Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination

Functions of nuclear factor Y in nervous system development, function and health

Nuclear factor Y is a ubiquitous heterotrimeric transcription factor complex conserved across eukaryotes that binds to CCAAT boxes, one of the most common motifs found in gene promoters and enhancers. Over the last 30 years, research has revealed that the nuclear factor Y complex controls many aspects of brain development, including differentiation, axon guidance, homeostasis, disease, and most recently regeneration. However, a complete understanding of transcriptional regulatory networks, including how the nuclear factor Y complex binds to specific CCAAT boxes to perform its function remains elusive. In this review, we explore the nuclear factor Y complex's role and mode of action during brain development, as well as how genomic technologies may expand understanding of this key regulator of gene expression.

NF-YCs modulate RNA polymerase II-mediated transcription to regulate FLM expression

The proper transition to flowering is a critical process for the success of plant reproduction and must be highly orchestrated. Nuclear Factor-Y subunit C (NF-YCs), which are closely related to histone H2A, exert diverse chromatin-mediated regulation over plant development events including flowering. However, the mechanisms by which NF-YCs regulate RNA polymerase II (Pol II) during gene transcription remain elusive. Here, we demonstrate that NF-YCs physically interact with EARLY FLOWERING 7 (ELF7), a core component of RNA Pol II-associated factor 1 complex (PAF1c), both in vitro and in vivo. We show that NF-YCs regulate flowering in an ELF7-dependent manner by repressing the expression of the floral repressor FLOWERING LOCUS M (FLM). Further analyses reveal that NF-YCs antagonize the binding of ELF7 to FLM chromatin, thereby suppressing ELF7-mediated RNA Pol II transcription at the FLM locus. Collectively, our findings uncover a novel chromatin-mediated regulatory mechanism in which NF-YCs, in association with ELF7, control the transcription of FLM to modulate flowering time.

Durum wheat nuclear factor Y (NF-Y) a subfamily: structure, phylogeny, and expression analysis in response to hormones and abiotic stresses

Nuclear factor-Y (NF-Y) transcription factors are heterotrimeric complexes that are widely distributed in eukaryotes and play essential roles in many biological processes. Although NF-YA proteins have been characterized in numerous plants, their contribution to the response of durum wheat (Triticum turgidum ssp. durum) to environmental factors has not been reported. Thus, this study was aimed at identification and characterization of Triticum turgidum TtNF-YA family members through genome-wide analysis. Twelve NF-YA genes were discovered in Triticum turgidum. Discovered genes were distributed across eight chromosomes, while their encoded proteins were localized in cell nucleus. Structure and motif pattern analyses revealed that the TtNF-YA genes were relatively conserved. The expression of TtNF-YAs genes was significantly induced by several stressors and their expression profiles differed in various tissues and at various development stages. Notably, TtNF-YA2 A-1 and TtNF-YA2B-1 exhibited the greatest increase in response to Polyethylene glycol, while TtNF-YA4 A and TtNF-YA4B-1 showed the highest increase under salt stress. Additionally, TtNF-YA5B-1 and TtNF-YA6 A-1 displayed pronounced upregulation when exposed to exogenous Abscisic acid, suggesting that TtNF-YA are involved in a series of cellular and developmental events. This finding was corroborated by the recognition of several cis-regulatory elements in the TtNF-YAs promoter region, associated with the applied treatments. Overexpression of TtNF-YA2 A-1, TtNF-YA2B-1, TtNF-YA4 A, TtNF-YA4 A-1, TtNF-YA4B-1, and TtNF-YA5 A-2 genes in Saccharomyces cerevisiae showed that these genes increase cell tolerance to multiple stresses. Our results will facilitate subsequent functional analysis of TtNF-YAs genes, which emerge as promising targets for genetic engineering for increasing wheat tolerance to multiple stresses.

Binding of NF-Y to transposable elements in mouse and human cells

BACKGROUND

Transposable Elements (TEs) represent a sizeable amount of mammalian genomes, providing regulatory sequences involved in shaping gene expression patterns. NF-Y is a Transcription factor -TF- trimer that binds to the CCAAT box, belonging to a selected group implicated in determining initiation of coding and noncoding RNAs.

RESULTS

We focus on NF-Y TE locations in 8 human and 8 mouse cells. Binding is exclusive for retroviral LTR12, MLT1 and MER in human and RLTR10 and IAPLTR in mouse cells. Cobinding and analysis of the DNA matrices signal enrichment of distinct TFs neighboring CCAAT in the three TE classes: MAFK/F/G in LTR12 and USF1/2 in MLT1 with precise alignment of sites, PKNOX1, MEIS2, PBX2/3 TALE TFs in MER57. The presence of "epigenetic" marks in human cells indicate prevalent co-association with open chromatin in MER, closed in LTR12 and mixed in MLT1. Based on chromatin features, these locations are mostly marked as enhancers, as confirmed by analysis of loci predicted to generate eRNAs.

CONCLUSIONS

These results are discussed in the context of functional data, suggesting a complex -positive and potentially-negative role of NF-Y on distinct classes of repetitive sequences.

Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels

NF-Y is a transcription factor trimer formed by Histone Fold subunits NF-YB/NF-YC and NF-YA, which confers sequence-specificity for the CCAAT box, an important cis regulatory element. The subunits are extremely conserved in all eukaryotes and in mammals they are typically encoded by single copy genes. We describe here the presence of a second NF-YA termed NF-YAr for retrogene in diverse groups of mammals (Cetacea, Ruminantia, Ursidae, Sciuridae, hippopotamus, and greater horseshoe bat). NF-YAr retrogenes are located on different chromosomes with respect to the parental gene; they are compact and intronless, or with few annotated introns. Phylogenetic and synteny analyses indicate multiple independent retrotransposition events in the different orders. Analysis of RNA-seq data of Bos taurus suggests expression confined to spermatozoa. Conservation of translation initiation signals around predicted start codons, and of 5'UTR sequences, are consistent with protein expression, suggesting that NF-YAr is a translated, retroposed NF-YA. 3D-informed structural considerations of the predicted protein sequences point at deleterious changes for CCAAT-binding and, potentially, for trimer formation. These findings indicate that multiple independent NF-YA retrotransposition events were fixed in selected orders of mammals, generating a second NF-YA with a strict tissue distribution.

