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Mol Neurobiol. 2019 Aug;56(8):5392-5415. doi: 10.1007/s12035-018-1465-2. Epub 2019 Jan 4.

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases.

Author information

1
Area of Neuroscience, SISSA, Trieste, Italy.
2
Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy.
3
Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
4
Department of Medical, Surgical and Health Sciences, Clinical Neurology Unit, Cattinara University Hospital, Trieste, Italy.
5
Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
6
Genome Biology of Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany.
7
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
8
RIKEN Omics Science Center, Yokohama, Japan.
9
Applied Genomics for Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany.
10
RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan.
11
Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
12
Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, WA, 6008, Australia.
13
Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
14
Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
15
Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
16
Area of Neuroscience, SISSA, Trieste, Italy. stefano.gustincich@iit.it.
17
Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy. stefano.gustincich@iit.it.

Abstract

Natural antisense transcripts are common features of mammalian genes providing additional regulatory layers of gene expression. A comprehensive description of antisense transcription in loci associated to familial neurodegenerative diseases may identify key players in gene regulation and provide tools for manipulating gene expression. We take advantage of the FANTOM5 sequencing datasets that represent the largest collection to date of genome-wide promoter usage in almost 2000 human samples. Transcription start sites (TSSs) are mapped at high resolution by the use of a modified protocol of cap analysis of gene expression (CAGE) for high-throughput single molecule next-generation sequencing with Helicos (hCAGE). Here we present the analysis of antisense transcription at 17 loci associated to hereditary Alzheimer's disease, Frontotemporal Dementia, Parkinson's disease, Amyotrophic Lateral Sclerosis, and Huntington's disease. We focused our analysis on libraries derived from brain tissues and primary cells. We also screened libraries from total blood and blood cell populations in the quest for peripheral biomarkers of neurodegenerative diseases. We identified 63 robust promoters in antisense orientation to genes associated to familial neurodegeneration. When applying a less stringent cutoff, this number increases to over 400. A subset of these promoters represents alternative TSSs for 24 FANTOM5 annotated long noncoding RNA (lncRNA) genes, in antisense orientation to 13 of the loci analyzed here, while the remaining contribute to the expression of additional transcript variants. Intersection with GWAS studies, sample ontology, and dynamic expression reveals association to specific genetic traits as well as cell and tissue types, not limited to neurodegenerative diseases. Antisense transcription was validated for a subset of genes, including those encoding for Microtubule-Associated Protein Tau, α-synuclein, Parkinsonism-associated deglycase DJ-1, and Leucin-Rich Repeat Kinase 2. This work provides evidence for the existence of additional regulatory mechanisms of the expression of neurodegenerative disease-causing genes by previously not-annotated and/or not-validated antisense long noncoding RNAs.

KEYWORDS:

Antisense transcription; Long noncoding RNA; Neurodegenerative diseases

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