Molecular cloning and preliminary functional analysis of two novel human KRAB zinc finger proteins, HKr18 and HKr19

Gene network analyses of larvae under different egg-protecting behaviors provide novel insights into immune response mechanisms of Amphioctopus fangsiao

Amphioctopus fangsiao was a representative economic species in cephalopods, which was vulnerable to marine bacteria. Vibrio anguillarum was a highly infectious pathogen that have recently been found to infect A. fangsiao and inhibit its growth and development. There were significant differences in the immune response mechanisms between egg-protected and egg-unprotected larvae. To explore larval immunity under different egg-protecting behaviors, we infected A. fangsiao larvae with V. anguillarum for 24 h and analyzed the transcriptome data about egg-protected and egg-unprotected larvae infected with 0, 4, 12, and 24 h using weighted gene co-expression networks (WGCNA) and protein-protein interaction (PPI) networks. Network analyses revealed a series of immune response processes after infection, and identified six key modules and multiple immune-related hub genes. Meanwhile, we found that ZNF family, such as ZNF32, ZNF160, ZNF271, ZNF479, and ZNF493 might play significant roles in A. fangsiao immune response processes. We first creatively combined WGCNA and PPI network analysis to deeply explore the immune response mechanisms of A. fangsiao larvae with different egg-protecting behaviors. Our results provided further insights into the immunity of V. anguillarum infected invertebrates, and laid the foundation for exploring the immune differences among cephalopods with different egg protecting behaviors.

Knockdown of ZNF479 inhibits proliferation and glycolysis of gastric cancer cells through regulating β-catenin/c-Myc signaling pathway

Gastric cancer is the fifth most common malignancy and the third most deadly tumor in the world. Zinc finger protein 479 (ZNF479) has been demonstrated to play crucial roles in hepatocellular carcinoma. However, the function of ZNF479 in gastric cancer remains to be clarified. The current study aimed to investigate the role of ZNF479 in gastric cancer progression and elucidate the potential molecular mechanism. In this study, Cell Count Kit-8 and colony formation assays demonstrated that knockdown of ZNF479 inhibited cell proliferation in AGS and SGC-7901 cells. Of note, knockdown of ZNF479 hinders tumor growth of xenograft tumor mice. What is more, knockdown of ZNF479 inhibited glucose uptake, lactate production, adenosine triphosphate level, and extracellular acidification ratio; increased oxygen consumption ratio in gastric cancer cells; and decreased the expression of glycolytic proteins both in vitro and in vivo. Furthermore, analysis mechanism suggests that ZNF479 participated in the regulation of gastric cancer progression through affecting the β-catenin/c-Myc signaling pathway. Collectively, ZNF479 plays a role as an oncogene through modulating β-catenin/c-Myc signaling pathway in the development of gastric cancer, which provides a new research target for future studies.

ZNF479 downregulates metallothionein-1 expression by regulating ASH2L and DNMT1 in hepatocellular carcinoma

Decreased expression of metallothionein-1 (MT-1) is associated with a poor prognosis in hepatocellular carcinoma (HCC). Here, we found that MT-1 expression was suppressed by 14-3-3ε, and MT-1 overexpression abolished 14-3-3ε-induced cell proliferation and tumor growth. We identified that 14-3-3ε induced expression of ZNF479, a novel potential transcriptional regulator by gene expression profiling and ZNF479 contributed to 14-3-3ε-suppressed MT-1 expression. ZNF479 induced the expression of DNMT1, UHRF1, and mixed-lineage leukemia (MLL) complex proteins (ASH2L and Menin), and increased tri-methylated histone H3 (H3K4me3) levels, but suppressed H3K4 (H3K4me2) di-methylation. ZNF479-suppressed MT-1 expression was restored by silencing of ASH2L and DNMT1. Furthermore, ZNF479 expression was higher in HCC tissues than that in the non-cancerous tissues. Expression analyses revealed a positive correlation between the expression of ZNF479 and DNMT1, UHRF1, ASH2L, and Menin, and an inverse correlation with that of ZNF479, ASH2L, Menin, and MT-1 isoforms. Moreover, correlations between the expression of ZNF479 and its downstream factors were more pronounced in HCC patients with hepatitis B. Here, we found that ZNF479 regulates MT-1 expression by modulating ASH2L in HCC. Approaches that target ZNF479/MLL complex/MT-1 or related epigenetic regulatory factors are potential therapeutic strategies for HCC.

KAP1 protein: an enigmatic master regulator of the genome

In mammalian cells, multiple cellular processes, including gene silencing, cell growth and differentiation, pluripotency, neoplastic transformation, apoptosis, DNA repair, and maintenance of genomic integrity, converge on the evolutionarily conserved protein KAP1, which is thought to regulate the dynamic organization of chromatin structure via its ability to influence epigenetic patterns and chromatin compaction. In this minireview, we discuss how KAP1 might execute such pleiotropic effects, focusing on genomic targeting mechanisms, protein-protein interactions, specific post-translational modifications of both KAP1 and associated histones, and transcriptome analyses of cells deficient in KAP1.