Q-rich activation domains: flexible 'rulers' for transcription start site selection?

Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term 'ruler' TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.

Regulation pattern of carotenoid biosynthesis induced by low light stress in Dunaliella

This research aims to explore the response mechanism of carotenoid synthesis in Dunaliella bardawil under low light stress (≤13.5 µmol·m-2·s-1). We analyzed carotenoid composition and its correlation with carotenogenic genes (CRTs) differential expression, promoter regulatory elements and transcription factors. DbPDS and DbZDS were significantly up-regulated under low light stress. Mutation experiments showed ACE, ASF1, CCACA-box, and CCAAT-box in DbZDS promoter key for low light regulation. In addition, CONSTANS (DbCO) and nuclear transcription factor YB (DbNF-YB) had a weak interaction and could bind to DbZDS gene promoter, whereas there was no interaction between DbZDS promoter and DbHY5 (ELONGATED HYPOCOTYL 5). We constructed a DbCO gene overexpressing strain, which significantly enhanced carotenoid content, notably increasing β-carotene levels to 2.3 times. These results significantly enhance our understanding of the regulation of low light stress in microalgae.

Identification of nuclear factor YA6 genes in sorghum and characterization of their involvement in drought tolerance

Nuclear factor Y alpha proteins (NF-YAs) are conserved transcription factor proteins crucial to plant growth and development that exhibit specific responses to biotic and abiotic stresses. Using bioinformatics approaches to investigate the NF-YA family in sorghum (Sorghum bicolor), we identified nine SbNF-YA genes unevenly distributed on four of the 10 sorghum chromosomes. Despite variations in gene structure, all encode proteins have the characteristic CBFB_NFYA domain and other predicted motifs. The secondary structure of SbNF-YA members is predominantly composed of α-helices and random coils. A phylogenetic analysis of NF-YAs of sorghum and other plant species indicated that SbNF-YAs are closely related to NF-YAs from maize (Zea mays) and distantly related to those in Arabidopsis (Arabidopsis thaliana). A colinearity analysis determined that six of the nine SbNF-YA genes arose from segmental duplication events. Transcriptome and RT-qPCR analyses showed that the expression levels of eight of the SbNF-YA genes (SbNF-YA5 being the exception) are responsive to drought stress to varying degrees. Notably, SbNF-YA1, SbNF-YA4, SbNF-YA6, SbNF-YA8, and SbNF-YA9 expression was significantly upregulated under the stress conditions, suggesting that they participate in drought response. When heterologously expressed in Arabidopsis, SbNF-YA6 conferred greater tolerance of drought stress imposed by treatment with the osmolyte mannitol, with the transgenic Arabidopsis lines showing superior germination rates; longer roots; higher fresh weight; higher activities of the enzymes peroxidase, superoxide dismutase, and catalase; and higher soluble protein and proline contents, compared to the wild type. Additionally, the transgenic Arabidopsis lines accumulated lower levels of hydrogen peroxide, superoxide anion, and malondialdehyde. The expression levels of several drought-responsive genes were elevated in transgenic Arabidopsis seedlings relative to the wild type, indicating that the heterologous expression of SbNF-YA6 enhances the drought tolerance of Arabidopsis.

The role of nuclear factor-Y (NF-Y) transcription factor in plant growth and development

The nuclear factor-Y (NF-Y) transcription factor, also known as heme-activator protein (HAP) or CCAAT-binding factor (CBF), is a critical transcription factor widely present in eukaryotes. The number of NF-Y subunits has significantly increased in higher plants compared to animals and fungi. The NF-Y complex is composed of three subunits: (1) NF-YA; (2) NF-YB; and (3) NF-YC. NF-YB and NF-YC contain histone fold domains (HFDs), which can interact with NF-YA or other transcription factors, or directly bind to the promoter CCAAT box to regulate the transcription of downstream genes. NF-Y plays a significant role in various plant processes, including growth and development. This review elucidates the structural and functional aspects of NF-Y subunits, identified NF-Y complexes, and their molecular regulatory mechanisms. Understanding these facets of NF-Y provides valuable insights into advancing crop genetic improvement and promoting sustainable agricultural practices.

Aging-dependent temporal regulation of MIR156 epigenetic silencing by CiLDL1 and CiNF-YB8 in chrysanthemum

Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown. Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin-MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine-specific demethylase CiLDL1 and the nuclear factor Y complex. CiLDL1 and CiNF-YB8 interact with the classical histone-like fold domain (HFD) of CiNF-YC1 and CiNF-YA3, which form distinct heterotrimers binding to the 'CCAAT' box in the promoter region of cin-MIR156ab. CiLDL1 and CiNF-YB8 have opposing effects on cin-MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin-MIR156ab locus. During aging, decreased CiNF-YB8 expression leads to a quantitative switch from the CiNF-YA3-CiNF-YC1-CiNF-YB8 heterotrimer to the CiNF-YA3-CiNF-YC1-CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin-MIR156ab locus, thus temporal silencing its expression. Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF-YB8 ensures proper aging-dependent flowering in chrysanthemum.

