A plant‐specific SWR1 chromatin‐remodeling complex couples histone H2A.Z deposition with nucleosome sliding

Abstract

Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin‐remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant‐specific SWR1 components: MBD9, a methyl‐CpG‐binding domain‐containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co‐regulating gene expression, development, and flowering time.

FHA2 is a plant‐specific ISWI subunit responsible for stamen development and plant fertility

“…We predict that the H2A.Z preference of FHA2 may enhance the association of the ISWI complex with H2A.Z-enriched chromatin loci and subsequently facilitate the coupling of nucleosome spacing and H2A.Z deposition. A recent study reported that the ISWI chromatin remodelers CHR11 and CHR17 can function as subunits of the H2A.Z deposition complex (Luo et al 2020), suggesting that nucleosome spacing is coupled with H2A.Z deposition. The interaction of FHA2 with H2A.Z documented in the current study reveals another mode of coupling between nucleosome spacing and H2A.Z deposition.…”

“…Histone octamer assembly and histone pull-down assay The histone octamer/dimer was assembled as previously described (Luo et al 2020). In brief, Arabidopsis histone H2A (HTA10, AT1G51060), H2A.Z (HTA9, AT1G52740), H2B (HTB1, AT1G07790), H3 (AT1G09200), and H4 (AT2G28740) were cloned into the pET28a vector without tags and were purified from E. coli strain BL21 (DE3) as the inclusion body.…”

Gene co‐expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress

“…Interestingly, our data indicate that transposable elements (TE) contribute significantly to the transcriptome divergence between the wild and cultivated chickpea species, with higher expression levels in both cultivars compared with wild relatives. Differences in transposase expression, enrichment of the endonuclease activity GO term ( Figure S6) and the species resolved expression of SWR1 complex subunit 6 (Data S3) could reflect differences in chromatin context and regulation between domesticated and wild species, and/or domestication-related differences in transposase distributions or frequencies (Berriri et al, 2016;He et al, 2019;Luo et al, 2020). Distinct TE distributions in wild and cultivated rice accessions (Li et al, 2017), and in pea (Kreplak et al, 2019), have been described.…”

A role for prefoldins in H2A.Z deposition inArabidopsis

“…Interestingly, affinity purification followed by mass spectrometry has also identified PFDs as ARP6-and SWC4-interacting proteins (Gomez-Zambrano et al, 2018;Luo et al, 2021;Potok et al, 2019;Sijacic et al, 2019). To obtain additional proof for the in vivo interaction between PFD and SWR1 subunits, we performed a co-immunoprecipitation assay between cMyc-ARP6 and YFP-PFD6 expressed in Nicotiana benthamiana leaves ( Figure 2B).…”