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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...) SCENIC results of the control and mTBI group. Major regulators were shown; their corresponding enriched DNA-binding motifs are shown in right column. (F) Ridge plot showing the expression of Tcf7l1. (G) Protein–protein interaction (PPI) networks of TFs and miRNAs in neuroblast (upper) and astrocyte, q...
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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
.... Here, to provide further evidence for this interaction, two additional approaches were used: (1) a PLA, showing that endogenous TRAP1 and TOMM40 produce an average of 13 spots/cell (Fig. 3A), and (2) coimmunoprecipitation experiments, showing binding between TRAP1 and TOMM40 when the TRAP1–GFP protein...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...(4×), FGFR2 (3×), ALK (2×), RET (2×), NTRK1 (1×), RASGRP1 (1×), and ROS1 (1×). Some of the affected proteins are direct interaction partners of KRAS (RASGRP1, BRAF, RAF1), suggesting that the corresponding fusion proteins might activate the same pathway as oncogenic KRAS. Indeed, a statistical...
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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
...of protein pairs sharing at least one location, calculated from different sets of proteins. ‘‘Random’’ was calculated as the average of 1000 randomly selected interaction sets with the same number of interactions as the original protein network. (B) Leave-two-out cross-validation with a DC-kNN classifier...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...such as immune cells and vasculature.LTR7-PLAAT4 emerged as a top TE-oncogene candidate in PAAD and other cancers. LTR7, regulated by HNF4A, may interact with m6A-modified HERV-H transcripts and TET1 to evade epigenetic silencing (Sun et al. 2023). Functionally, PLAAT4 participates in lipid metabolism, and our...
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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
...association of cytosolic proteins, thereby altering their molecular interactions and cellular functions. A chimeric protein has been identified that encompasses parts of the matrilin (MATN) and lysosomal-associated protein transmembrane (LAPTM) genes (Maeda et al. 2005). In accord with our hypothesis...
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Methods: High-Throughput Expression of C. elegans Proteins
- Chi-Hao Luan,
- Shihong Qiu,
- James B. Finley,
- Mike Carson,
- Rita J. Gray,
- Wenying Huang,
- David Johnson,
- Jun Tsao,
- Jérôme Reboul,
- Philippe Vaglio,
- David E. Hill,
- Marc Vidal,
- Lawrence J. DeLucas,
- and Ming Luo
Genome Res. October 15, 2004 14: 2102-2110; doi:10.1101/gr.2520504
...simple organism have yielded many insights about the biology of higher organisms, including humans. For example, programmed cell death (apoptosis) was discovered in C. elegans (see, e.g., Ellis and Horvitz 1986 ). Proteome scale studies of protein structure, function, and interactions have become a new...
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Methods: Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- Eivind Valen,
- Giovanni Pascarella,
- Alistair Chalk,
- Norihiro Maeda,
- Miki Kojima,
- Chika Kawazu,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Dejan Lazarevic,
- Dario Motti,
- Troels Torben Marstrand,
- Man-Hung Eric Tang,
- Xiaobei Zhao,
- Anders Krogh,
- Ole Winther,
- Takahiro Arakawa,
- Jun Kawai,
- Christine Wells,
- Carsten Daub,
- Matthias Harbers,
- Yoshihide Hayashizaki,
- Stefano Gustincich,
- Albin Sandelin,
- and Piero Carninci
Genome Res. February 2009 19: 255-265; Published in Advance December 11, 2008, doi:10.1101/gr.084541.108
...cerebellum PEP. ( B ) The Dlgap1 gene has four PEPs, one from each brain tissue. All of these are overlapping known 5′-ends inferred by cDNAs. There are five 14-amino-acid-long repeats in the N-terminal end of the corresponding protein that affects the ability to interact with other proteins. Repeats...
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Methods: Fluorescent Detection and Isolation of DNA Variants Using Stabilized RecA-Coated Oligonucleotides
- Michael C. Rice,
- Brandy M. Heckman,
- Yi Liu,
- and Eric B. Kmiec
Genome Res. January 2004 14: 116-125; Published in Advance December 12, 2003, doi:10.1101/gr.1386204
.... Information gained from sequencing initiatives has been organized into interactive databases, which can be used to profile individual DNA samples and detect variations within and among populations ( Smigielski et al. 2000 ; Daly et al. 2001 ; Gabriel et al. 2002 ). In their simplest form, gene variations...
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ARTICLE: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation
- Nicholas R. Thomson,
- Corin Yeats,
- Kenneth Bell,
- Matthew T.G. Holden,
- Stephen D. Bentley,
- Morag Livingstone,
- Ana M. Cerdeño-Tárraga,
- Barbara Harris,
- Jon Doggett,
- Doug Ormond,
- Karen Mungall,
- Kay Clarke,
- Theresa Feltwell,
- Zahra Hance,
- Mandy Sanders,
- Michael A. Quail,
- Claire Price,
- Bart G. Barrell,
- Julian Parkhill,
- and David Longbottom
Genome Res. May 2005 15: 629-640; Published in Advance April 18, 2005, doi:10.1101/gr.3684805
...with protein–protein interactions and are present as functional domains in a variety of proteins including the protective M proteins of Streptococci , hemagglutinins of H. influenzae and transcriptional regulators (for review, see Lupas 1996 ), and this is perhaps consistent with their proposed role...

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