Genome-Wide Identification and Expression Pattern Analysis of Nuclear Factor Y B/C Genes in Pinus koraiensis, and Functional Identification of LEAFY COTYLEDON 1

The nuclear factor Y (NF-Y) transcription factor is widely involved in various plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress responses. This study presents a comprehensive genome-wide identification and expression profile of transcription factors NF-YB and NF-YC in Pinus koraiensis. Eight NF-YB and seven NF-YC transcription factors were identified through bioinformatics analysis, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. We evaluate the expression patterns of NF-YB/C genes in various tissues and somatic embryo maturation processes through the transcriptomics of ABA-treated tissues from multiple nutritional tissues, reproductive tissues, and somatic embryo maturation processes. The Leafy cotyledon1 (LEC1) gene belongs to the LEC1-type gene in the NF-YB family, numbered PkNF-YB7. In this study, we characterized the function of PkLEC1 during somatic embryonic development using genetic transformation techniques. The results indicate that PkNF-YB/C transcription factors are involved in the growth and development of nutritional tissues and reproductive organs, with specific high expression in PkNF-YB7 embryogenic callus, somatic embryos, zygotic embryos, and macropores. Most PkNF YB/C genes do not respond to ABA treatment during the maturation culture process. Compared with the absence of ABA, PkNF-YB8 was up-regulated in ABA treatment for one week (4.1 times) and two weeks (11.6 times). However, PkNF-YC5 was down-regulated in both one week (0.6 times) and two weeks (0.36 times) of culture, but the down-regulation trend was weakened in tissues treated with ABA (0.72-0.83 times). In addition, the promoter of PkNF YB/Cs was rich in elements that respond to various plant hormones, indicating their critical role in hormone pathways. The overexpression of PkLEC1 stimulated the generation of early somatic embryos from callus tissue with no potential for embryogenesis, enhancing the somatic embryogenesis ability of P. koraiensis callus tissue.

The role(s) of NF-Y in development and differentiation

NF-Y is a conserved sequence-specific trimeric Transcription Factor -TF- binding to the CCAAT element. We review here the role(s) in development, from pre-implantation embryo to terminally differentiated tissues, by rationalizing and commenting on genetic, genomic, epigenetic and biochemical studies. This effort brings to light the impact of NF-YA isoforms on stemness and differentiation, as well as binding to distal vs promoter proximal sites and connections with selected TFs.

PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production

The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) PhpCNF-Y complex can infiltrate constitutive heterochromatin via its histone-fold domains to transcribe repeat elements. PhpCNF-Y collaborates with a Zn-finger containing TF to bind repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, PhpCNF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain multiple cryptic introns which are required for the generation of small interfering RNAs (siRNAs) via a mechanism involving the spliceosome and RNAi machinery. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for heterochromatin nucleation at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.

Molecular condensation of the CO/NF-YB/NF-YC/FT complex gates floral transition in Arabidopsis

The plant master photoperiodic regulator CONSTANS (CO) interacts with Nuclear Factor-Y subunits B2 (NF-YB2) and C9 (NF-YC9) and transcriptionally activates the florigen gene FLOWERING LOCUS T (FT), regulating floral transition. However, the molecular mechanism of the functional four-component complex assembly in the nucleus remains elusive. We report that co-phase separation of CO with NF-YB2/NF-YC9/FT precisely controls heterogeneous CO assembly and FT transcriptional activation. In response to light signals, CO proteins form functional percolation clusters from a diffuse distribution in a B-box-motif-dependent manner. Multivalent coassembly with NF-YC9 and NF-YB2 prevents inhibitory condensate formation and is necessary to maintain proper CO assembly and material properties. The intrinsically disordered region (IDR) of NF-YC9, containing a polyglutamine motif, fine-tunes the functional properties of CO/NF-YB/NF-YC condensates. Specific FT promoter recognition with polyelectrolyte partitioning also enables the fluidic functional properties of CO/NF-YB/NF-YC/FT condensates. Our findings offer novel insights into the tunable macromolecular condensation of the CO/NF-YB/NF-YC/FT complex in controlling flowering in the photoperiod control.

Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation

In sexually reproducing organisms, life begins with the fusion of transcriptionally silent gametes, the oocyte and sperm. Although initiation of transcription in the embryo, known as zygotic genome activation (ZGA), is universally required for development, the transcription factors regulating this process are poorly conserved. In this Perspective, we discuss recent insights into the mechanisms of ZGA in totipotent mammalian embryos, namely ZGA regulation by several transcription factors, including by orphan nuclear receptors (OrphNRs) such as the pioneer transcription factor NR5A2, and by factors of the DUX, TPRX and OBOX families. We performed a meta-analysis and compiled a list of pan-ZGA genes, and found that most of these genes are indeed targets of the above transcription factors. Remarkably, more than a third of these ZGA genes appear to be regulated both by OrphNRs such as NR5A2 and by OBOX proteins, whose motifs co-occur in SINE B1 retrotransposable elements, which are enriched near ZGA genes. We propose that ZGA in mice is activated by recruitment of multiple transcription factors to SINE B1 elements that function as enhancers, and discuss a potential relevance of this mechanism to Alu retrotransposable elements in human ZGA.

Plant Nuclear Factor Y (NF-Y) Transcription Factors: Evolving Insights into Biological Functions and Gene Expansion

Gene expansion is a common phenomenon in plant transcription factor families; however, the underlying molecular mechanisms remain elusive. Examples of gene expansion in transcription factors are found in all eukaryotes. One example is plant nuclear factor Y (NF-Y) transcription factors. NF-Y is ubiquitous to eukaryotes and comprises three independent protein families: NF-YA, NF-YB, and NF-YC. While animals and fungi mostly have one of each NF-Y subunit, NF-Y is greatly expanded in plants. For example, humans have one each of NF-YA, NF-YB, and NF-YC, while the model plant Arabidopsis has ten each of NF-YA, NF-YB, and NF-YC. Our understanding of the plant NF-Y, including its biological roles, molecular mechanisms, and gene expansion, has improved over the past few years. Here we will review its biological roles and focus on studies demonstrating that NF-Y can serve as a model for plant gene expansion. These studies show that NF-Y can be classified into ancestrally related subclasses. Further, the primary structure of each NF-Y contains a conserved core domain flanked by non-conserved N- and C-termini. The non-conserved N- and C-termini, under pressure for diversifying selection, may provide clues to this gene family's retention and functional diversification following gene duplication. In summary, this review demonstrates that NF-Y expansion has the potential to be used as a model to study the gene expansion and retention of transcription factor families.

