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# **Full-length mRNA Sequencing Uncovers a Widespread Coupling between Transcription and mRNA Processing**
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By: Yahya Anvar, PhD [✍](mailto:s.y.anvar@lumc.nl) <br>
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Department of Human Genetics <br>
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Leiden University Medical Center <br>
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1. [Materials and Preprocessing]()
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1. [Data Characteristics]()
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1. [Prerequisites]()
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1. [Defining Unique Features]()
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1. [Statistical Analysis]()
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1. [Pathway Analysis]()
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1. [Annotation of Alternative Exons]()
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1. [Polyadenylation Sites Sequence Motif Analysis]()
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1. [Tandem 3' UTR Analysis]()
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1. [Sequence Motif Analysis Relative to Acceptor and Donor Sites]()
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1. [RNA Binding Motif Analysis]()
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1. [Scripts]()
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1. [Reported Bugs and Fixes]()
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1. [Citation]()
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1. [Authors Affiliation]()
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### **Summary** <br>
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The multilayered control of gene expression requires tight coordination of regulatory mechanisms at the transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells and three human tissues, we found an unforeseen number of genes that demonstrate mutually inclusive or exclusive alternative transcription and mRNA processing events, which can span the entire length of mRNA molecules. Furthermore, alternative poly(A) sites that are coupled with alternative splicing events are depleted for known poly(A) signals and enriched for MBNL binding motifs, supporting a dual role of MBNL proteins in regulating splicing and polyadenylation. We predict thousands of open-reading frames from the sequence of full-length mRNAs, allowing for a more sensitive proteogenomics analysis of MCF-7 mass-spectrometry data. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a framework to reveal largely unresolved mechanisms that coordinate transcription and mRNA processing.<br>
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