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2,899 Newest Publications of Cold Spring Harbor Laboratory Press
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Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors [RESEARCH]
01-04-2011 | Feber, Andrew; Wilson, Gareth A.; Zhang, Lu; Presneau, Nadege; Idowu, Bernadine; Down, Thomas A.; Rakyan, Vardhman K ..., Genome Research, 2011
Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of ...
RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology [RESEARCH]
01-04-2011 | Lawson, Andrew R.J.; Hindley, Guy F.L.; Forshew, Tim; Tatevossian, Ruth G.; Jamie, Gabriel A.; Kelly, Gavin P.; Neal ..., Genome Research, 2011
Gene fusions involving members of the RAF family of protein kinases have recently been identified as characteristic aberrations of low-grade astrocytomas, the most common tumors of the central nervous system in children. While it has been shown that these fusions cause constitutive ...
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes [Research Papers]
01-04-2011 | Fasolo, Joseph; Sboner, Andrea; Sun, Mark G.F.; Yu, Haiyuan; Chen, Rui; Sharon, Donald; Kim, Philip M.; Gerstein, Ma ..., Genes & Development, 2011
Protein kinases are key regulators of cellular processes. In spite of considerable effort, a full understanding of the pathways they participate in remains elusive. We globally investigated the proteins that interact with the majority of yeast protein kinases using protein microarrays. ...
Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition [Research Papers]
01-04-2011 | Chen, Jing; Melton, Collin; Suh, Nayoung; Oh, Jeong Su; Horner, Kathleen; Xie, Fang; Sette, Claudio; Blelloch, Rober ..., Genes & Development, 2011
Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here we used a systems approach by combining polysome ...
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells [Research Papers]
01-04-2011 | Min, Irene M.; Waterfall, Joshua J.; Core, Leighton J.; Munroe, Robert J.; Schimenti, John; Lis, John T., Genes & Development, 2011
Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome's primary transcription units in different cell states can identify the genes and steps in the ...
Psidin, a conserved protein that regulates protrusion dynamics and cell migration [Research Papers]
01-04-2011 | Kim, Ji Hoon; Cho, Aeri; Yin, Hongyan; Schafer, Dorothy A.; Mouneimne, Ghassan; Simpson, Kaylene J.; Nguyen, Kim-Vy; ..., Genes & Development, 2011
Dynamic assembly and disassembly of actin filaments is a major driving force for cell movements. Border cells in the Drosophila ovary provide a simple and genetically tractable model to study the mechanisms regulating cell migration. To identify new genes that regulate cell movement in vivo, ...
Pancreatic cancers require autophagy for tumor growth [Research Papers]
01-04-2011 | Yang, Shenghong; Wang, Xiaoxu; Contino, Gianmarco; Liesa, Marc; Sahin, Ergun; Ying, Haoqiang; Bause, Alexandra; Li, ..., Genes & Development, 2011
Macroautophagy (autophagy) is a regulated catabolic pathway to degrade cellular organelles and macromolecules. The role of autophagy in cancer is complex and may differ depending on tumor type or context. Here we show that pancreatic cancers have a distinct dependence on autophagy. ...
SKIP counteracts p53-mediated apoptosis via selective regulation of p21Cip1 mRNA splicing [Research Papers]
01-04-2011 | Chen, Yupeng; Zhang, Lirong; Jones, Katherine A., Genes & Development, 2011
The Ski-interacting protein SKIP/SNW1 functions as both a splicing factor and a transcriptional coactivator for induced genes. We showed previously that transcription elongation factors such as SKIP are dispensable in cells subjected to DNA damage stress. However, we report here that SKIP is ...
RAP80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci [Research Papers]
01-04-2011 | Hu, Yiduo; Scully, Ralph; Sobhian, Bijan; Xie, Anyong; Shestakova, Elena; Livingston, David M., Genes & Development, 2011
In response to DNA double-strand breaks (DSBs), BRCA1 forms biochemically distinct complexes with certain other DNA damage response proteins. These structures, some of which are required for homologous recombination (HR)-type DSB repair, concentrate at distinct nuclear foci that demarcate ...
Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells [Research Communications]
01-04-2011 | Wu, Hao; D'Alessio, Ana C.; Ito, Shinsuke; Wang, Zhibin; Cui, Kairong; Zhao, Keji; Sun, Yi Eve; Zhang, Yi, Genes & Development, 2011
Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a ...
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