title: Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.
abstract: Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
authors: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China.
authors: Jie
authors: J
authors: Lv
authors: Wei
authors: W
authors: Cui
authors: Hongbo
authors: H
authors: Liu
authors: Hongjuan
authors: H
authors: He
authors: Youcheng
authors: Y
authors: Xiu
authors: Jing
authors: J
authors: Guo
authors: Hui
authors: H
authors: Liu
authors: Qi
authors: Q
authors: Liu
authors: Tiebo
authors: T
authors: Zeng
authors: Yan
authors: Y
authors: Chen
authors: Yan
authors: Y
authors: Zhang
authors: Qiong
authors: Q
authors: Wu
mesh_terms: D000818:Animals; D001921:Brain / Q000196:embryology* / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics*; D057890:Epigenomics; D020869:Gene Expression Profiling; D051379:Mice; D034622:RNA Interference; D062085:RNA, Long Noncoding / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding; D038621:Regulatory Sequences, Ribonucleic Acid
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