Genetics III-Essay assignment

Selama kuliah ini matkul isinya hampir semuanya berkaitan sama DNA dan kawan-kawannya yang saya nggak paham. Rasanya semakin dipelajari semuanya terlihat semakin rumit, apalagi mereka itu nggak gampang bisa dilihat dengan mata jadi seakan semuanya itu cuma teori dan imajinasi dari para peneliti. Tapi memang sekarang ini ya jamannya molekular biologi. 
Tulisan di bawah ini salah satu contoh writing assignment di kelas Genetics III, mungkin bisa membantu kalo ada temen-temen yang punya tugas serupa ^^
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KLF4 (Kruppel-like factor 4)


The Kruppel-like factor (KLF) family is a group of zinc finger containing transcription factors, which are identical with the Drosophila Kruppel protein. The characteristic that distinguishes the KLF family from other zinc finger containing transcriptional factors is the presence of three highly conserved C2H2 containing zinc finger motifs at the C terminus. These fingers enable KLFs to bind to the GC-box or CACCC-boxes on DNA with different affinities.
Kruppel-like factor 4 (KLF4) is one of the member of the KLF family of transcription factors and encodes a polypeptide of 483 amino acids. It contains two potent nuclear localization signals (NLSs), one within the three zinc fingers and the other in a cluster of basic amino acids immediately adjacent to the first zinc finger. These two NLSs define a subfamily of three closely related KLFs: KLF1, KLF2, and KLF4. KLF4 binds to the promoter region of its own gene and can activate its own transcription and generally can act both as activator and as repressor. In humans, the protein is encoded by the KLF4 gene. The KLF4 gene is conserved in drosophila, chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebra fish, and frog.




Figure 1: Structure of KLF4. KLF4 has an N-terminal transcriptional activation domain, followed by a transcriptional repression domain, containing two lysine residues K225 and K229. These residues are acetylated by p300/CBP, which interacts with the activation domain. There lies a potential PEST sequence between the activation and repression domains. The C-terminus has a DNA binding domain containing three zinc fingers, which recognize and bind to the GC/CACCC target sequences in the nucleus. A Nuclear Localization Signal (NLS) (6 a.a.) is placed between the DNA binding and repression domains, which facilitates the transport of KLF4 into the nucleus. Please note that the size of each domain is not exactly proportional. (Hima Vangapandu and Walden Ai,2009)

Expression of the KLF4 gene is developmentally regulated and its higher expression is occurred in the later stage of fetal development. In adults, KLF4 is highly enriched in epithelial tissues, including the skin, lung, and intestine. Expression of KLF4 can also be found in a select number of other organs including the testis, thymus, and in vascular endothelial cells. Forced expression of KLF4 in cultured cells results in the inhibition of DNA synthesis.
KLF4 regulates proliferation, differentiation for instance goblet cell differentiation in the intestine and eye conjunctiva, apoptosis and somatic cell reprogramming which already proven by Takahashi and Yamanaka in 2006 that they reprogrammed somatic cells into pluripotent stem cells using KLF4 in combination with three other transcription factors: Oct4, Sox2 and c-Myc. It also regulates the expression of key transcription factors during embryonic development and maintains embryonic stem cells by inhibiting cell cycle progression. In addition, KLF4 seems to play a redundant role along with other KLF family proteins in embryonic stem (ES) cell self-renewal. There are still many other functions that are owned by KLF4 such as it maintains normal tissue homeostasis and it acts as a transcriptional activator of epithelial genes and as a repressor of mesenchymal genes. Evidence also suggests that KLF4 is a tumor suppressor in certain cancers, including colorectal cancer, but sometimes it can be an oncogene depending on differing cellular context and cancer types.