TaFAR9 and TaFAR10 synergistically regulate fertility conversion of photo-thermo-sensitive genic male sterility lines in wheat by modulating ROS homeostasis

Photo-thermo-sensitive genic male sterility (PTGMS), which exhibits varying fertility levels under different environmental conditions, is a crucial method for heterosis utilization in wheat. However, the mechanisms underlying fertility conversion remain unclear. In the study, three BS type PTGMS lines were analyzed to study fertility conversion characteristics. The results indicated that the fertility conversion occurred during meiosis and was accompanied by an increase in reactive oxygen species (ROS) under a sterile environment. TaFAR9 encoding a novel fatty acyl CoA reductase was identified using transcriptome sequencing. Expression analysis suggested that TaFAR9 was localized in the endoplasmic reticulum (ER), with high expression levels in anthers. Furthermore, the down-regulation of TaFAR9 expression displayed characteristics of male sterility, accompanied by the accumulation of ROS. Cytological analysis revealed abnormal development in the anther and pollen walls of TaFAR9-silenced lines. Additionally, TaFAR9 and TaFAR10 were confirmed to physically interact using molecular docking simulation, yeast two-hybrid, luciferase complementation, and bimolecular fluorescence complementation assays. The reduced expression of TaFAR10 also exhibited male sterility and ROS burst. Moreover, the co-silencing of TaFAR9 and TaFAR10 produced sterility phenotypes that were similar to those observed when silencing TaFAR9 or TaFAR10 individually. Transcriptome analysis suggested that the ROS burst in BSMV: TaFAR9/10 anthers can result in cellular metabolic disorders. These findings indicate that TaFAR9 and TaFAR10 may form heterodimers that synergistically regulate fertility conversion in PTGMS lines by modulating ROS metabolism. And this study offers a fresh insight into the regulatory processes involved in fertility conversion in PTGMS lines.

Genome-Wide Identification and Expression Profiles of Nuclear Factor Y A Transcription Factors in Blueberry Under Abiotic Stress

Nuclear Factor Y A (NF-YA) transcription factors are widely involved in multiple plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress response. This study presents a comprehensive genome-wide identification and expression profiling of NF-YA transcription factors in blueberry (Vaccinium corymbosum), an important economic crop with good adaptability, under abiotic stress conditions. Given the economic significance and health benefits of blueberries, understanding their responses to environmental stresses, such as salt, drought, and temperature extremes, is crucial. A total of 24 NF-YA transcription factors were identified through bioinformatics analyses, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. The expression patterns of these NF-YA genes were evaluated in various tissues (roots, stems, and leaves) and under different stress treatments (abscisic acid, salt, and cold) using quantitative real-time PCR (qRT-PCR). The results indicated that most VcNF-YA genes exhibited higher expression levels in stems and leaves compared to roots. Most VcNF-YAs were responsive to the stress treatment. Furthermore, cis-acting element analysis revealed that the promoters of VcNF-YAs were enriched with elements responsive to abiotic stress, suggesting their pivotal role in stress adaptation. This research unveils the expressional responses of NF-YA transcription factors in blueberry upon abiotic stresses and lays the groundwork for future studies on improving crop adaptation.

Genomic binding of NF-Y in mouse and human cells

NF-Y is a Transcription Factor that regulates transcription through binding to the CCAAT-box. To understand its strategy, we analyzed 16 ChIP-seq datasets from human and mouse cells. Shared loci, mostly located in promoters of expressed genes of cell cycle, metabolism and gene expression pathways, are associated with histone marks of active chromatin and specific modules of TFs. Other peaks are in enhancers and Transposable Elements -TE- of retroviral origin in human and mouse. We evaluated the relationship with USF1, a common synergistic partner in promoters and MLT1 TEs, upon NF-YB inactivation: USF1 binding decreases in promoters, modestly in MLT1, suggesting a pioneering role of NF-Y in formers, not in the latters. These data define a common set of NF-Y functional targets across different mammalian cell types, suggesting a pioneering role in promoters with respect to TEs.

p53 target ANKRA2 cooperates with RFX7 to regulate tumor suppressor genes

The transcription factor regulatory factor X 7 (RFX7) has been identified as a tumor suppressor that is recurrently mutated in lymphoid cancers and appears to be dysregulated in many other cancers. RFX7 is activated by the well-known tumor suppressor p53 and regulates several other known tumor suppressor genes. However, what other factors regulate RFX7 and its target genes remains unclear. Here, reporter gene assays were used to identify that RFX7 regulates the tumor suppressor gene PDCD4 through direct interaction with its X-box promoter motif. We utilized mass spectrometry to identify factors that bind to DNA together with RFX7. In addition to RFX7, we also identified RFX5, RFXAP, RFXANK, and ANKRA2 that bind to the X-box motif in the PDCD4 promoter. We demonstrate that ANKRA2 is a bona fide direct p53 target gene. We used transcriptome analyses in two cell systems to identify genes regulated by ANKRA2, its sibling RFXANK, and RFX7. These results revealed that ANKRA2 functions as a critical cofactor of RFX7, whereas RFXANK regulates largely distinct gene sets.

Identification and expression analysis of nuclear factor Y transcription factor genes under drought, cold and Eldana infestation in sugarcane (Saccharum spp. hybrid)

BACKGROUND

The Nuclear Factor Y (NF-Y) transcription factor (TF) gene family plays a crucial role in plant development and response to stress. Limited information is available on this gene family in sugarcane.

