NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors

SummaryGene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. Given that the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone-like) mouse photoreceptors. We identified a large-scale, sharp transition in the transcriptome landscape between postnatal days 6 and 10 concordant with rod morphogenesis. Rod-specific temporal DNA methylation corroborated gene expression patterns. De novo assembly and alternative splicing analyses revealed previously unannotated rod-enriched transcripts and the role of NRL in transcript maturation. Furthermore, we defined the relationship of NRL with other transcriptional regulators and downstream cognate effectors. Our studies provide the framework for comprehensive system-level analysis of the GRN underlying the development of a single sensory neuron, the rod photoreceptor

Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL

PURPOSE. Transcriptome analysis by next generation sequencing allows qualitative and quantitative profiling of expression patterns associated with development and disease. However, most transcribed sequences do not encode proteins, and little is known about the functional relevance of noncoding (nc) transcriptome in neuronal subtypes. The goal of this study was to perform a comprehensive analysis of long noncoding (lncRNAs) and antisense (asRNAs) RNAs expressed in mouse retinal photoreceptors

Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL

PURPOSE. Transcriptome analysis by next generation sequencing allows qualitative and quantitative profiling of expression patterns associated with development and disease. However, most transcribed sequences do not encode proteins, and little is known about the functional relevance of noncoding (nc) transcriptome in neuronal subtypes. The goal of this study was to perform a comprehensive analysis of long noncoding (lncRNAs) and antisense (asRNAs) RNAs expressed in mouse retinal photoreceptors

TRPM1 Mutations are the Most Common Cause of Autosomal Recessive Congenital Stationary Night Blindness (CSNB) in the Palestinian and Israeli Populations

International audiencePrecise genetic and phenotypic characterization of congenital stationary night blindness (CSNB) patients is needed for future therapeutic interventions. The aim of this study was to estimate the prevalence of CSNB in our populations and to study clinical and genetic aspects of the autosomal recessive (AR) form of CSNB. This is a retrospective cohort study of Palestinian and Israeli CSNB patients harboring mutations in TRPM1 underwent comprehensive ocular examination. Genetic analysis was performed using homozygosity mapping and sequencing. 161 patients (from 76 families) were recruited for this study, leading to a prevalence of 1:6210 in the vicinity of Jerusalem, much higher than the worldwide prevalence. 61% of the families were consanguineous with AR inheritance pattern. Biallelic pathogenic TRPM1 mutations were identified in 36 families (72 patients). Two founder mutations explain the vast majority of cases: a nonsense mutation c.880A>T (p.Lys294*) identified in 22 Palestinian families and a large genomic deletion (36,445 bp) encompassing exons 2–7 of TRPM1 present in 13 Ashkenazi Jewish families. Most patients were myopic (with mean BCVA of 0.40 LogMAR) and all had absent rod responses in full field electroretinography. To the best of our knowledge, this is the largest report of a clinical and genetic analysis of patients affected with CSNB due to TRPM1 mutations

Exome Sequencing Identifies a Founder Frameshift Mutation in an Alternative Exon of <em>USH1C</em> as the Cause of Autosomal Recessive Retinitis Pigmentosa with Late-Onset Hearing Loss

<div><p>We used a combined approach of homozygosity mapping and whole exome sequencing (WES) to search for the genetic cause of autosomal recessive retinitis pigmentosa (arRP) in families of Yemenite Jewish origin. Homozygosity mapping of two arRP Yemenite Jewish families revealed a few homozygous regions. A subsequent WES analysis of the two index cases revealed a shared homozygous novel nucleotide deletion (c.1220delG) leading to a frameshift (p.Gly407Glufs*56) in an alternative exon (#15) of <em>USH1C</em>. Screening of additional Yemenite Jewish patients revealed a total of 16 homozygous RP patients (with a carrier frequency of 0.008 in controls). Funduscopic and electroretinography findings were within the spectrum of typical RP. While other <em>USH1C</em> mutations usually cause Usher type I (including RP, vestibular dysfunction and congenital deafness), audiometric screening of 10 patients who are homozygous for c.1220delG revealed that patients under 40 years of age had normal hearing while older patients showed mild to severe high tone sensorineural hearing loss. This is the first report of a mutation in a known USH1 gene that causes late onset rather than congenital sensorineural hearing loss. The c.1220delG mutation of <em>USH1C</em> accounts for 23% of RP among Yemenite Jewish patients in our cohort.</p> </div

Ocular Phenotype of patients who are homozygous for the <i>USH1C</i> c.1220delG mutation.

<p>(A, C, E) Color fundus photographs of three patients aged 13 (MOL0486 II:3), 33 (TB16-R12), and 72 (MOL1023-1) years old, respectively. Note the increasing severity of fundus changes with age, and the presence of dense bone spicule-like pigmentation. (B, D, F) Corresponding fundus autofluorescence imaging of the macular area in the three patients shown in A,C,E. Note hyeprfluorescent rings around the foveas in the younger patients, and hypofluorescent areas of atrophy that encroach upon the macula in the 33 year-old patient and invade the macula in the 72 year-old. (G, H, I) Horizontal optical coherence tomography (OCT) cross-sections through the fovea in the 13 yo (panel G), 33 yo (H) and 72 yo (I) <i>USH1C</i> patients showing progressive loss of retinal and particularly photoreceptor layer thickness with age. Intra-retinal cysts of fluid (cystoid macular edema) are evident in two of the cases (H, I).</p

Family trees and segregation analysis of the <i>USH1C</i> c.1220delG mutation.

<p>A. Structure of the two families that were selected for whole exome sequencing. The family number is indicated above the corresponding family tree. Filled symbols represent affected individuals, whereas clear symbols represent unaffected individuals. Generation numbers are depicted on the left and individual numbers below each symbol. The <i>USH1C</i> genotype is presented as: M/M, homozygous for the c.1220delG mutation; M/+, heterozygous; +/+, homozygous for the wildtype allele. Index cases are marked with an arrow. B. Sequence chromatograms of part of <i>USH1C</i> exon 15 of a control individual (top), a heterozygote (middle), and a patient who is homozygous for the mutation (bottom). The c.1220delG mutation (boxed) results in a frameshift (p.Gly407Glufs*56).</p

Audiometric results of patients who are homozygous for the <i>USH1C</i> c.1220delG mutation.

<p>A. Patient MOL0486 II:3 (13 yo) with normal hearing function. B. Patient MOL0887-3 (44 yo) with severe SNHL, particularly at higher frequencies (descending pattern). C,D. Hearing threshold versus age at a frequency of 4,000 Hz (C) and 8,000 Hz (D). At younger ages, normal hearing function is evident, but after the age of 40 years, sensitivity is markedly reduced. For each of the 10 patients, the data from both the right and left ears is presented, showing symmetry between both ears.</p

Data on sequence variants identified by the whole exome sequencing analysis.

*<p>- The two variants are: c.1220delG in <i>USH1C</i> and c.218_219insC in <i>VPS11</i>. The latter was found in about 73% of ethnicity-matched exomes and is therefore predicted to be a population-specific polymorphism.</p>**<p>- The two variants are: c.1220delG in <i>USH1C</i> and c.705_706delTT in <i>PKD1L2</i>. The latter was found in about 20% of ethnicity-matched exomes and is therefore predicted to be a population-specific polymorphism.</p