Fig. 6: NKAPL co-localizes with R-loops at GA-rich sites and promotes R-loop formation. | Nature Communications

Fig. 6: NKAPL co-localizes with R-loops at GA-rich sites and promotes R-loop formation.

From: NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit

Fig. 6

a Representative genomic regions showing ssDRIP-seq signals in P21 wild-type testes. b Distribution of ssDRIP-seq signals for biological duplicates in different genomic regions. promoter, ±2 kb of TSS; terminal regions, ±2 kb of TTS. Bounds of box represent the interquartile range (IQR) from the 25th to the 75th percentile with the median as the horizontal line, while whiskers extend to the most extreme data points (outliers excluded) within 1.5×IQR.***p < 0.001. c ssDRIP-seq signals within ±10 kb of TSS. Red: forward strand signal; Blue: reverse strand signal. d The top enriched motif identified by MEME from germline R-loops in mouse testis as well as recently published R-loops in human and mouse cells. e NKAPL eCLIP binding signals at targeted loci generally co-localized with corresponding R-loop signals. f R-loop signal profiles within −10 kb/ +10 kb of NKAPL eCLIP binding sites. g R-loop signals by ssDRIP-seq at NKAPL target genes versus those genes without NKAPL eCLIP peaks. h Relative R-loop signals at NKAPL eCLIP binding sites in wild-type and Nkapl KO testes at P21. i Comparison of R-loop signal occupancy in wild-type and Nkapl KO on genes across ±10 kb genomic region flanking TSS. j Model for NKAPL function in the release of paused Pol II and R-loop formation. Transcription initiation complex containing SOX30/HDAC3 assembles at promoters and recruits Pol II. NKAPL interacts with the SOX30/HDAC3 initiation complex dynamically and transiently, and occupies at promoter regions indirectly. Initiation occurs with the opening of double-stranded DNA, and a short nascent RNA is synthesized before the transcription machinery pauses promoter proximally. Promoter-proximal stalled Pol II produces more levels of short RNAs, which re-anneal with its template DNA strand to form three-stranded RNA/DNA hybrid structures (R-loops). NKAPL binds promoter-associated nascent RNAs, and co-localizes with R-loops at GA-rich loci, where it interacts with RNA-DNA hybrid structures to enable R-loop formation and efficient Pol II elongation. Nkapl knockout causes prolonged Pol II pause and a pronounced reduction of R-loops, resulting in a stalled initiation complex containing SOX30/HDAC3.

Back to article page