OBJECTIVES

To identify sugarcane NF-Y genes through bioinformatic analysis and phylogenetic association and investigate the expression of these genes in response to abiotic and biotic stress.

METHODS

Sugarcane NF-Y genes were identified using comparative genomics from functionally annotated Poaceae and Arabidopsis species. Quantitative PCR and transcriptome analysis assigned preliminary functional roles to these genes in response to water deficit, cold and African sugarcane borer (Eldana saccharina) infestation.

RESULTS

We identify 21 NF-Y genes in sugarcane. Phylogenetic analysis revealed three main branches representing the subunits with potential discrepancies present in the assignment of numerical names of some NF-Y putative orthologs across the different species. Gene expression analysis indicated that three genes, ShNF-YA1, A3 and B3 were upregulated and two genes, NF-YA4 and A7 were downregulated, while three genes were upregulated, ShNF-YB2, B3 and C4, in the plants exposed to water deficit and cold stress, respectively. Functional involvement of NF-Y genes in the biotic stress response were also detected where three genes, ShNF-YA6, A3 and A7 were downregulated in the early resistant (cv. N33) response to Eldana infestation whilst only ShNF-YA6 was downregulated in the susceptible (cv. N11) early response.

CONCLUSIONS

Our research findings establish a foundation for investigating the function of ShNF-Ys and offer candidate genes for stress-resistant breeding and improvement in sugarcane.

Nuclear factor Y, a key player in neuronal gene regulation

Establishing a functional nervous system is a complex process requiring tightly controlled gene expression programs to achieve the correct differentiation of distinct neuronal subtypes. The molecular programs required for neurons to acquire neuron-type-specific, and core pan-neuronal features mostly rely on sequence-specific transcription factors (TFs), which recognize and bind to cis-regulatory motifs present in the promoters of target genes. Recently, we investigated the role and mode of action of the NF-Y complex, a ubiquitously expressed transcriptional master regulator, in the Caenorhabditis elegans nervous system. We found that NFYA-1 is a pervasive regulator of neuron-specific and pan-neuronal gene batteries that are essential for neuronal development and function. Furthermore, we concluded that NFYA-1 acts cell autonomously by either directly binding to conserved motifs in target gene promoter regions or indirectly by regulating other transcriptional regulators to fine-tune gene expression. However, further studies are required to fully define the impact of the NF-Y complex on nervous system regulatory networks and how NF-Y coordinates with other TFs in this regard.

Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L

Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.

ZmNF-YA1 Contributes to Maize Thermotolerance by Regulating Heat Shock Response

Zea mays (maize) is a staple food, feed, and industrial crop. Heat stress is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers heat stress tolerance in maize. The nf-ya1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The nf-ya1 mutant was more temperature-sensitive than the wild-type (WT), while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were observed in the mutant, followed by WT and overexpression lines after heat stress treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in nf-ya1 and its wild-type control W22 in response to heat stress. Based on their expression profiles, the heat stress response-related differentially expressed genes (DEGs) in nf-ya1 compared to WT were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of the DEGs in different clades was performed to elucidate the roles of ZmNF-YA1-mediated transcriptional regulation and their contribution to maize thermotolerance. The loss function of ZmNF-YA1 led to the failure induction of DEGs in GO terms of protein refolding, protein stabilization, and GO terms for various stress responses. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of abscisic acid (ABA), ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype.

Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar

The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.

Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y

Transcription factors (TFs) play a central role in gene regulation, and their malfunction can result in a plethora of severe diseases. TFs are therefore interesting therapeutic targets, but their involvement in protein-protein interaction networks and the frequent lack of well-defined binding pockets render them challenging targets for classical small molecules. As an alternative, peptide-based scaffolds have proven useful, in particular with an α-helical active conformation. Peptide-based strategies often require extensive structural optimization efforts, which could benefit from a more detailed understanding of the dynamics in inhibitor/protein interactions. In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.

Transcription factors as molecular switches regulating plant responses to drought stress

Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.

Nuclear factor Y-A3b binds to the SINGLE FLOWER TRUSS promoter and regulates flowering time in tomato

The control of flowering time is essential for reproductive success and has a major effect on seed and fruit yield and other important agricultural traits in crops. Nuclear factors Y (NF-Ys) are transcription factors that form heterotrimeric protein complexes to regulate gene expression required for diverse biological processes, including flowering time control in plants. However, to our knowledge, there has been no report on mutants of individual NF-YA subunits that promote early flowering phenotype in plants. In this study, we identified SlNF-YA3b, encoding a member of the NF-Y transcription factor family, as a key gene regulating flowering time in tomato. Knockout of NF-YA3b resulted in an early flowering phenotype in tomato, whereas overexpression of NF-YA3b delayed flowering in transgenic tomato plants. NF-YA3b was demonstrated to form heterotrimeric protein complexes with multiple NF-YB/NF-YC heterodimers in yeast three-hybrid assays. Biochemical evidence indicated that NF-YA3b directly binds to the CCAAT cis-elements of the SINGLE FLOWER TRUSS (SFT) promoter to suppress its gene expression. These findings uncovered a critical role of NF-YA3b in regulating flowering time in tomato and could be applied to the management of flowering time in crops.

