The WD40-Repeat Proteins NFC101 and NFC102 Regulate Different Aspects of Maize Development through Chromatin Modification

Abstract

The maize (Zea mays) nucleosome remodeling factor complex component101 (nfc101) and nfc102 are putative paralogs encoding WD-repeat proteins with homology to plant and mammalian components of various chromatin modifying complexes. In this study, we generated transgenic lines with simultaneous nfc101 and nfc102 downregulation and analyzed phenotypic alterations, along with effects on RNA levels, the binding of NFC101/NFC102, and Rpd3-type histone deacetylases (HDACs), and histone modifications at selected targets. Direct NFC101/NFC102 binding and negative correlation with mRNA levels were observed for indeterminate1 (id1) and the florigen Zea mays CENTRORADIALIS8 (ZCN8), key activators of the floral transition. In addition, the abolition of NFC101/NFC102 association with repetitive sequences of different transposable elements (TEs) resulted in tissue-specific upregulation of nonpolyadenylated RNAs produced by these regions. All direct nfc101/nfc102 targets showed histone modification patterns linked to active chromatin in nfc101/nfc102 downregulation lines. However, different mechanisms may be involved because NFC101/NFC102 proteins mediate HDAC recruitment at id1 and TE repeats but not at ZCN8. These results, along with the pleiotropic effects observed in nfc101/nfc102 downregulation lines, suggest that NFC101 and NFC102 are components of distinct chromatin modifying complexes, which operate in different pathways and influence diverse aspects of maize development.

Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

“…We cloned and sequenced cDNAs derived from the ZCN7 and ZCN8 antisense RNAs of B73 and teosinte plants and found that they encode very short putative open reading frames with no homology to known proteins (Supplemental Fig. S4; Mascheretti et al, 2013). Therefore, these antisense transcripts may represent long noncoding RNAs (lncRNAs).…”

“…A recent report used a combination of RNA blotting with strand-specific probes and RT-PCR with locusand strand-specific primers to show that ZCN8 produces three transcript isoforms (Mascheretti et al, 2013). These isoforms correspond to (1) the processed sense mRNA, which accumulates only in mature leaf; (2) a very low amount of unspliced sense-strand premRNA present both in meristematic enriched regions and in mature leaf; and (3) an unspliced antisense RNA strand, which represents the prevalent form of unspliced transcript and is produced not only in leaves but also in various other tissues (Fig.…”

“…ChIP assays of id1 mutant immature leaves indicate that the majority of histone marks analyzed are not related to id1 function, suggesting that additional factors must be involved. For example, some of these factors could be chromatin-remodeling complexes containing the WD-repeat proteins NFC101/ NFC102, which directly bind ZCN8 to negatively regulate its expression and H3K4me2 levels in meristem-enriched tissues (Mascheretti et al, 2013).…”

“…S6). We selected histone marks that are usually located within genes and that were previously analyzed for florigen genes of other plant species (Jiang et al, 2008;Adrian et al, 2010;He, 2012;Sun et al, 2012;Gu et al, 2013;Mascheretti et al, 2013;López-González et al, 2014). Four histone marks usually associated with active transcription were selected for chromatin analysis.…”

“…One possibility is that ID1 protein operates by means of epigenetic mechanisms to promote the formation of a transcriptionally competent ZCN8 chromatin in immature leaf, which is maintained throughout leaf development to enable the production of florigenic signals in the mature leaf. The relevance of epigenetic mechanisms in maize flowering was demonstrated recently with the finding that the nucleosome remodeling factor complex component101 (nfc101) and nfc102 genes encode WD-repeat proteins that bind both id1 and ZCN8 sequences, thus regulating their expression and chromatin modifications (Mascheretti et al, 2013).…”