Localization and differential expression of the Krüppel-associated box zinc finger proteins 1 and 54 in early mouse development

Upon fertilization, the zygotic genome is activated. To ensure the transcription of specific genes and avoid promiscuous gene expression, a chromatin-mediated repressive state is established. To characterize potential heterochromatin factors present during the first cleavage, two putative transcriptional repressors, zinc finger protein (ZFP1) and ZFP54, belonging to the Krüppel-associated box (KRAB) zinc finger family, were isolated. ZFP1 and ZFP54 contain an N-terminally located KRAB repressor domain followed by 8 and 12 repeats of Krüppel zinc-finger motifs, respectively. Reverse transcription (RT) and quantitative (q) PCR show that maternally contributed Zfp1 and Zfp54 mRNA are detected throughout preimplantation development. α-Amanitin-treated zygotes revealed that maternal Zfp1 and Zfp54 are fully degraded at the two-cell stage. Microinjections of in vitro-transcribed mRNA encoding a gfp-fused reporter gene into zygotes demonstrated the intracellular distribution of ZFP1-green fluorescent protein (GFP) and ZFP54-GFP colocalized with a DNA marker in the two-cell embryo. The KRAB domain was essential to colocalize with DNA, and deletion of the KRAB domain in ZFP1-GFP and ZFP54-GFP localized in nucleoli and in a ubiquitously manner, respectively. Taken together, this suggests a role for ZFP1 and ZFP54 in transcriptional regulation in early development.

Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes

Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have continued in each mammalian group. One such family encodes KRAB-zinc finger (KRAB-ZNF) proteins, which function as transcriptional repressors. One particular subfamily of KRAB-ZNF genes, including ZNF91, has expanded specifically in primates to comprise more than 110 loci in the human genome. Genes of the ZNF91 subfamily reside in large gene clusters near centromeric regions of human chromosomes 19 and 7 with smaller clusters or isolated copies in other locations. Phylogenetic analysis indicates that many of these genes arose before the split between the New and Old World monkeys, but the ZNF91 subfamily has continued to expand and diversify throughout the evolution of apes and humans. Paralogous loci are distinguished by divergence within their zinc finger arrays, indicating selection for proteins with different regulatory targets. In addition, many loci produce multiple alternatively spliced transcripts encoding proteins that may serve separate and perhaps even opposing regulatory roles because of the modular motif structure of KRAB-ZNF genes. The tissue-specific expression patterns and rapid structural divergence of ZNF91 subfamily genes suggest a role in determining gene expression differences between species and the evolution of novel primate traits.

A novel Krüppel-Associated Box identified in a panel of mammalian zinc finger proteins

Krüppel-related zinc finger proteins probably constitute the largest individual family of transcription factors in mammals. These proteins often carry a potent repressor domain called the Krüppel Associated Box (KRAB), which is known to effectively repress transcription through interaction with transcriptional intermediary factor 1beta (TIF1beta). Here we report the isolation and characterization of a novel human KRAB A zinc finger protein, HZF12. The gene encoding HZF12 is located on Chromosome (Chr) 19p13.11-p12, and a 4.4-kb transcript from this gene is expressed in a variety of adult and fetal tissues. Two additional, larger transcripts are expressed in testis only. Interestingly, the KRAB A domain of HZF12 is followed by a 21-amino acid domain, encoded by a separate exon. This domain, which we designate KRAB C, was also identified in more than 25 additional human, mouse, and rat KRAB zinc finger proteins. On the basis of results from a previous study, we conclude that this novel KRAB domain strengthens the interaction with TIF1beta, thereby improving the ability of these KRAB zinc finger proteins to recruit TIF1beta to specific sites.

MZF6D, a novel KRAB zinc-finger gene expressed exclusively in meiotic male germ cells

Spermatogenesis takes place in the seminiferous tubule in the testes and culminates in the production of spermatozoa (male gametes). Here we report the identification of a novel mouse zinc-finger gene, MZF6D, which is selectively expressed in meiotic spermatocytes. The MZF6D protein contains an N-terminally located repressor domain, a KRAB domain, followed by at least seven successive Krüppel zinc-finger motifs. The KRAB domain of MZF6D, which consists of a KRAB A box and the newly identified KRAB C box, has previously been shown to interact with TIF1beta, which is the common corepressor of all KRAB zinc-finger proteins. Northern blot analysis shows that the expression of MZF6D is restricted to testes. This was confirmed by RT-PCR analysis of a panel of mouse tissues. In situ hybridization of sections from adult mouse testes localizes the expression to meiotic spermatocytes, suggesting a specific role for MZF6D in the regulation of spermatogenesis.

Rat tenascin-R gene: structure, chromosome location and transcriptional activity of promoter and exon 1

Tenascin-R is an extracellular matrix protein expressed exclusively in the central nervous system where it is thought to play a relevant role in regulating neurite outgrowth. We have i) cloned the cDNA of the rat tenascin-R 5' region; ii) defined its genomic organization, obtaining the sequence of two novel untranslated exons; iii) mapped the gene to rat chromosome 13q23 and suggested a previously unreported synteny between rat chromosome 13q23, human chromosome 1q24, and mouse chromosome 4E; and iv) sequenced and characterized the elements responsible for its neural cell-restricted transcription. We found that two discrete regions of the rat gene (the first in the proximal promoter, the second in the first exon) are independently able to activate to a high degree the transcription of a reporter gene in either human or rat neuroblastoma cell lines but not in other cell lines. Based on this observation, we re-evaluated the arrangement of transcriptionally active regions in the human tenascin-R gene we recently cloned and found that the human gene also contains an exon sequence able to initiate and sustain transcription independently of promoter sequences.