Searching journal content for articles similar to Sterne-Weiler et al. 23 (10): 1615.

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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: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...the limitations of the methods above. Transcript isoforms in polysome sequencing (TrIP-seq) (Floor and Doudna 2016) and fractionation and high-throughput RNA sequencing (Frac-seq) (Sterne-Weiler et al. 2013) have been used to quantify isoform-level translation by coupling polysome association with short...
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Research: Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
- Alina Chakraborty,
- Mandy Cadix,
- Sébastien Relier,
- Nicolò Taricco,
- Tina Alaeitabar,
- Alexandre Devaux,
- Céline M. Labbé,
- Sylvain Martineau,
- Amélie Heneman-Masurel,
- Pierre Gestraud,
- Alberto Inga,
- Nicolas Servant,
- Stéphan Vagner,
- and Martin Dutertre
Genome Res. July 2022 32: 1271-1284; Published in Advance July 20, 2022, doi:10.1101/gr.276192.121
...that may have a function in cell response to Doxo, we designed isoform-specific siRNAs targeting nine IPA isoforms (within their last exon, which is absent in the corresponding LE isoform) that are up-regulated by Doxo in the cytosol and that are up-regulated and/or abundant in polysomes. For eight IPA...
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Research: Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency
- Yonggui Fu,
- Liutao Chen,
- Chengyong Chen,
- Yutong Ge,
- Mingjing Kang,
- Zili Song,
- Jingwen Li,
- Yuchao Feng,
- Zhanfeng Huo,
- Guopei He,
- Mengmeng Hou,
- Shangwu Chen,
- and Anlong Xu
Genome Res. November 2018 28: 1656-1663; Published in Advance September 18, 2018, doi:10.1101/gr.231506.117
...reveals isoform-specific recruitment to polyribosomes. Genome Res 23: 1615–1623. ↵Truesdell SS, Mortensen RD, Seo M, Schroeder JC, Lee JH, LeTonqueze O, Vasudevan S. 2012. MicroRNA-mediated mRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear microRNP. Sci Rep 2...
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Method: Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing
- Laura M. Agosto,
- Matthew R. Gazzara,
- Caleb M. Radens,
- Simone Sidoli,
- Josue Baeza,
- Benjamin A. Garcia,
- and Kristen W. Lynch
Genome Res. December 2019 29: 2046-2055; Published in Advance November 14, 2019, doi:10.1101/gr.248435.119
...sequences (Wang et al. 2008). Of note, analysis of all junctions (including those in >80% or <20% of transcripts) reveals that 91% fall in the CDS, suggesting that AJs may be somewhat selected against within the CDS. In sum, this analysis identified 3929 genes that express at least two readily detectable m...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...FU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel...
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