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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...(Lewis et al. 2003) but can also result in a variety of genetic diseases (Scotti and Swanson 2016; Zhang et al. 2022; Kurolap et al. 2023). In other cases, the resulting changes in sequence lead to protein products with distinct functions. For example, in human embryonic stem cells, an AS event...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...RNA expression profiling in postmortem brains from individuals with ASD and controls and identified 60 circRNAs and three coregulated modules that were perturbed in ASD. By integrating circRNA, microRNA, and mRNA dysregulation data derived from the same cortex samples, we identified 8170 ASD-associated circRNA-microRNA...
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Method: Next-generation sequencing identifies the natural killer cell microRNA transcriptome
- Todd A. Fehniger,
- Todd Wylie,
- Elizabeth Germino,
- Jeffrey W. Leong,
- Vincent J. Magrini,
- Sunita Koul,
- Catherine R. Keppel,
- Stephanie E. Schneider,
- Daniel C. Koboldt,
- Ryan P. Sullivan,
- Michael E. Heinz,
- Seth D. Crosby,
- Rakesh Nagarajan,
- Giridharan Ramsingh,
- Daniel C. Link,
- Timothy J. Ley,
- and Elaine R. Mardis
Genome Res. November 2010 20: 1590-1604; Published in Advance October 8, 2010, doi:10.1101/gr.107995.110
...Next-generation sequencing identifies the natural killer cell microRNA transcriptome Todd A. Fehniger 1 , 4 , Todd Wylie 2 , 4 , Elizabeth Germino 1 , Jeffrey W. Leong 1 , Vincent J. Magrini 2 , Sunita Koul 3 , Catherine R...
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Research: Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing
- Florian Caiment,
- Carole Charlier,
- Tracy Hadfield,
- Noelle Cockett,
- Michel Georges,
- and Denis Baurain
Genome Res. December 2010 20: 1651-1662; Published in Advance October 13, 2010, doi:10.1101/gr.108787.110
...Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing Florian Caiment 1 , Carole Charlier 1 , Tracy Hadfield 2 , Noelle Cockett 2 , Michel Georges 1 , 3 and Denis...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...in evolutionary biology. In addition to protein sequence changes, gene expression alterations due to regulatory mutations are thought to underlie many or even most phenotypic innovations (King and Wilson 1975). MicroRNAs (miRNAs) are short (approximately 22 nucleotides) noncoding RNA molecules that bind...
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Methods: Next-generation tag sequencing for cancer gene expression profiling
- A. Sorana Morrissy,
- Ryan D. Morin,
- Allen Delaney,
- Thomas Zeng,
- Helen McDonald,
- Steven Jones,
- Yongjun Zhao,
- Martin Hirst,
- and Marco A. Marra
Genome Res. October 2009 19: 1825-1835; Published in Advance June 18, 2009, doi:10.1101/gr.094482.109
...analysis for a greater range of transcripts. Tag-seq libraries provide an excellent resource for the discovery of known and novel transcripts with expression changes relevant to disease processes, and highlight the applicability of next-generation tag sequencing to gene expression profiling. Methods Tag...
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RESOURCE: A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
- Evgeny A. Glazov,
- Pauline A. Cottee,
- Wesley C. Barris,
- Robert J. Moore,
- Brian P. Dalrymple,
- and Mark L. Tizard
Genome Res. June 2008 18: 957-964; Published in Advance May 9, 2008, doi:10.1101/gr.074740.107
.... , McDonald, H. , Zeng, T. , Hirst, M. , et al. ( 2008 ) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells . Genome Res. 18 : 610 – 621 . ↵ Okamura, K. , Hagen, J.W. , Duan, H. , Tyler, D.M. , Lai, E.C. ( 2007 ) The mirtron pathway generates...
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Method: P-value-based regulatory motif discovery using positional weight matrices
- Holger Hartmann,
- Eckhart W. Guthöhrlein,
- Matthias Siebert,
- Sebastian Luehr,
- and Johannes Söding
Genome Res. January 2013 23: 181-194; Published in Advance September 18, 2012, doi:10.1101/gr.139881.112
...that are coregulated under microRNA (miRNA) knock-downs. The 8-mer miRNA seeds were imported from miRBase 16.0 (Griffiths-Jones et al. 2006). While Linhart et al. (2008) used experimentally validated transcription factor PWMs from release 8.0 of the TRANSFAC database (Wingender et al. 1996), we could only access...
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Method: Observation of dually decoded regions of the human genome using ribosome profiling data
- Audrey M. Michel,
- Kingshuk Roy Choudhury,
- Andrew E. Firth,
- Nicholas T. Ingolia,
- John F. Atkins,
- and Pavel V. Baranov
Genome Res. November 2012 22: 2219-2229; Published in Advance May 16, 2012, doi:10.1101/gr.133249.111
.... 2010). Ribosome profiling is based on the isolation of mRNA fragments protected by ribosomes followed by massively parallel sequencing of cDNA libraries derived from the ribosome protected fragments (RPFs). The technique allows mapping the locations of translating ribosomes on the entire set of m...
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LETTER: In-depth characterization of the microRNA transcriptome in a leukemia progression model
- Florian Kuchenbauer,
- Ryan D. Morin,
- Bob Argiropoulos,
- Oleh I. Petriv,
- Malachi Griffith,
- Michael Heuser,
- Eric Yung,
- Jessica Piper,
- Allen Delaney,
- Anna-Liisa Prabhu,
- Yongjun Zhao,
- Helen McDonald,
- Thomas Zeng,
- Martin Hirst,
- Carl L. Hansen,
- Marco A. Marra,
- and R. Keith Humphries
Genome Res. November 2008 18: 1787-1797; Published in Advance October 10, 2008, doi:10.1101/gr.077578.108
....48 Dynamic Array System (Fluidigm Corporation) and TaqMan MicroRNA Assays (Applied Biosystems) according to the manufacturer’s instructions. The reverse transcriptase reaction using TaqMan stem-loop primers was performed according to the protocol of Tang et al. (2006) . Cooperative miRNA target prediction...

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