Search Results - "Burge, Christopher B"

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins by Lambert, Nicole, Robertson, Alex, Jangi, Mohini, McGeary, Sean, Sharp, Phillip A., Burge, Christopher B.

“…Specific protein-RNA interactions guide posttranscriptional gene regulation. Here, we describe RNA Bind-n-Seq (RBNS), a method that comprehensively…”
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Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues by Merkin, Jason, Russell, Caitlin, Chen, Ping, Burge, Christopher B.

“…Most mammalian genes produce multiple distinct messenger RNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess…”
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Splicing regulation: from a parts list of regulatory elements to an integrated splicing code by Wang, Zefeng, Burge, Christopher B

“…Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in…”
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Widespread Regulation of Translation by Elongation Pausing in Heat Shock by Shalgi, Reut, Hurt, Jessica A., Krykbaeva, Irina, Taipale, Mikko, Lindquist, Susan, Burge, Christopher B.

“…Global repression of protein synthesis is a hallmark of the cellular stress response and has been attributed primarily to inhibition of translation initiation,…”
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Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment by Klattenhoff, Carla A., Scheuermann, Johanna C., Surface, Lauren E., Bradley, Robert K., Fields, Paul A., Steinhauser, Matthew L., Ding, Huiming, Butty, Vincent L., Torrey, Lillian, Haas, Simon, Abo, Ryan, Tabebordbar, Mohammadsharif, Lee, Richard T., Burge, Christopher B., Boyer, Laurie A.

“…Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here,…”
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Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells by Kröger, Cornelia, Afeyan, Alexander, Mraz, Jasmin, Eaton, Elinor Ng, Reinhardt, Ferenc, Khodor, Yevgenia L., Thiru, Prathapan, Bierie, Brian, Ye, Xin, Burge, Christopher B., Weinberg, Robert A.

“…Carcinoma cells residing in an intermediate phenotypic state along the epithelial–mesenchymal (E–M) spectrum are associated with malignant phenotypes, such as…”
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Transcriptional Amplification in Tumor Cells with Elevated c-Myc by Lin, Charles Y., Lovén, Jakob, Rahl, Peter B., Paranal, Ronald M., Burge, Christopher B., Bradner, James E., Lee, Tong Ihn, Young, Richard A.

“…Elevated expression of the c-Myc transcription factor occurs frequently in human cancers and is associated with tumor aggression and poor clinical outcome. The…”
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Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins by Wang, Eric T., Cody, Neal A.L., Jog, Sonali, Biancolella, Michela, Wang, Thomas T., Treacy, Daniel J., Luo, Shujun, Schroth, Gary P., Housman, David E., Reddy, Sita, Lécuyer, Eric, Burge, Christopher B.

“…The muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in myotonic dystrophy (DM), in which…”
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Analysis and design of RNA sequencing experiments for identifying isoform regulation by Airoldi, Edoardo M, Burge, Christopher B, Katz, Yarden, Wang, Eric T

“…The mixture of isoforms model (MISO) assesses the confidence in estimates of the abundance of spliced exons or isoforms from paired-end RNA-seq data and…”
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Most mammalian mRNAs are conserved targets of microRNAs by Friedman, Robin C, Farh, Kyle Kai-How, Burge, Christopher B, Bartel, David P

“…MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed…”
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Promoter directionality is controlled by U1 snRNP and polyadenylation signals by Almada, Albert E., Wu, Xuebing, Kriz, Andrea J., Burge, Christopher B., Sharp, Phillip A.

“…Asymmetric sequence determinants flanking gene transcription start sites are shown to control directionality of transcription elongation in mammalian cells by…”
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Revisiting Global Gene Expression Analysis by Lovén, Jakob, Orlando, David A., Sigova, Alla A., Lin, Charles Y., Rahl, Peter B., Burge, Christopher B., Levens, David L., Lee, Tong Ihn, Young, Richard A.

“…Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states…”
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Distal Alternative Last Exons Localize mRNAs to Neural Projections by Taliaferro, J. Matthew, Vidaki, Marina, Oliveira, Ruan, Olson, Sara, Zhan, Lijun, Saxena, Tanvi, Wang, Eric T., Graveley, Brenton R., Gertler, Frank B., Swanson, Maurice S., Burge, Christopher B.

“…Spatial restriction of mRNA to distinct subcellular locations enables local regulation and synthesis of proteins. However, the organizing principles of mRNA…”
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Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock by Shalgi, Reut, Hurt, Jessica A., Lindquist, Susan, Burge, Christopher B.

“…During heat shock and other proteotoxic stresses, cells regulate multiple steps in gene expression in order to globally repress protein synthesis and…”
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Quantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins by Findlay, Scott D., Romo, Lindsay, Burge, Christopher B.

“…Many non-coding variants associated with phenotypes occur in 3ʹ untranslated regions (3ʹ UTRs), and may affect interactions with RNA-binding proteins (RBPs) to…”
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Widespread PERK-dependent repression of ER targets in response to ER stress by Gonen, Nir, Sabath, Niv, Burge, Christopher B., Shalgi, Reut

“…The UPR (Unfolded Protein Response) is a well-orchestrated response to ER protein folding and processing overload, integrating both transcriptional and…”
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Biased Chromatin Signatures around Polyadenylation Sites and Exons by Spies, Noah, Nielsen, Cydney B., Padgett, Richard A., Burge, Christopher B.

“…Core RNA-processing reactions in eukaryotic cells occur cotranscriptionally in a chromatin context, but the relationship between chromatin structure and…”
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Cotargeting among microRNAs in the brain by Cherone, Jennifer M, Jorgji, Vjola, Burge, Christopher B

“…MicroRNAs (miRNAs) play roles in diverse developmental and disease processes. Distinct miRNAs have hundreds to thousands of conserved mRNA binding sites but…”
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Quantitative visualization of alternative exon expression from RNA-seq data by Katz, Yarden, Wang, Eric T, Silterra, Jacob, Schwartz, Schraga, Wong, Bang, Thorvaldsdóttir, Helga, Robinson, James T, Mesirov, Jill P, Airoldi, Edoardo M, Burge, Christopher B

“…Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA…”
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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data by Ramsköld, Daniel, Wang, Eric T, Burge, Christopher B, Sandberg, Rickard

“…The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We characterized the features of…”
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