title: The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury.
abstract: Spinal cord injury (SCI) remains one of the most debilitating neurological disorders and the majority of SCI patients are in the chronic phase. Previous studies of SCI have usually focused on few genes and pathways at a time. In particular, the biological roles of long non-coding RNAs (lncRNAs) have never been characterized in SCI. Our study is the first to comprehensively investigate alterations in the expression of both coding and long non-coding genes in the sub-chronic and chronic stages of SCI using RNA-Sequencing. Through pathway analysis and network construction, the functions of differentially expressed genes were analyzed systematically. Furthermore, we predicted the potential regulatory function of non-coding transcripts, revealed enriched motifs of transcription factors in the upstream regulatory regions of differentially expressed lncRNAs, and identified differentially expressed lncRNAs homologous to human genomic regions which contain single-nucleotide polymorphisms associated with diseases. Overall, these results revealed critical pathways and networks that exhibit sustained alterations at the sub-chronic and chronic stages of SCI, highlighting the temporal regulation of pathological processes including astrogliosis. This study also provided an unprecedented resource and a new catalogue of lncRNAs potentially involved in the regulation and progression of SCI.
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.|Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA.
authors.forename: Raquel Cuevas-Diaz
authors.initials: RC
authors.lastname: Duran
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.|Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Yan
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.|Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA.
authors.forename: Yiyan
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Department of Bioengineering, Rice University, Houston, TX 77005, USA.
authors.forename: Xingfan
authors.initials: X
authors.lastname: Huang
authors.affiliation: Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Raymond
authors.initials: R
authors.lastname: Grill
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Dong H
authors.initials: DH
authors.lastname: Kim
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.|Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA.
authors.forename: Qilin
authors.initials: Q
authors.lastname: Cao
authors.affiliation: The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.|Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA.
authors.forename: Jia Qian
authors.initials: JQ
authors.lastname: Wu
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D062085:RNA, Long Noncoding / Q000032:analysis*; D012333:RNA, Messenger / Q000032:analysis*; D017207:Rats, Sprague-Dawley; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013119:Spinal Cord Injuries / Q000473:pathology*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger