Non-histone binding functions of PHD fingers

Gaurav, Nitika; Kutateladze, Tatiana G.

doi:10.1016/j.tibs.2023.03.005

Cited by 9 publications

(8 citation statements)

References 58 publications

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“…S6B,D, Table S3), however none of them was specific to H3. PHD fingers have been reported to bind non-H3 partners, like DNA, histone 4, or other proteins (Bienz, 2006; Black & Kutateladze, 2023; Gaurav & Kutateladze, 2023; L. Liu et al, 2012; Oppikofer et al, 2017). The combination of the PHD and PHD-zinc-finger-like domain in the DevPFs may enable the paralogs to simultaneously recognize two adjacent histone modifications, as demonstrated for tandem PHD domains (Zeng et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

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Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing

Häußermann,

Singh,

Swart

2024

Preprint

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The unicellular eukaryoteParamecium tetraureliacontains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sexual reproduction, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique Internal Eliminated Sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IESs excision occurs. InDevPF2knockdown (KD) long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed inDevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced byDevPF1-andDevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.

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Section: Discussionmentioning

confidence: 99%

Section: Implications Of the Phd Domain For Devpf1 And Devpf2 Functionsmentioning

confidence: 99%

Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing

Häußermann,

Singh,

Swart

2024

Preprint

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“…The PHD is a structural pattern common to all eukaryotic genomes [ 36 , 37 ]. Previous studies have shown that the PHD as a bridge between protein and histone binding, regulating gene expression and modifications [ 38 , 39 ].…”

Section: Discussionmentioning

confidence: 99%

PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway

Cheng,

Cao,

Yao

et al. 2023

Cell Death Dis

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At present, non-small cell lung cancer (NSCLC) is still one of the leading causes of cancer-related deaths. Chemotherapy remains the standard treatment for NSCLC. However, the emergence of chemoresistance is one of the major obstacles to lung cancer treatment. Plant homologous structural domain finger protein 23 (PHF23) plays crucial roles in multiple cell fates. However, the clinical significance and biological role of PHF23 in NSCLC remain elusive. The Cancer Genome Atlas data mining, NCBI/GEO data mining, and western blotting analysis were employed to characterize the expression of PHF23 in NSCLC cell lines and tissues. Statistical analysis of immunohistochemistry and the Kaplan–Meier Plotter database were used to investigate the clinical significance of PHF23. A series of in vivo and in vitro assays, including assays for colony formation, cell viability, 5-ethynyl-2’-deoxyuridine (EDU incorporation) and Transwell migration, flow cytometry, RT-PCR, gene set enrichment analysis, co-immunoprecipitation analysis, and a xenograft tumor model, were performed to demonstrate the effects of PHF23 on the chemosensitivity of NSCLC cells and to clarify the underlying molecular mechanisms. PHF23 is overexpressed in NSCLC cell lines and tissues. High PHF23 levels correlate with short survival times and a poor response to chemotherapy in NSCLC patients. PHF23 overexpression facilitates cell proliferation, migration and sensitizes NSCLC cells to Cisplatin and Docetaxel by promoting DNA damage repair. Alpha-actinin-4 (ACTN4), as a downstream regulator, interacts with PHD domain of PHF23. Moreover, PHF23 is involved in ACTN4 stabilization by inhibiting its ubiquitination level. These results show that PHF23 plays an important role in the development and progression of NSCLC and suggest that PHF23 may serve as a therapeutic target in NSCLC patients.

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“…These genes predominantly encode Vernalization Insensitive 3-like proteins, characterized by Oberon-like, PHD finger domain (PHD), and Fibronectin Type III (FN3) domains (refer to Supplementary Figure S1). These Vernalization Insensitive 3-like proteins feature a plant homeodomain (PHD) that suppresses the FLOWERING LOCUS C (FLC) gene family, thus inhibiting flowering during vernalization [26][27][28].…”

Section: Differential Gene Screening Identified Genes Associated With...mentioning

confidence: 99%

Identification of a Rye Spring Mutant Derived from a Winter Rye Variety by High-Altitude Environment Screening Using RNA Sequencing Technology

Wang,

Liu,

et al. 2024

Genes

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Wintergrazer-70 and Ganyin No1 are high-yield forage varieties suitable for cultivation in high-altitude areas of Tibet (4300 m above sea level). Ganyin No1 was developed from Wintergrazer-70, with the latter serving as its parent variety. Ganyin No1 was identified as a spring variety, and subsequent RNA sequencing was conducted. RNA sequencing analysis identified 4 differentially expressed genes related to vernalization and 28 genes related to photoperiod regulation. The Sc7296g5-i1G3 gene is related to the flowering inhibition of rye, which may be related to the phenotypic difference in the Ganyin No1 variety in winter and spring. This finding provides valuable insights for future research on Ganyin No1, especially in addressing feed shortages in Tibet during winter and spring.

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Non-histone binding functions of PHD fingers

Cited by 9 publications

References 58 publications

Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing

Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing

PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway

Identification of a Rye Spring Mutant Derived from a Winter Rye Variety by High-Altitude Environment Screening Using RNA Sequencing Technology

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