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Should Genome Editing Replace Embryo Selection Following PGT?
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
An improvement came in the early 1990s with the introduction of zinc finger nucleases (ZFNs) and transcription-activator-like effector nucleases (TALENs), which could be engineered in order to induce DSBs at specified sites. ZFNs utilize zinc finger protein domains that bind to a 3-bp motif in a modular manner, making them ideal as building units for the creation of sequence-specific DNA binding nucleases (19). TALENs, on the other hand, recognize a single base in each repeat domain, allowing up to four different domains to be mixed and matched to generate a novel DNA binding protein. However, both of these programmable nucleases are associated with an appreciable incidence of “off-target” effects, defined as non-specific cleavage of the DNA at locations other than the intended target site, potentially resulting in cytotoxicity (19,21). Furthermore, since the target specificity is determined by modification of the DNA binding domain, the application of these nucleases is limited to cases where successful engineering of binding domains is possible, at significant cost of time and resources.
ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
In Figure 9.2 we can see a perfect example of why quality control is important. CTCF is a zinc finger protein which co-localizes with the Cohesin complex. SMC3 is a sub unit of the Cohesin complex, and we would therefore expect to see that the SMC3signal profile has high correlation with the CTCF signal profile. This is true for the second biological replicate of SMC3, while the first replicate (SMC3_r1) clusters with the input samples. This indicates that the sample likely has low enrichment. We can see that the ChIP and Input samples form separate clusters. This implies that the ChIP samples have an enrichment of fragments. Additionally, we see that the biological replicates of other experiments cluster together.
Genetics of Endocrine Disorders and Diabetes Mellitus
Published in George H. Gass, Harold M. Kaplan, Handbook of Endocrinology, 2020
Bess Adkins Marshall, Abby Solomon Hollander
GHF-1, which is also known as Pit-1 or GC1, is a pituitary-specific factor that has been found to bind to two cis-acting elements within the GH promoter.14 The gene and protein have been sequenced in humans and rodents. At the amino acid level, there is 96% identity between the human and mouse sequences, and at the DNA level, identity is 90%, indicating a high level of conservation of structure and function.10 GHF-1 is a member of the POU domain family of transcriptional regulators. The POU-domain proteins have important developmental and transcriptional functions. During development of the fetal mouse, the detectability of GHF-1 protein accumulation coincides with the earliest time that GH transcription is evident, indicating that GHF-1 plays a role in pituitary cell differentiation.15 A zinc finger protein involved in GHF-1 activation of the GH promoter has recently been described.16 This protein, called Zn-15, binds to a sequence of GH called the GH-Z box. The binding of Zn-15 to GH appears to be critical for GHF-1-dependent GH expression.
Clear cell carcinoma of the ovary and venous thromboembolism: a systematic review and meta-analysis
Published in Current Medical Research and Opinion, 2023
Hamidreza Didar, Farah Farzaneh, Hanieh Najafiarab, Kosar Namakin, Kimiya Gohari, Ali Sheidaei, Sepehr Ramezani
Therefore, multiple analyses were performed based on the geographic location of studies, the tumor stage at the incidence of VTE, and study types. Among all locations, the pooled prevalence of VTE among OCCC patients was higher in Japan (26.15%), which was two times higher than China (13.61%). A meta-analysis by Kristin S. Weeks on the VTE risk in ovarian cancer patients59 demonstrated that Japanese women with ovarian cancer had a higher risk of VTE events (20%) compared with Chinese women (8%). However, most studies demonstrating VTE events in OCCC were performed in Japan, while few studies were carried out in China. A study revealed that amplification of Zinc Finger Protein 217 (ZNF217) was noticeably higher in Japanese clear cell tumor samples as compared with Korean and German specimens. ZNF217 may promote neoplastic transformation by promoting cell survival during the telomeric crisis, leading to the survival of tumor cells and promoting later stages of malignancy60. VTE prevalence was higher among patients with advanced stages almost in all studies. Shuang Ye et al.41 revealed the higher prevalence of VTE in the advanced stages of OCCC (21.9%) than in the early stages (8.2%). Moreover, Matsuura et al.50 showed that VTE was more common in the advanced stages of OCCC (66.66% [16/24]) than in the early stages (28.57% [12/42]). These findings indicate a possible connection between the amplification of ZNF217 and the promotion of clear cell carcinoma to advanced stages in Japanese women compared to others. More VTE events are expected at more advanced cases.
miR-34a inhibits proliferation, migration and invasion of paediatric neuroblastoma cells via targeting HNF4α
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2019
Hepatocyte nuclear factor 4α (HNF4α) belongs to the steroid hormone receptor superfamily, which can regulate cell differentiation and metabolism at the transcriptional level. Human HNF4α is located on 20q13.12 chromosome. It is a highly conserved zinc finger protein, which can be activated by various pathways such as acetylated phosphorylation. It binds with the target gene promoter sequence to form a dimer and regulates chromosomal structure, hepatocyte polarization and cholesterol metabolism [21]. Some studies found that HNF4α can be used as a marker for the diagnosis of invasive mucinous adenocarcinoma, and has inhibitory effect on colon cancer. Knocking out HNF4α can promote the metastasis of colon cancer and contribute to the occurrence and development of colon cancer [22,23]. In neuroblastoma cells, HNF4α can promote cell invasion, metastasis and angiogenesis by targeting MMP-14. The lower differentiation of neuroblastoma and higher expression level of HNF4α, the shorter survival time of patients [24]. In this study, HNF4αwas knocked down by RNA interference in SH-SY5Y cells, the ability of proliferation, migration and invasion was decreased (p < .05), and the expression of MMP-2 and MMP-14 was down-regulated at mRNA and protein levels (p < .05). Overexpression of HNF4α reversed the inhibitory effect of miR34a on proliferation, migration and invasion of SH-SY5Y cells.
Paget’s disease of bone: an update on epidemiology, pathogenesis and pharmacotherapy
Published in Expert Opinion on Orphan Drugs, 2018
Luigi Gennari, Domenico Rendina, Tommaso Picchioni, Simone Bianciardi, Maria Materozzi, Ranuccio Nuti, Daniela Merlotti
This gene encodes for a zinc finger protein that together with ZMYND8 and ZNF592, is part of the recently described transcriptional regulator complex Z3 [81]. The P397R mutation probably acts as a gain of function change, since it involves a nuclear localization signal and has been associated with enhanced availability of this transcription factor in the nucleus [80]. Although the exact function of ZNF687 in bone metabolism remains unknown, the gene is highly expressed during either osteoclastogenesis or osteoblastogenesis and is dramatically upregulated in the tumor tissue of individuals with GCT and PDB [80]. In addition, osteoclast derived from peripheral blood mononuclear cells of P397R mutation carriers are larger and shows a greater number of nuclei per cell than those derived from the control individuals, both representing peculiar features of pagetic osteoclasts [80].