The ANKRD42 Gene - Dissertation Example

 The ANKRD42 Gene The ANKRD42 is an acronym for Ankyrin Repeat Domain containing protein 42. It is conserved in Homo sapiens who are the hosts (ncbi.nlm.nih.gov). It is also referred to as polyclonal ANKRD42 antibody, Anti-ANKRD42 antibody, Ankryin Repeat domain 42 antibody or SARP, PPP1R79. It is a rabbit polyclonal ANKRD42 antibody that is raised against the N terminal of the gene (Kozlov, 2014). SARP is a 389 amino acid protein that exists in the form of two isoforms that are spliced alternatively and contain 9 ANK repeats. The features of ANKRD42 gene are annotated in the two cDNA clones. The gene is found at the highest levels in the sperm and testis. ANKRD42 is universally expressed and is encoded be a gene that is located on chromosome 11 in humans. The chromosome has over 1400 genes and makes up about 4% of the human genome (Hoh, 2010). Ankryins can be defined as membrane adaptor molecules that perform the crucial role of coupling integral proteins of the membrane to the cytoskeleton network based on the spectrin. The ANKRD42 gene is a promoter which lacks in methylation is all cell lines at any point in time. Mutations of this gene results in some severe genetic diseases such as hereditary spherocytosis and cardiac arrhythmias. It has been proposed that the gene is a participant in the regulation of DNA-dependent transcription process. As a protein, it is expected to have molecular functions such binding of DNA and activity of transcription factor. However, the function of Ankryin protein has not been widely studied and hence it has not been fully clarified in research. UCSC Genes track are utilised to show the predictions of the genes based on data obtained from various sources such as Refseq, GenBank and CCDS. It entails the use of the support of a GenBank RNA sequence and aone or more additional lines of evidence. The RNAs from RefSeq however do not require the provision of additional evidence. Both protein coding and acknowledged non-coding transcripts are used to provide results in the tests. Colour keys utilised include black, dark blue, medium blue and light blue. When all the unique transcripts are generated on a graph, protein prediction is generated and a designated program is used to determine whether a transcript is protein coding. If so, the program determines the locations of the start and stop codons. The length of the protein, the presence of the Kozak consensus sequence at the start codon and the length of the reference predicted protein are weighed by the program as positive (Hsu et.al, 2006). From the research, the results show that the ANKRD42 gene was found to exhibit bright bands of the expected size. Ciliated cells exhibited strong immuno-reactivity in cilia, neuronal cells were moderately stained while other normal cells exhibited weak stains or negative expression. The gene is well expressed with the expression being detected in normal cells including the testis, brain cerebellum, foetal brain, heart, rathke’s pouches, cecum, urinary bladder, spinal cord, prostate, salivary gland, thymus, skeletal muscle and small intestine among other tissues. Due to this it was put aside and no further tests were conducted to investigate its potential as a cancer marker. MAEL Gene The MAEL gene is described as maelstrom spermatogenic transposon silencer which creates a protein that was initially located in Drosophila melanogaster in the nuage perinuclear structure (Findley et.al, 2003). It is believed to have a functionality that is similar to the dpinfle gene class. The gene Maelstrom is a protein-coding gene that is associated with diseases such as gonorrhoea and essential hypertension. The gene encode a novel protein that is distributed in the cytoplasm of the nurse cell as well as the oocyte until the protein disappears in the stage 7 of oogenesis. The MAEL gene is essential in spermatogenesis by preventing the mobilization of transposable elements (TEs) which it inhibits during the process. This ensures the germline integrity. It also ensures the inhibition of transposable elements during meiosis by the piRNA metabolic process. This entails the formation of complexes of Piwi-associated RNAs (piRNAs) and Piwi proteins and the governing of the methylation and inhibition of jumping genes (Pek et.al, 2009). The association of MAEL gene with piP-bodies could suggest that it plays a role in the secondary piRNAs metabolic process. Recently, MAEL has been associated with human cancer. From previous experiments, MAEL expression was shown in various cancer cell types including breast cancer, lung cancer, colon cancer and breast cancer. This suggests that MAEL gene is a constituent of the class of testis or cancer gene (Xiao et.al, 2010). From the experiment, the MAEL gene was expressed in normal tissues at the expected size of the gene (417bp). The expression was in the testis, brain cerebellum and the brain as a whole, foetal brain, spinal cord, prostrate and small intestine. Since the function of the gene is unknown it is difficult to conclude but from the expression results it can be concluded that this gene was not a perfect candidate for computerized tomography (CT). However, further analysis would be necessary to draw strong conclusions. Further analysis of this gene in several cancer lines revealed its expression in the testis. Digital differential display experiments reveal that the gene in human tissue is only expressed in the testis. However, it is also expressed in some cancer cell lines. Treatment with the dimethylating agent 5'-Aza-2-Deoxycytidine regulated the expression significantly which suggests that the gene is associated with cancer gene and is regulated by DNA methylation. FSCN3 Gene FSCN3 is an acronym that stands for Fascin 3 which is designated testis fascin. It is also known as testis fascin and in humans, it is a protein that is encoded by the FSCN3 gene. The gene is a protein that is involved in the spermatid development that is specific to the testis and is actin bundling. It is a characterization of a spermatid-specific murine paralog of the actin-bundling protein fascin (FSCN1).). The gene is located in chromosome 7q31.3. Its molecular function entails protein binding, actin filament binding and bridging (Tubb