Expression profiling of Nuclear Factor-Y (NF-Y) transcription factors during dehydration and salt stress in finger millet reveals potential candidate genes for multiple stress tolerance

MAIN CONCLUSION

Expression profiling of NF-Y transcription factors during dehydration and salt stress in finger millet genotypes contrastingly differing in tolerance levels identifies candidate genes for further characterization and functional studies. The Nuclear Factor-Y (NF-Y) transcription factors are known for imparting abiotic stress tolerance in different plant species. However, there is no information on the role of this transcription factor family in naturally drought-tolerant crop finger millet (Eleusine coracana L.). Therefore, interpretation of expression profiles against drought and salinity stress may provide valuable insights into specific and/or overlapping expression patterns of Eleusine coracana Nuclear Factor-Y (EcNF-Y) genes. Given this, we identified 59 NF-Y (18 NF-YA, 23 NF-YB, and 18 NF-YC) encoding genes and designated them EcNF-Y genes. Expression profiling of these genes was performed in two finger millet genotypes, PES400 (dehydration and salt stress tolerant) and VR708 (dehydration and salt stress sensitive), subjected to PEG-induced dehydration and salt (NaCl) stresses at different time intervals (0, 6, and 12 h). The qRT-PCR expression analysis reveals that the six EcNF-Y genes namely EcNF-YA1, EcNF-YA5, EcNF-YA16, EcNF-YB6, EcNF-YB10, and EcNF-YC2 might be associated with tolerance to both dehydration and salinity stress in early stress condition (6 h), suggesting the involvement of these genes in multiple stress responses in tolerant genotype. In contrast, the transcript abundance of finger millet EcNF-YA5 genes was also observed in the sensitive genotype VR708 under late stress conditions (12 h) of both dehydration and salinity stress. Therefore, the EcNF-YA5 gene might be important for adaptation to salinity and dehydration stress in sensitive finger millet genotypes. Therefore, this gene could be considered as a susceptibility determinant, which can be edited to impart tolerance. The phylogenetic analyses revealed that finger millet NF-Y genes share strong evolutionary and functional relationship to NF-Ys governing response to abiotic stresses in rice, sorghum, maize, and wheat. This is the first report of expression profiling of EcNF-Ys genes identified from the finger millet genome and reveals potential candidate for enhancing dehydration and salt tolerance.

C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies

In humans, specific aberrations in β-globin results in sickle cell disease and β-thalassemia, symptoms of which can be ameliorated by increased expression of fetal globin (HbF). Two recent CRISPR-Cas9 screens, centered on ∼1500 annotated sequence-specific DNA binding proteins and performed in a human erythroid cell line that expresses adult hemoglobin, uncovered four groups of candidate regulators of HbF gene expression. They are (1) members of the nucleosome remodeling and deacetylase (NuRD) complex proteins that are already known for HbF control; (2) seven C2H2 zinc finger (ZF) proteins, including some (ZBTB7A and BCL11A) already known for directly silencing the fetal γ-globin genes in adult human erythroid cells; (3) a few other transcription factors of different structural classes that might indirectly influence HbF gene expression; and (4) DNA methyltransferase 1 (DNMT1) that maintains the DNA methylation marks that attract the MBD2-associated NuRD complex to DNA as well as associated histone H3 lysine 9 methylation. Here we briefly discuss the effects of these regulators, particularly C2H2 ZFs, in inducing HbF expression for treating β-hemoglobin disorders, together with recent advances in developing safe and effective small-molecule therapeutics for the regulation of this well-conserved hemoglobin switch.

Histone dynamics responding to internal and external cues underlying plant development

Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.

Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L

Rapeseed (Brassica napus) is one of the important oil crops worldwide. Its production is often threatened by drought stress. Here, we identify a transcription factor (BnaA9.NF-YA7) that negatively regulates drought tolerance through genome-wide association study in B. napus. The presence of two SNPs within a CCAAT cis element leads to downregulation of BnaA9.NF-YA7 expression. In addition, the M63I (G-to-C) substitution in the transactivation domain can activate low level expression of BnaA4.DOR, which is an inhibitory factor of ABA-induced stomatal closure. Furthermore, we determine that Bna.ABF3/4s directly regulate the expression of BnaA9.NF-YA7, and BnaA9.NF-YA7 indirectly suppresses the expression of Bna.ABF3/4s by regulation of Bna.ASHH4s. Our findings uncover that BnaA9.NF-YA7 serves as a supplementary role for ABA signal balance under drought stress conditions, and provide a potential molecular target to breed drought-tolerant B. napus cultivars.

Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.)

Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants.

Expression and function of NF-Y subunits in cancer

NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.

Nuclear factor Y is a pervasive regulator of neuronal gene expression

Nervous system function relies on the establishment of complex gene expression programs that provide neuron-type-specific and core pan-neuronal features. These complementary regulatory paradigms are controlled by terminal selector and parallel-acting transcription factors (TFs), respectively. Here, we identify the nuclear factor Y (NF-Y) TF as a pervasive direct and indirect regulator of both neuron-type-specific and pan-neuronal gene expression. Mapping global NF-Y targets reveals direct binding to the cis-regulatory regions of pan-neuronal genes and terminal selector TFs. We show that NFYA-1 controls pan-neuronal gene expression directly through binding to CCAAT boxes in target gene promoters and indirectly by regulating the expression of terminal selector TFs. Further, we find that NFYA-1 regulation of neuronal gene expression is important for neuronal activity and motor function. Thus, our research sheds light on how global neuronal gene expression programs are buffered through direct and indirect regulatory mechanisms.

Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response

The process of flowering in plants is a pivotal stage in their life cycle, and the CONSTANS-like (COL) protein family, known for its photoperiod sensing ability, plays a crucial role in regulating plant flowering. Over the past two decades, homologous genes of COL have been identified in various plant species, leading to significant advancements in comprehending their involvement in the flowering pathway and response to abiotic stress. This article presents novel research progress on the structural aspects of COL proteins and their regulatory patterns within transcription complexes. Additionally, we reviewed recent information about their participation in flowering and abiotic stress response, aiming to provide a more comprehensive understanding of the functions of COL proteins.

