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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...localization, stability, and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESCs) and neural progenitor...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...versus predicted completeness using the GF and GG model established in C. elegans in four other model organisms.Further gene model refinement by applying proteotranscriptomicsTo provide experimental evidence for the predicted ORFs at the protein level, we measured the proteome of the same C. elegans...
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...from 7 to 12, polysomes. Proteins from each fraction were analyzed by WB with the indicated antibodies. (C) Subcellular fractionation of HeLa cells showing the presence of indicated proteins into cytosolic (cyto) and mitochondrial (mito) fractions. VCL and GAPDH have been used as markers of cytosol...
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Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
...and translated small ORFs (smORFs) with up to 100 amino acids (aa) (Ramamurthi and Storz 2014), as their protein-coding potential is difficult to assess bioinformatically (Ladoukakis et al. 2011). These small proteins localize to specific subcellular compartments and perform cellular functions as any other...
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Method: Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes
- Li Zhao,
- Yiyun Chen,
- Amol Onkar Bajaj,
- Aiden Eblimit,
- Mingchu Xu,
- Zachry T. Soens,
- Feng Wang,
- Zhongqi Ge,
- Sung Yun Jung,
- Feng He,
- Yumei Li,
- Theodore G. Wensel,
- Jun Qin,
- and Rui Chen
Genome Res. May 2016 26: 660-669; Published in Advance February 24, 2016, doi:10.1101/gr.198911.115
...fractions provides invaluable information regarding both protein abundance and subcellular localization. When integrated with other data sets, it can greatly enhance our ability to predict gene function genome-wide. In this study, we performed a comprehensive proteomic analysis on the light...
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Method: Proteome-wide discovery of mislocated proteins in cancer
- KiYoung Lee,
- Kyunghee Byun,
- Wonpyo Hong,
- Han-Yu Chuang,
- Chan-Gi Pack,
- Enkhjargal Bayarsaikhan,
- Sun Ha Paek,
- Hyosil Kim,
- Hye Young Shin,
- Trey Ideker,
- and Bonghee Lee
Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
...protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called...
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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
...-translational modifications, subcellular localization information, and identification of interaction partners of proteins. Due to enormous advances in mass spectrometry instrumentation, biochemical fractionation methods, and computational approaches, proteomics hasmatured into a statewhere the description of complete...
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Methods: Predicting Subcellular Localization via Protein Motif Co-Occurrence
- Michelle S. Scott,
- David Y. Thomas,
- and Michael T. Hallett
Genome Res. October 2004 14: 1957-1966; doi:10.1101/gr.2650004
...are organized into organelles and suborganelles that generate appropriate environments for their specialized functions. Thus, subcellular localization often offers important clues toward determining the function of an uncharacterized protein. The mechanisms of targeting of proteins to various subcellular...
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Methods: Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
- Nathalie Harder,
- Felipe Mora-Bermúdez,
- William J. Godinez,
- Annelie Wünsche,
- Roland Eils,
- Jan Ellenberg,
- and Karl Rohr
Genome Res. November 2009 19: 2113-2124; Published in Advance October 1, 2009, doi:10.1101/gr.092494.109
...migration dynamics (e.g., Chen et al. 2009). Automated classification methods have also been used on static images to distinguish different phenotype classes, providing information on the structure and location of subcellular phenotypes at a single cell level (e.g., Conrad et al. 2004; Huang and Murphy 2004...
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Research: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
- Milana Frenkel-Morgenstern,
- Vincent Lacroix,
- Iakes Ezkurdia,
- Yishai Levin,
- Alexandra Gabashvili,
- Jaime Prilusky,
- Angela del Pozo,
- Michael Tress,
- Rory Johnson,
- Roderic Guigo,
- and Alfonso Valencia
Genome Res. July 2012 22: 1231-1242; Published in Advance May 15, 2012, doi:10.1101/gr.130062.111
..., the expression and subcellular localization of the MATN–LAPTM chimera differ from those of the parental wild-type genes participating in the chimera (Maeda et al. 2005). Similarly, the TWE-PRIL chimeric protein that comprises two tumor necrosis factors,TWEAK andAPRIL, contains the TWEAK cytoplasmic and TM...
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