Widespread transcription at neuronal activity-regulated enhancers

Abstract

We used genome-wide sequencing methods to study stimulus-dependent enhancer function in neurons. We identified ∼12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. Remarkably, RNAPII at enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs) within enhancer domains defined by the presence of histone H3 that is mono-methylated at lysine 4 (H3K4me1). The level of eRNA expression at neuronal enhancers positively correlates with the level of mRNA synthesis at nearby genes, suggesting that eRNA synthesis occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis. These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis.

PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth

“…Mouse embryonic cortical neurons were prepared and seeded as in Kim et al (2010). For direct neuron transfection, MISSION shRNA lentivirus constructs for PQBP1 (Sigma) and a nontargeting shRNA vector (Addgene Plasmid 1864) were transfected into neurons on the day of seeding with Lipofectamine 2000 (Invitrogen).…”

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

“…For example, EP300, a histone acetyltransferase, activates transcription via acetylating the histones. Therefore, the binding sites of EP300 were often used to predict enhancers (Visel et al, 2009); (iii) It was reported that RNA polymerase II (RNAPII) binds to thousands of enhancers (Kim et al, 2010). Therefore, binding sites of POLR2A, the largest subunit of RNAPII, are considered to be the active regulatory regions; (iv) DNase I hypersensitivity sites (DHS) represent the open chromatin regions, many of which cover the enhancers (Thurman et al, 2012); (v) Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) coupled with sequencing is another method to identify large numbers of active regulatory elements including enhancers (Gaulton et al, 2010); (vi) Some histone modification patterns reflect different chromatin states.…”

LncRNAs: Bridging environmental sensing and gene expression

“…1 Over the past 50 years, many different classes of ncRNAs have been described, including microRNAs (miRNAs), 2,3 small nucleolar RNAs (snoRNAs), 4,5 small nuclear RNAs (snRNAs), 6 small Cajal body-specific RNAs (scaRNAs), 7 enhancer RNAs (eRNAs), 8 and long non-coding RNAs (lncRNAs). 9 LncRNAs are a diverse class of ncRNAs found in all eukaryotes from mammals 10 to unicellular organisms, such as Trichomonas vaginalis, 11 Plasmodium falciparum, 12 and the budding yeast Saccharomyces cerevisiae.…”