Nuclear factor OsNF-YC5 modulates rice seed germination by regulating synergistic hormone signaling

Regulation of seed dormancy/germination is of great importance for seedling establishment and crop production. Nuclear factor-Y (NF-Y) transcription factors regulate plant growth and development, as well as stress responses; however, their roles in seed germination remain largely unknown. In this study, we reported that NF-Y gene OsNF-YC5 knockout increased, while its overexpression reduced, the seed germination in rice (Oryza sativa L.). ABA-induced seed germination inhibition assays showed that the osnf-yc5 mutant was less sensitive but OsNF-YC5-overexpressing lines were more sensitive to exogenous ABA than the wild type. Meanwhile, MeJA treatment substantially enhanced the ABA sensitivity of OsNF-YC5-overexpressing lines during seed germination. Mechanistic investigations revealed that the interaction of OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9) with OsNF-YC5 enhanced the stability of OsNF-YC5 by protein phosphorylation, while the interaction between JASMONATE ZIM-domain protein 9 (OsJAZ9) and OsNF-YC5 repressed OsNF-YC5 transcriptional activity and promoted its degradation. Furthermore, OsNF-YC5 transcriptionally activated ABA catabolic gene OsABA8ox3, reducing ABA levels in germinating seeds. However, the transcriptional regulation of OsABA8ox3 by OsNF-YC5 was repressed by addition of OsJAZ9. Notably, OsNF-YC5 improved seed germination under salinity conditions. Further investigation showed that OsNF-YC5 activated the high-affinity K+ transporter gene (OsHAK21) expression, and addition of SAPK9 could increase the transcriptional regulation of OsHAK21 by OsNF-YC5, thus substantially reducing the ROS levels to enhance seed germination under salt stress. Our findings establish that OsNF-YC5 integrates ABA and JA signaling during rice seed germination, shedding light on the molecular networks of ABA-JA synergistic interaction.

Characterization of NF-Y gene family and their expression and interaction analysis in Phalaenopsis orchid

The complex of Nuclear Factor Ys (NF-Ys), a family of heterotrimeric transcription factors composed of three unique subunits (NF-YA, NF-YB, and NF-YC), binds to the CCAAT box of eukaryotic promoters to activate or repress transcription of the downstream genes involved into various biological processes in plants. However, the systematic characterization of NF-Y gene family has not been elucidated in Phalaenopsis. A total of 24 NF-Y subunits (4 NF-YA, 9 NF-YB, and 11 NF-YC subunits) were identified in Phalaenopsis genome, whose exon/intron structures were highly differentiated among the PhNF-Y subunits. The distribution of motifs between coding regions of PhNF-YA and PhNF-YB/C was distinct. Segmental and tandem duplication events among paralogous PhNF-Ys were occurred. Six pairs of orthologous NF-Ys from Phalaenopsis and Arabidopsis and five pairs of orthologous NF-Ys from Phalaenopsis and rice involved in the phylogenetic gene synteny were identified. The various cis-elements being responsive to low-temperature, drought and ABA were distributed in the promoters of PhNF-Ys. qRT-PCR analysis indicated all of PhNF-Ys displayed the spatial specificity of expression in different tissues. Moreover, the expression levels of multiple PhNF-Ys significantly changed responding to low-temperature and ABA treatment. Yeast two hybrid and bimolecular fluorescence complementation assays approved the interaction of PhNF-YA1/3 with PhNF-YB6/PhNF-YC7, respectively, as well as PhNF-YB6 with PhNF-YC7. PhNF-YA1/3, PhNF-YB6, and PhNF-YC7 proteins were all localized in the nucleus. Further, transient overexpression of PhNF-YB6 and PhNF-YC7 promoted PhFT3 and repressed PhSVP expression in Phalaenopsis. These findings will facilitate to explore the role of PhNF-Ys in floral transition in Phalaenopsis orchid.

Epigenetic silencing of callose synthase by VIL1 promotes bud-growth transition in lily bulbs

In plants, restoring intercellular communication is required for cell activity in buds during the growth transition from slow to fast growth after dormancy release. However, the epigenetic regulation of this phenomenon is far from understood. Here we demonstrate that lily VERNALIZATION INSENSITIVE 3-LIKE 1 (LoVIL1) confers growth transition by mediating plasmodesmata opening via epigenetic repression of CALLOSE SYNTHASE 3 (LoCALS3). Moreover, we found that a novel transcription factor, NUCLEAR FACTOR Y, SUBUNIT A7 (LoNFYA7), is capable of recruiting the LoVIL1-Polycomb Repressive Complex 2 (PRC2) and enhancing H3K27me3 at the LoCALS3 locus by recognizing the CCAAT cis-element (Cce) of its promoter. The LoNFYA7-LoVIL1 module serves as a key player in orchestrating the phase transition from slow to fast growth in lily bulbs. These studies also indicate that LoVIL1 is a suitable marker for the bud-growth-transition trait following dormancy release in lily cultivars.

NF-YA isoforms with alternative splicing of exon-5 in Aves

NF-YA, the regulatory subunit of the trimeric CCAAT-binding transcription factor NF-Y, is present in vertebrates in two major alternative spliced isoforms: NF-YAl and NF-YAs, differing for the presence of exon-3. NF-YAx, a third isoform without exon-3/-5, was reported only in human neuronal cells and tumors. These events affect the Trans-Activation Domain. We provide here evidence for the expression of NF-YAx and for the existence of a new isoform, NF-YAg, skipping only exon-5. These isoforms are abundant in Aves, but not in reptiles, and are the prevalent transcripts in the initial phases of embryo development in chicken. Finally, we analyzed NF-YAg and NF-YAx amino acid sequence using AlphaFold: absence of exon-5 denotes a global reduction of β-stranded elements, while removal of the disordered exon-3 sequence has limited effects on TAD architecture. These data identify an expanded program of NF-YA isoforms within the TAD in Aves, implying a role during early development.

Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis

Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.

