Identification of Novel PHD-Finger Genes in Pepper by Genomic Re-Annotation and Comparative Analyses

BackgroundThe plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays important roles in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.ResultsWe performed genome-wide re-annotation in Arabidopsis, rice, pepper, potato, and tomato to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper.ConclusionsOur data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.

Chromatin Enrichment for Proteomics in Plants (ChEP-P) Implicates the Histone Reader ALFIN-LIKE 6 in Jasmonate Signalling

BackgroundCovalent modifications of core histonesgoverndownstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. ResultsHere, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsivegenes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach,that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. ConclusionsAltered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli. Our study shows that ChEP-P is well suited to gain holistic insights into chromatin-related processes in plants. Data are available via ProteomeXchange with identifier PXD026541.

A Novel Splice Variant of the Inhibitor of Growth 3 Lacks the Plant Homeodomain and Regulates Epithelial–Mesenchymal Transition in Prostate Cancer Cells

Inhibitor of growth 3 (ING3) is one of five members of the ING tumour suppressor family, characterized by a highly conserved plant homeodomain (PHD) as a reader of the histone mark H3K4me3. ING3 was reported to act as a tumour suppressor in many different cancer types to regulate apoptosis. On the other hand, ING3 levels positively correlate with poor survival prognosis of prostate cancer (PCa) patients. In PCa cells, ING3 acts rather as an androgen receptor (AR) co-activator and harbours oncogenic properties in PCa. Here, we show the identification of a novel ING3 splice variant in both the human PCa cell line LNCaP and in human PCa patient specimen. The novel ING3 splice variant lacks exon 11, ING3∆ex11, which results in deletion of the PHD, providing a unique opportunity to analyse functionally the PHD of ING3 by a natural splice variant. Functionally, overexpression of ING3Δex11 induced morphological changes of LNCaP-derived 3D spheroids with generation of lumen and pore-like structures within spheroids. Since these structures are an indicator of epithelial–mesenchymal transition (EMT), key regulatory factors and markers for EMT were analysed. The data suggest that in contrast to ING3, ING3Δex11 specifically modulates the expression of key EMT-regulating upstream transcription factors and induces the expression of EMT markers, indicating that the PHD of ING3 inhibits EMT. In line with this, ING3 knockdown also induced the expression of EMT markers, confirming the impact of ING3 on EMT regulation. Further, ING3 knockdown induced cellular senescence via a pathway leading to cell cycle arrest, indicating an oncogenic role for ING3 in PCa. Thus, the data suggest that the ING3Δex11 splice variant lacking functional PHD exhibits oncogenic characteristics through triggering EMT in PCa cells.

ING Proteins: Tumour Suppressors or Oncoproteins

The INhibitor of Growth family was defined in the mid-1990s by the identification of a tumour suppressor, ING1, and subsequent expansion of the family based essentially on sequence similarities. However, later work and more recent investigations demonstrate that at least a few ING proteins are actually required for normal proliferation of eukaryotic cells, from yeast to human. ING proteins are also part of a larger family of chromatin-associated factors marked by a plant homeodomain (PHD), which mediates interactions with methylated lysine residues. Herein, we discuss the role of ING proteins and their various roles in chromatin signalling in the context of cancer development and progression.

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

Background The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. Results In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. Conclusion This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

Background: The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.Results: In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.Conclusion: This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

NuA3 HAT antagonizes the Rpd3S and Rpd3L HDACs to optimize mRNA and lncRNA expression dynamics

In yeast, NuA3 histone acetyltransferase (NuA3 HAT) promotes acetylation of histone H3 lysine 14 (H3K14) and transcription of a subset of genes through interaction between the Yng1 plant homeodomain (PHD) finger and H3K4me3. Although NuA3 HAT has multiple chromatin binding modules with distinct specificities, their interdependence and combinatorial actions in chromatin binding and transcription remain unknown. Modified peptide pulldown assays reveal that the Yng1 N-terminal region is important for the integrity of NuA3 HAT by mediating the interaction between core subunits and two methyl-binding proteins, Yng1 and Pdp3. We further uncover that NuA3 HAT contributes to the regulation of mRNA and lncRNA expression dynamics by antagonizing the histone deacetylases (HDACs) Rpd3S and Rpd3L. The Yng1 N-terminal region, the Nto1 PHD finger and Pdp3 are important for optimal induction of mRNA and lncRNA transcription repressed by the Set2-Rpd3S HDAC pathway, whereas the Yng1 PHD finger–H3K4me3 interaction affects transcriptional repression memory regulated by Rpd3L HDAC. These findings suggest that NuA3 HAT uses distinct chromatin readers to compete with two Rpd3-containing HDACs to optimize mRNA and lncRNA expression dynamics.

Plant homeodomain proteins provide a mechanism for how leaves grow wide

ABSTRACTThe mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNA-seq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem cell-organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and stimulates cell divisions in the same cells in which it is transcribed.