et.al, 2002). Transposon activity is generally controlled tightly to ensure the integrity of the germline. This repression of the transposon is achieved with the aid of a germ cell specific organelle referred to as nuage. Studies carried out to test this hypothesis have entailed the disruption of a Drosophilia nuage protein MAEL and the results observed to view the expression of the transposable elements. The results from these experiments suggest that MAEL plays a crucial role in the depression of transposable elements in the male germline. Previous experimentation has identified the FSCN3 expression to be highly specific to the testis. In situ hybridization, the FSCN3 gene prevents its expression to elongating spermatids. From the antibodies raised against the FSCN3 protein, it is identified as a band at 56kD in testis, epididymis, and epididymis spermatozoa. This suggests that the testis fascin is localized in mature spermatozoa. In normal adults, the fascin gene is strongly expressed in vascular endothelial, neuronal and dendritic cells of the lymphoid tissue, the oesophagus and the uterine cervix (Pelosi et al, 2003). Despite the expression being homogenous to postnatal stages, some differential expression is visible during embryonic and foetal development. The gene is also widely expressed in the nervous system and gastrointestinal tract but it is absent in the liver. Hence, it is observed that the expression of the gene is highly tissue specific and cell specific throughout human development. The expression is however time specific during human growth and development with more reactivity being observed in early embryo stages. There is no mechanism to explain the up regulation of fascin protein levels in normal tissues. However, it can be assumed that the fascin gene plays a role in the interaction between cells, cell division and cell growth. From the experiment, the FSCN3 gene was expressed at the expected size of the gene (512bp). The expression was in the testis. Since the function of the gene is unknown, it is difficult to conclude. However, from the expression results it can be concluded that this gene was not a perfect candidate for computerized tomography (CT). Further analysis would still be required to draw strong conclusions. ZDHHC11 Gene It is an acronym for zinc finger, DHHC domain type containing 11. The gene type is protein coding and it is located in humans (Homo sapiens) in the Chromosome 5 - NC_000005.10. It is also known as ZNF399 and is a 412 amino acid multi-pass membrane protein, which contains one DHHC-type zinc finger. The protein is referred to as probable palmitoyl-transferase ZDHHC11. The gene encoding ZDHHC11 is located in the human chromosome 5p15.33. This chromosome contains 181 million base pairs and comprises nearly 6% of the human genome (Ohno et.al, 2006). The zinc-finger proteins have DNA-binding domains with a variety of functions that include forms of transcriptional repression or activation. The gene is thought to perform as a palmitoyl-transferase that catalyses the transformation of palmitoyl-CoA and a protein conjugated in cysteine to form an S-palmitoyl protein and a free CoA. The ZDHHC11 gene may be used as a potential biomarker in identifying and diagnosing high-risk patients with disease progression in bladder cancer. This gene codes for transcriptional factors that can be defined as gene products that are nor directly accessible by conventional antibody assays. In the characterization of transcriptional regulation network in spermatogenesis and the male reproduction process a silico-based approach is utilized to identify the candidacy of the gene in identifying transcriptional factors. From the experiment, the ZDHHC11 gene showed clear expression with bands of the correct size as expected in the gene. It was expressed in the testis, brain cerebellum, spinal cord and prostrate. Hence, it qualifies as a perfect candidate for computerized tomography. The positive nuclear staining of a limited number of male germ cells and the consequent staining of a male germ cells with perinuclear staining indicate that the ZDHHC11 gene is highly expressed in the tissues with normal cells. Hence, these results suggest that it would be fairly easy to observe the results of a CT analysis when this gene is used. In the cancer cell line, the gene produced clear bands with testis and prostrate adenocarcinoma (PC-3). However, faint bands each of the proper estimated size of the gene were detected in different cancer cell lines including Colon adenocarcinoma (HT29), Colon adenocarcinoma (LoVo), Colon adenocarcinoma (SW480), Caucasian malignant melanoma (G361), Malignant melanoma (MM127), Melanoma (COLO800), Melanoma (COLO857) and T-cell leukemia (Jurkat). Hence it can be concluded that the ZDHHC11 gene is a perfect candidate for CT. However, further analysis such as cloning of CT genes and analysis that is more detailed is necessary to determine its applicability. Bibliography Abaan O. et al., 2013. The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology. Cancer Res, 73(14) p.4372-82. Findley S., et al., 2003. Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog. Aubergine, in nuage. Dev, 130 p.859–871. Hoh, R., 2010. The Ciliated Cell Transcriptome. Carlifornia: Stanford University. Ohno, Y., et al. 2006. Intracellular Localization and Tissue-Specific Distribution of Human and Yeast DHHC Cysteine-Rich Domain-Containing Proteins. Biophys. Acta, 1761 p.474-483. Pek J., Lim A. and Kai, T., 2009. Drosophila Maelstrom Ensures Proper Germline Stem Cell Lineage Differentiation By Repressing Microrna-7. Dev. Cell. 17 p.417-424. Pelosi, G. et al., 2003. Independent Prognostic Value Of Fascin Immunoreactivity in Stage I Non-Small Cell Lung Cancer. Br J Cancer, 88 p.537–547. Tubb, B., 2002. Testis Fascin (FSCN3): A Novel Paralog Of The Actin-bundling Protein Fascin Expressed Specifically in the Elongate Spermatid Head. Exp Cell Res 275:92–109. Vignjevic, D., et al., 2007. Fascin, A Novel Target Of Beta-Catenin-TCF Signaling, Is Expressed At The Invasive Front Of Human Colon Cancer. Cancer Res, 67 p.6844–6853. Xiao, L., et al., 2010. Identification of a novel human cancer/testis gene MAEL that is regulated by DNA methylation. Molecular Biology Reports, 37 p.2355-2360. Read More