NFYC-37 promotes tumor growth by activating the mevalonate pathway in bladder cancer

Dysregulation of transcription is a hallmark of cancer, including bladder cancer (BLCA). CRISPR-Cas9 screening using a lentivirus library with single guide RNAs (sgRNAs) targeting human transcription factors and chromatin modifiers is used to reveal genes critical for the proliferation and survival of BLCA cells. As a result, the nuclear transcription factor Y subunit gamma (NFYC)-37, but not NFYC-50, is observed to promote cell proliferation and tumor growth in BLCA. Mechanistically, NFYC-37 interacts with CBP and SREBP2 to activate mevalonate pathway transcription, promoting cholesterol biosynthesis. However, NFYC-50 recruits more of the arginine methyltransferase CARM1 than NFYC-37 to methylate CBP, which prevents the CBP-SREBP2 interaction and subsequently inhibits the mevalonate pathway. Importantly, statins targeting the mevalonate pathway can suppress NFYC-37-induced cell proliferation and tumor growth, indicating the need for conducting a clinical trial with statins for treating patients with BLCA and high NFYC-37 levels, as most patients with BLCA have high NFYC-37 levels.

Analysis of gene duplication within the Arabidopsis NUCLEAR FACTOR Y, subunit B (NF-YB) protein family reveals domains under both purifying and diversifying selection

Gene duplication is an evolutionary mechanism that provides new genetic material. Since gene duplication is a major driver for molecular evolution, examining the fate of duplicated genes is an area of active research. The fate of duplicated genes can include loss, subfunctionalization, and neofunctionalization. In this manuscript, we chose to experimentally study the fate of duplicated genes using the Arabidopsis NUCLEAR FACTOR Y (NF-Y) transcription factor family. NF-Y transcription factors are heterotrimeric complexes, composed of NF-YA, NF-YB, and NF-YC. NF-YA subunits are responsible for nucleotide-specific binding to a CCAAT cis-regulatory element. NF-YB and NF-YC subunits make less specific, but essential complex-stabilizing contacts with the DNA flanking the core CCAAT pentamer. While ubiquitous in eukaryotes, each NF-Y family has expanded by duplication in the plant lineage. For example, the model plant Arabidopsis contains 10 each of the NF-Y subunits. Here we examine the fate of duplicated NF-YB proteins in Arabidopsis, which are composed of central histone fold domains (HFD) and less conserved flanking regions (N- and C-termini). Specifically, the principal question we wished to address in this manuscript was to what extent can the 10 Arabidopsis NF-YB paralogs functionally substitute the genes NF-YB2 and NF-YB3 in the promotion of photoperiodic flowering? Our results demonstrate that the conserved histone fold domains (HFD) may be under pressure for purifying (negative) selection, while the non-conserved N- and C-termini may be under pressure for diversifying (positive) selection, which explained each paralog's ability to substitute. In conclusion, our data demonstrate that the N- and C-termini may have allowed the duplicated genes to undergo functional diversification, allowing the retention of the duplicated genes.

OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice

The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.

Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP

Apolipoprotein (apo) E4 is the major genetic risk factor for Alzheimer's disease. While neurons generally produce a minority of the apoE in the central nervous system, neuronal expression of apoE increases dramatically in response to stress and is sufficient to drive pathology. Currently, the molecular mechanisms of how apoE4 expression may regulate pathology are not fully understood. Here, we expand upon our previous studies measuring the impact of apoE4 on protein abundance to include the analysis of protein phosphorylation and ubiquitylation signaling in isogenic Neuro-2a cells expressing apoE3 or apoE4. ApoE4 expression resulted in a dramatic increase in vasodilator-stimulated phosphoprotein (VASP) S235 phosphorylation in a protein kinase A (PKA)-dependent manner. This phosphorylation disrupted VASP interactions with numerous actin cytoskeletal and microtubular proteins. Reduction of VASP S235 phosphorylation via PKA inhibition resulted in a significant increase in filopodia formation and neurite outgrowth in apoE4-expressing cells, exceeding levels observed in apoE3-expressing cells. Our results highlight the pronounced and diverse impact of apoE4 on multiple modes of protein regulation and identify protein targets to restore apoE4-related cytoskeletal defects.

BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells

Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of regulator of imprinted sites (BORIS), also known as CCCTC binding factor-like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of melanoma cells from an intermediate melanocytic state toward a more mesenchymal-like state. However, the mechanism underlying this transcriptional switch remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in melanoma cells harboring an intermediate melanocytic state. The gene set that gained promoter accessibility, following ectopic BORIS expression, showed enrichment for biological processes associated with melanoma invasion, while promoters of genes associated with proliferation showed reduced accessibility. Integration of ATAC-seq and RNA-seq data demonstrated that increased chromatin accessibility was associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes were associated with repressed activity of tumor suppressors and proliferation factors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of melanoma cells toward a mesenchymal-like genetic signature.

Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications

Histone modifications are epigenetic mechanisms, termed relative to genetics, and they refer to the induction of heritable changes without altering the DNA sequence. It is widely known that DNA sequences precisely modulate plant phenotypes to adapt them to the changing environment; however, epigenetic mechanisms also greatly contribute to plant growth and development by altering chromatin status. An increasing number of recent studies have elucidated epigenetic regulations on improving plant growth and adaptation, thus making contributions to the final yield. In this review, we summarize the recent advances of epigenetic regulatory mechanisms underlying crop flowering efficiency, fruit quality, and adaptation to environmental stimuli, especially to abiotic stress, to ensure crop improvement. In particular, we highlight the major discoveries in rice and tomato, which are two of the most globally consumed crops. We also describe and discuss the applications of epigenetic approaches in crop breeding programs.

Single-cell genetic models to evaluate orphan gene function: The case of QQS regulating carbon and nitrogen allocation

We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.

The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans

Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].

The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans

Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].