RNA polymerase II-independent recruitment of SPT6L at transcription start sites in Arabidopsis

Abstract

SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.

Genome‐wide occupancy of Arabidopsis SWI/SNF chromatin remodeler SPLAYED provides insights into its interplay with its close homolog BRAHMA and Polycomb proteins

“…ChIP‐seq data were analyzed as previously described (Chen et al ., 2019; Shu et al ., 2019). Briefly, the sequenced reads were aligned to the Arabidopsis genome (TAIR10) by Bowtie mapper with default settings (Langmead et al ., 2009; Lamesch et al ., 2012).…”

Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity Mapping

“…We collected published chromatin accessibility data and ChIP-seq data in which experimental materials and developmental stages are similar to the A. thaliana material used for STARR-seq and iSTARR-seq in this study. These raw data were downloaded from published study in GEO database, including DNase-seq 48 , ATAC-seq 44 , H3K4me1 46 , H3K27ac 46 , H3K9ac 44 , H3K36ac 45 , H3K56ac 41 , H3K36me3 43 , H3K4me3 40 , H3K27me3 46 , H3K9me2 39 , H2A 47 , H2A.Z 47 , RNAPII 42 . We performed trimming, mapping and filtering to these epigenetic data for subsequent analysis.…”

“…Enhancers identified by iSTARR-seq may carry different epigenetic marks at their endogenous genomic loci. To characterize the epigenetic states of enhancers, we collected datasets of chromatin accessibility, RNAPII binding, DNA methylation and histone modifications in the leaf cells of A. thaliana [39][40][41][42][43][44][45][46][47][48] (Supplementary list 4). Enhancers are ranked by the overall signal intensity of multiple epigenetic features ( Fig.…”

“…thaliana material used for STARR-seq and iSTARR-seq in this study. These raw data were downloaded from published study in GEO database, including DNase-seq 48 , ATAC-seq 44 42 . We performed trimming, mapping and filtering to these epigenetic data for subsequent analysis.…”

Creativity comes from interactions: modules of protein interactions in plants

“…Arabidopsis contains two SPT6 paralogs, known as SPT6 and SPT6-LIKE (SPT6L). SPT6L regulates apical-basal polarity during embryonic development; SPT6L knockouts display embryo or seedling lethality due to severe developmental defects [10,11]. The SH2 domain is necessary for full SPT6L function; however, SPT6L∆SH2 partially rescues embryonic development, suggesting that the SPT6L SH2 domain is likely the predominant feature mediating RNAPII association and that additional features may also allow lower-affinity RNAPII binding [11].…”