ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

Abstract

The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are recognized remains poorly understood. Here, we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1 and AtALBA2) functioning as the genic R-loop readers in Arabidopsis. While AtALBA1 binds to the DNA-RNA hybrid, AtALBA2 associates with single-stranded DNA in the R-loops in vitro. In vivo, these two proteins interact and colocalize in the nucleus, where they preferentially bind to genic regions with active epigenetic marks in an R-loop–dependent manner. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. The formation of DNA breaks in alba mutants originates from unprotected R-loops. Our results reveal that the AtALBA1 and AtALBA2 protein complex is the genic R-loop reader crucial for genome stability in Arabidopsis.

The ALBA RNA-binding proteins function redundantly to promote growth and flowering in Arabidopsis

“…In Arabidopsis, there are six ALBA genes (Figure 1). Two previous reports have given them different names (Honkanen et al, 2016; Yuan et al, 2019). Although Honkanen et al (2016) study was first, given the extensive analysis of Yuan et al (2019), we will follow their ALBA gene nomenclature.…”

“…Two previous reports have given them different names (Honkanen et al, 2016; Yuan et al, 2019). Although Honkanen et al (2016) study was first, given the extensive analysis of Yuan et al (2019), we will follow their ALBA gene nomenclature. There are three shorter-form ALBA genes, ALBA1 (AT1G29250), ALBA2 (AT2G34160) and ALBA3 (AT3G04620); and three longer-form ALBA genes being ALBA4 (AT1G76010), ALBA5 (AT1G20220) and ALBA6 (AT3G07030) (Figure 1).…”

“…Firstly, T-DNA insertional mutations in ALBA long-form genes of either Arabidopsis (At1g76010 and At1g20220) or the liverwort Marchantia polymorpha , inhibited root hair growth (Honkanen et al, 2016). In another study, the short-form ALBA proteins were found to bind DNA-RNA hybrids in vitro , that they localized to both the nucleus and cytoplasm, where they could form either homo- or heterodimers with one another (Yuan et al, 2019). In the nucleus, they were shown to be R-loop readers, binding throughout the genome at locations consistent with the presence of R-loops, where their function is to stabilize the genome (Yuan et al, 2019).…”

“…In another study, the short-form ALBA proteins were found to bind DNA-RNA hybrids in vitro , that they localized to both the nucleus and cytoplasm, where they could form either homo- or heterodimers with one another (Yuan et al, 2019). In the nucleus, they were shown to be R-loop readers, binding throughout the genome at locations consistent with the presence of R-loops, where their function is to stabilize the genome (Yuan et al, 2019). Therefore, the short-form ALBA proteins appear to have a clear role in the nucleus related to DNA-binding.…”

Comprehensive Classification of the RNase H-like domain-containing Proteins in Plants

“…In addition, there are three RNase H1 enzymes with different organelle localization and the chloroplast-localized RNase H1 is critical for maintaining chloroplast genome integrity in Arabidopsis [26]. Furthermore, R-loops can perform their function as chromatin features and read by proteins such as ALBA proteins in Arabidopsis and GADD45A (growth arrest and DNA damage inducible alpha) proteins in mammals [27,28]. Therefore, RNHLS proteins might regulate R-loops in development tissues and response to hormones in plants whose gene expression should be fine-tuned.…”