title: mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
abstract: The volume of RNA-Seq data sets in public repositories has been expanding exponentially, providing unprecedented opportunities to study gene expression regulation. Because degraded RNA samples, such as those collected from post-mortem tissues, can result in distinct expression profiles with potential biases, a particularly important step in mining these data is quality control. Here we develop a method named mRIN to directly assess mRNA integrity from RNA-Seq data at the sample and individual gene level. We systematically analyse large-scale RNA-Seq data sets of the human brain transcriptome generated by different consortia. Our analysis demonstrates that 3' bias resulting from partial RNA fragmentation in post-mortem tissues has a marked impact on global expression profiles, and that mRIN effectively identifies samples with different levels of mRNA degradation. Unexpectedly, this process has a reproducible and gene-specific component, and transcripts with different stabilities are associated with distinct functions and structural features reminiscent of mRNA decay in living cells.
authors.affiliation: MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.|Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, New York 10032, USA.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Feng
authors.affiliation: MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
authors.forename: Xuegong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, New York 10032, USA.
authors.forename: Chaolin
authors.identifier: http://orcid.org/0000-0002-8310-7537
authors.initials: C
authors.lastname: Zhang
mesh_terms: D001344:Autopsy; D001921:Brain / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D004586:Electrophoresis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D000069550:Machine Learning; D020871:RNA Stability; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D012333:RNA, Messenger