Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors

• Published in: eLife Vol. 13
• Main Authors: Corso Diaz, Ximena, Liang, Xulong, Preston, Kiam, Tegshee, Bilguun, English, Milton A, Nellissery, Jacob, Yadav, Sharda Prasad, Marchal, Claire, Swaroop, Anand
• Format: Journal Article
• Language: English
• Published: England eLife Science Publications, Ltd 06.03.2025; eLife Sciences Publications Ltd; eLife Sciences Publications, Ltd
• Subjects: Animals; Basic-Leucine Zipper Transcription Factors - genetics; Basic-Leucine Zipper Transcription Factors - metabolism; Cell cycle; Chromatin; DNA binding proteins; DNA helicase; Epigenetic inheritance; Epigenetics; Experiments; Eye Proteins - genetics; Eye Proteins - metabolism; Gene expression; Gene Expression Regulation; Genes; Genetics and Genomics; Humans; Leucine zipper proteins; Mass spectrometry; Mice; Mutation; Photoreceptors; Protein Binding; protein interaction; Proteins; R-loops; Retina; retinal development; Retinal Rod Photoreceptor Cells - metabolism; RNA; RNA helicase; RNA polymerase; RNA processing; RNA-binding protein; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Scientific imaging; Transcription factors; Yeast; United States; Massachusetts; California; mouse; RNA-binding protein; genetics; protein interaction; genomics; retinal development; gene expression
• DOI: 10.7554/eLife.103259
• ISSN: 2050-084X

RNA-binding proteins (RBPs) perform diverse functions including the regulation of chromatin dynamics and the coupling of transcription with RNA processing. However, our understanding of their actions in mammalian neurons remains limited. Using affinity purification, yeast-two-hybrid and proximity ligation assays, we identified interactions of multiple RBPs with neural retina leucine (NRL) zipper, a Maf-family transcription factor critical for retinal rod photoreceptor development and function. In addition to splicing, many NRL-interacting RBPs are associated with R-loops, which form during transcription and increase during photoreceptor maturation. Focusing on DHX9 RNA helicase, we demonstrate that its expression is modulated by NRL and that the NRL–DHX9 interaction is positively influenced by R-loops. ssDRIP-Seq analysis reveals both stranded and unstranded R-loops at distinct genomic elements, characterized by active and inactive epigenetic signatures and enriched at neuronal genes. NRL binds to both types of R-loops, suggesting an epigenetically independent function. Our findings suggest additional functions of NRL during transcription and highlight complex interactions among transcription factors, RBPs, and R-loops in regulating photoreceptor gene expression in the mammalian retina.