ArticleBMC genomics2014
Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- mComputational and structural biotechnology journal · 2022Article
- VECTOR: An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.Genes · 2021Article
- X-Chromosome Inactivation and Autosomal Random Monoallelic Expression as "Faux Amis".Frontiers in cell and developmental biology · 2021Review
- Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2020Article
- Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation.Cell death discovery · 2020Article
- Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- A microRNA cluster in the Fragile-X region expressed during spermatogenesis targets FMR1.EMBO reports · 2019Article
- Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs.Journal of molecular neuroscience : MN · 2019Article
- Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA.Biology methods & protocols · 2019Review
- Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941.Molecular biology and evolution · 2018Article
- Challenges of CRISPR/Cas9 applications for long non-coding RNA genes.Nucleic acids research · 2017Article
- Building an RNA Sequencing Transcriptome of the Central Nervous System.The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry · 2016Review
- Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells.Nucleic acids research · 2016Article
- Upstream binding of idling RNA polymerase modulates transcription initiation from a nearby promoter.The Journal of biological chemistry · 2015Article
- Probabilistic bidirectional promoter switches: noncoding RNA takes control.Molecular therapy. Nucleic acids · 2014Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundComprehensive annotation of transcripts expressed in a given tissue is a critical step towards the understanding of regulatory and functional pathways that shape the transcriptome.
resultsHere, we reconstructed a cumulative transcriptome of the human prefrontal cortex (PFC) based on approximately 300 million strand-specific RNA sequence (RNA-seq) reads collected at different stages of postnatal development. We find that more than 50% of reconstructed transcripts represent novel transcriptome elements, including 8,343 novel exons and exon extensions of annotated coding genes, 11,217 novel antisense transcripts and 29,541 novel intergenic transcripts or their fragments showing canonical features of long non-coding RNAs (lncRNAs). Our analysis further led to a surprising discovery of a novel class of bidirectional promoters (NBiPs) driving divergent transcription of mRNA and novel lncRNA pairs and displaying a distinct set of sequence and epigenetic features. In contrast to known bidirectional and unidirectional promoters, NBiPs are strongly associated with genes involved in neuronal functions and regulated by neuron-associated transcription factors.
conclusionsTaken together, our results demonstrate that large portions of the human transcriptome remain uncharacterized. The distinct sequence and epigenetic features of NBiPs, as well as their specific association with neuronal genes, further suggest existence of regulatory pathways specific to the human brain.
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