which, in turn, may cause the accumulation of defective mitochondria and, ultimately, neurodegeneration in Parkinson{\&}apos;s disease.},
archivePrefix = {arXiv},
arxivId = {139},
author = {Vives-Bauza, C. and Zhou, C. and Huang, Y. and Cui, M. and de Vries, R. L. A. and Kim, J. and May, J. and Tocilescu, M. A. and Liu, W. and Ko, H. S. and Magrane, J. and Moore, D. J. and Dawson, V. L. and Grailhe, R. and Dawson, T. M. and Li, C. and Tieu, K. and Przedborski, S.},
doi = {10.1073/pnas.0911187107},
eprint = {139},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Vives-Bauza et al. - 2010 - PINK1-dependent recruitment of Parkin to mitochondria in mitophagy.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {jan},
number = {1},
pages = {378--383},
pmid = {273559200066},
publisher = {National Academy of Sciences},
title = {{PINK1-dependent recruitment of Parkin to mitochondria in mitophagy}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0911187107},
volume = {107},
year = {2010}
}
@manual{Gentleman2017,
annote = {R package version 1.58.1},
author = {Gentleman, R. and Carey, V. and Huber, W. and Hahne, F.},
title = {{Genefilter: Methods for filtering genes from high-throughput experiments. R package version 1.53.0.}},
url = {https://www.bioconductor.org/packages/3.3/bioc/html/genefilter.html},
year = {2015}
}
@article{Mochida2015,
abstract = {Macroautophagy (hereafter referred to as autophagy) degrades various intracellular constituents to regulate a wide range of cellular functions, and is also closely linked to several human diseases. In selective autophagy, receptor proteins recognize degradation targets and direct their sequestration by double-membrane vesicles called autophagosomes, which transport them into lysosomes or vacuoles. Although recent studies have shown that selective autophagy is involved in quality/quantity control of some organelles, including mitochondria and peroxisomes, it remains unclear how extensively it contributes to cellular organelle homeostasis. Here we describe selective autophagy of the endoplasmic reticulum (ER) and nucleus in the yeast Saccharomyces cerevisiae. We identify two novel proteins, Atg39 and Atg40, as receptors specific to these pathways. Atg39 localizes to the perinuclear ER (or the nuclear envelope) and induces autophagic sequestration of part of the nucleus. Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes. Atg39-dependent autophagy of the perinuclear ER/nucleus is required for cell survival under nitrogen-deprivation conditions. Atg40 is probably the functional counterpart of FAM134B, an autophagy receptor for the ER in mammals that has been implicated in sensory neuropathy. Our results provide fundamental insight into the pathophysiological roles and mechanisms of 'ER-phagy' and 'nucleophagy' in other organisms.},
author = {Mochida, Keisuke and Oikawa, Yu and Kimura, Yayoi and Kirisako, Hiromi and Hirano, Hisashi and Ohsumi, Yoshinori and Nakatogawa, Hitoshi},
doi = {10.1038/nature14506},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
month = {jun},
number = {7556},
pages = {359--362},
pmid = {26040717},
title = {{Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus}},
url = {http://www.nature.com/doifinder/10.1038/nature14506},
volume = {522},
year = {2015}
}
@article{Jin2013,
abstract = {Defective mitochondria exert deleterious effects on host cells. To manage this risk, mitochondria display several lines of quality control mechanisms: mitochondria-specific chaperones and proteases protect against misfolded proteins at the molecular level, and fission/fusion and mitophagy segregate and eliminate damage at the organelle level. An increase in unfolded proteins in mitochondria activates a mitochondrial unfolded protein response (UPR(mt)) to increase chaperone production, while the mitochondrial kinase PINK1 and the E3 ubiquitin ligase PARK2/Parkin, whose mutations cause familial Parkinson disease, remove depolarized mitochondria through mitophagy. It is unclear, however, if there is a connection between those different levels of quality control (QC). Here, we show that the expression of unfolded proteins in the matrix causes the accumulation of PINK1 on energetically healthy mitochondria, resulting in mitochondrial translocation of PARK2, mitophagy and subsequent reduction of unfolded protein load. Also, PINK1 accumulation is greatly enhanced by the knockdown of the LONP1 protease. We suggest that the accumulation of unfolded proteins in mitochondria is a physiological trigger of mitophagy.},
author = {Jin, Seok Min and Youle, Richard J.},
doi = {10.4161/auto.26122},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Jin, Youle - 2013 - The accumulation of misfolded proteins in the mitochondrial matrix is sensed by PINK1 to induce PARK2Parkin-mediated.pdf:pdf},
isbn = {1554-8627$\backslash$r1554-8635},
issn = {15548635},
journal = {Autophagy},
keywords = {LONP,Mitochondria,Mitophagy,PARK2/Parkin,PINK1,Unfolded protein response},
month = {nov},
number = {11},
pages = {1750--1757},
pmid = {24149988},
publisher = {Taylor {\&} Francis},
title = {{The accumulation of misfolded proteins in the mitochondrial matrix is sensed by PINK1 to induce PARK2/Parkin-mediated mitophagy of polarized mitochondria}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24149988 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4028334},
volume = {9},
year = {2013}
}
@article{Ntambi2000,
abstract = {The major function of adipocytes is to store triacylglycerol in periods of energy excess and to mobilize this energy during times of deprivation. The short-term control of these lipogenic and lipolytic processes is carefully modulated by hormonal signals from the bloodstream, which provide an inventory of the body's metabolic state. Long-term changes in fat storage needs are accomplished by altering both the size and number of fat cells within the body because terminally differentiated adipocytes cannot divide. Alterations in the number of fat cells within the body must be accomplished by the differentiation of preadipocytes, which act as the renewable source of adipocytes. Our understanding of the events that occur during preadipocyte differentiation has advanced considerably in the last few years and has relied mainly on the use of tissue culture models of adipogenesis. This article will discuss the various models used for studying the preadipocyte differentiation process, with the mouse 3T3-L1 cell culture line described in detail. We focus on those genetic events that link effectors to induction of adipocyte gene expression.},
