Rbfox1 Is Expressed in the Mouse Brain in the Form of Multiple Transcript Variants and Contains Functional E Boxes in Its Alternative Promoters

Abstract

The RNA-binding protein RBFOX1 is an important regulator of neuron development and neuronal excitability. Rbfox1 is a dosage-sensitive gene and in both mice and humans, decreased expression of Rbfox1 has been linked to neurodevelopmental disorders. Alternative promoters drive expression of Rbfox1 transcript isoforms that encode an identical protein. The tissue-and developmental stage-specific expression of these isoforms, as well as the underlying regulatory mechanisms, are, however, unclear. Here, we set out to capture all of the Rbfox1 transcript isoforms and identify transcriptional mechanisms that regulate brain-specific Rbfox1 expression. Isoform sequencing identified multiple alternative Rbfox1 transcript variants in the mouse cerebral cortex, including transcripts with novel first exons, alternatively spliced exons and 3-truncations. Quantitative RT-PCR determined the expression of the alternative first exons in the developing cerebral cortex and different subregions of the juvenile brain. Alternative first exons were found to be highly stage-and subregion specific in their expression patterns suggesting that they fulfill specific functions during cortex development and in different brain regions. Using reporter assays we found that the promoter regions of the two first exons E1B and E1C/E1C.1 contain several functional E-boxes. Together, we provide an extensive picture of Rbfox1 isoform expression. We further identified important regulatory mechanisms that drive neuron-specific Rbfox1 expression. Thus, our study forms the basis for further research into the mechanisms that ensure physiological Rbfox1 expression in the brain. It also helps to understand why, in patients with neurodevelopmental disorders deletion of individual RBFOX1 transcript isoforms could affect brain function.

Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in theRBFOX1locus

“…5A ). We hypothesized that, since we are quantifying Rbfox1 expression by RT-qPCR using primers in one exon that is common to all the different Rbfox1 isoforms ( 42 ), we were probably obtaining an average expression, but it is possible that the 2xHAR.505 element is controlling some but not all the isoforms. Thus, to gain more insight into the activity of this regulatory element, we performed RT-qPCRs to quantify the expression of each one of the different Rbfox1 isoforms at P8 in the cortex using specific primers for each Rbfox1 isoform.…”

Identifying Aging and Alzheimer Disease–Associated Somatic Variations in Excitatory Neurons From the Human Frontal Cortex

“… 35 RBFOX1 is a neuron-specific splicing factor predicted to regulate neuronal splicing networks clinically implicated in neurodevelopmental disorders. 36 , 37 The increased somatic mutations in RBFOX1 with age indicates neurodevelopmental disorders may also associate with human brain aging.…”

The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data

“…The other alteration observed concerns the RBFOX1 gene, which is located on chromosome 16, cytoband p13.3 (5,239,738-7,713,340 (GRCh38/hg38), and includes 25 exons for a total length of about 2,473,603 bases, with 40 transcripts and 178 orthologues. RBFOX1 is a dose-sensitive gene that encodes splicing factors specifically expressed in neurons and muscles and is an important regulator of development and neuronal excitability [ 29 , 30 , 31 ]. Reduced RBFOX1 expression has been associated with neurodevelopmental disorders; indeed, CNVs comprising RBFOX1 are implicated in mental retardation, epilepsy, schizoaffective disorder (SCZ) [ 29 , 32 ], bipolar disorder (BD), attention deficit hyperactivity disorder (ADHD), ID [ 33 ] and ASD [ 34 ].…”