author = {Ntambi, J M and Young-Cheul, K},
doi = {Test},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Ntambi, Young-Cheul - 2000 - Adipocyte differentiation and gene expression.pdf:pdf},
isbn = {0022-3166},
issn = {0022-3166},
journal = {The Journal of nutrition},
month = {dec},
number = {12},
pages = {3122S--3126S},
pmid = {11110885},
publisher = {American Society for Nutrition},
title = {{Adipocyte differentiation and gene expression.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11110885},
volume = {130},
year = {2000}
}
@article{Sica2015,
abstract = {Autophagy constitutes a prominent mechanism through which eukaryotic cells preserve homeostasis in baseline conditions and in response to perturbations of the intracellular or extracellular microenvironment. Autophagic responses can be relatively non-selective or target a specific subcellular compartment. At least in part, this depends on the balance between the availability of autophagic substrates ("offer") and the cellular need of autophagic products or functions for adaptation ("demand"). Irrespective of cargo specificity, adaptive autophagy relies on a panel of sensors that detect potentially dangerous cues and convert them into signals that are ultimately relayed to the autophagic machinery. Here, we summarize the molecular systems through which specific subcellular compartments-including the nucleus, mitochondria, plasma membrane, reticular apparatus, and cytosol-convert homeostatic perturbations into an increased offer of autophagic substrates or an accrued cellular demand for autophagic products or functions.},
author = {Sica, Valentina and Galluzzi, Lorenzo and {Bravo-San Pedro}, Jos{\'{e}} Manuel and Izzo, Valentina and Maiuri, Maria Chiara and Kroemer, Guido},
doi = {10.1016/j.molcel.2015.07.021},
isbn = {1097-4164 (Electronic)$\backslash$r1097-2765 (Linking)},
issn = {10974164},
journal = {Molecular Cell},
month = {aug},
number = {4},
pages = {522--539},
pmid = {26295960},
title = {{Organelle-Specific Initiation of Autophagy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276515005791},
volume = {59},
year = {2015}
}
@article{Scott1982,
abstract = {The differentiation of most mammalian cells is preceded by growth arrest in the G1 phase of the cell cycle, but the characteristics of this state have not been established. We now report that the growth arrest that precedes the differentiation of BALB/c 3T3 T mouse proadipocytes must occur at a distinct state in G1 designated GD. GD-arrested cells are characterized by their ability to differentiate in the absence of DNA synthesis and by their unique sensitivity to the mitogenic effect of isobutylmethylxanthine. Proadipocytes induced to become G1 growth arrested at other states by culture in medium deficient in growth factor or nutrients, by contrast, are unable to differentiate in the absence of DNA synthesis and are not stimulated to proliferate by isobutylmethylxanthine even when they are exposed to differentiation-promoting medium prior to arrest. These data support the conclusion that, prior to the expression of a differentiated phenotype, proadipocytes must arrest their growth at a distinct state in the G1 phase of the cell cycle, GD. These data also provide the basis for the hypothesis that carcinogenesis is associated with defects in the coupling of growth arrest and differentiation at the GD state.},
author = {Scott, R E and Florine, D L and Wille, J J and Yun, K},
doi = {10.1073/pnas.79.3.845},
file = {:Users/MahShaaban/Library/Application Support/Mendeley Desktop/Downloaded/Scott et al. - 1982 - Coupling of growth arrest and differentiation at a distinct state in the G1 phase of the cell cycle GD.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = {feb},
number = {February},
pages = {845--849},
pmid = {6174983},
publisher = {National Academy of Sciences},
title = {{Coupling of growth arrest and differentiation at a distinct state in the G1 phase of the cell cycle: GD.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6174983 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC345849},
volume = {79},
year = {1982}
}
@article{Kanehisa2017,
abstract = {The eukaryotic RNA exosome is an essential, multi-subunit complex that catalyzes RNA turnover, maturation, and quality control processes. Its non-catalytic donut-shaped core includes 9 subunits that associate with the 3' to 5' exoribonucleases Rrp6, and Rrp44/Dis3, a subunit that also catalyzes endoribonuclease activity. Although recent structures and biochemical studies of RNA bound exosomes from S. cerevisiae revealed that the Exo9 central channel guides RNA to either Rrp6 or Rrp44 using partially overlapping and mutually exclusive paths, several issues related to RNA recruitment remain. Here, we identify activities for the highly basic Rrp6 C-terminal tail that we term the 'lasso' because it binds RNA and stimulates ribonuclease activities associated with Rrp44 and Rrp6 within the 11-subunit nuclear exosome. Stimulation is dependent on the Exo9 central channel, and the lasso contributes to degradation and processing activities of exosome substrates in vitro and in vivo. Finally, we present evidence that the Rrp6 lasso may be a conserved feature of the eukaryotic RNA exosome.},
archivePrefix = {arXiv},
arxivId = {1611.06654},
author = {Kanehisa, Minoru and Furumichi, Miho and Tanabe, Mao and Sato, Yoko and Morishima, Kanae},
doi = {10.1093/nar/gkw1092},
eprint = {1611.06654},
isbn = {2076792171},
issn = {13624962},
journal = {Nucleic Acids Research},
month = {jan},
number = {D1},
pages = {D353--D361},
pmid = {27899565},
title = {{KEGG: New perspectives on genomes, pathways, diseases and drugs}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27899662 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5210567 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1092},
volume = {45},
year = {2017}
}