Figure 2: Multiple context-dependent functions of KLF4. Up regulation or over expression of KLF4 promotes cell differentiation, inhibits cell proliferation, and induces cell cycle arrest, down-regulates apoptosis for maintaining tissue homeostasis. It functions as a tumor suppressor in cancers of some tissues and as an oncogene in some tissues like those of breast. KLF4 is instrumental in stem cell renewal and generation of induced pluripotent stem cells (iPS cells). (Hima Vangapandu and Walden Ai,2009)

KLF4 has been shown to be down-regulated by integration of different signaling pathways, including Notch and Wnt. These signaling pathways are responsible in expression in stem cells, cancer cells, and tumorigenesis. It contributes to the down-regulation of p21WAF1/CIP1, a critical checkpoint protein that inhibits cell cycle progression and is essential in mediating the cell cycle arrest at both the G1/S and G2/M boundaries. KLF4 mediates the cell cycle checkpoint function of the tumor suppressor p53 suggesting that it may itself act as a tumor suppressor. KLF4 can also down-regulate the level of beta-catenin to inhibit beta-catenin-mediated transcription. In addition, KLF4 inhibits expression of the cell cycle-promoting genes CCND1 (cyclin D1) and CCNB1 (cyclin B1).  In response to DNA damage, KLF4 suppresses transcription of the gene that encodes cyclin E and prevents chromosomal amplification.




Figure 3. Both Krüppel-like transcription factor 4 (KLF4) and p21 (also known as CIP1/WAF1) are targets of multiple tumour-suppressor pathways. KLF4 has been shown to mediate p53–p21 signalling in response to DNA damage23, 62. We speculate that KLF4 is also a mediator of transforming growth factor-beta (TGFbeta)–p21 and adenomatosis polyposis coli (APC)–p21 signalling, thereby relaying signals elicited by multiple key tumour-suppressor pathways. (Benjamin D. Rowland and Daniel S. Peeper,2006)




Figure 4. Many oncogenic signaling pathways have contradictory effects, depending on the setting, which allows them to function as either stimulators or inhibitors of cellular proliferation. (Explanation only shown that related to KLF4). a | Although Krüppel-like transcription factor 4 (KLF4) represses transcription of TP53 (the gene that encodes p53), thereby preventing senescence and inducing resistance to drug-induced apoptosis, it activates p21 (also known as CIP1/WAF1)-dependent cell-cycle arrest. d | When KLF4 is expressed in cells that express an activated form of Ras (RasV12), however, their mutual inhibition of anti-proliferative signaling results in oncogenic transformation. e | A similar mechanism could occur in cells that co-express KLF4 and E1A. (Benjamin D. Rowland and Daniel S. Peeper,2006)

Another example of KLF4 regulation is that KLF4 interacts with p300 histone acetyltransferase and regulates gene transcription by modulating histone acetylation. In case of iPSC, The KLF4 C terminus which contains three tandem zinc fingers is required for activation of the target gene Nanog. It functions upstream of Nanog in ES cell self-renewal and in preventing ES cell differentiation.





Figure 5. Klf4 as part of a transcriptional regulatory circuit for somatic cell reprogramming. A model of the transcriptional hierarchy of the reprogramming transcription factors: Klf4, Sox2, Oct4, and c-Myc. Klf4 is shown as an upstream regulator of feed-forward transcription loops; it binds the promoters of Oct4, Sox2, c-Myc, and the downstream target Nanog. Klfs 2 and 5 can substitute for Klf4 in somatic cell reprogramming. (Beth B. McConnell and Vincent W. Yang, 2010)





References
Benjamin D. Rowland and Daniel S. Peeper. KLF4, p21 and context-dependent opposing forces in cancer. Nature Reviews Cancer.[Online]2006; 6, 11-23.Available from:  http://www.nature.com/nrc/journal/v6/n1/full/nrc1780.html [Accessed October 25th 2014].
Beth B. McConnell and Vincent W. Yang. Mammalian Krüppel-Like Factors in Health and Diseases. Physiological Reviews.[Online]2010; (.Available from:  10.1152/physrev.00058.2009 [Accessed November 6th 2014].
Hima Vangapandu and Walden Ai. Kruppel like factor 4 (KLF4): a transcription factor with diverse context-dependent functions. Gene Ther Mol Biol. [Online]2009; 194-204.[.Available from:  http://www.gtmb.org/pages/13/HTML/17.%20Ai%20et%20al%20194-204.htm [Accessed November 4th 2014].
Kazutoshi Takahashi and Shinya Yamanaka. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell Stem Cell. .[Online]2006;126(4):663-676.Available from: http://dx.doi.org/10.1016/j.cell.2006.07.024 [Accessed November 6th 2014].
Shinya Yamanaka. Strategies and New Developments in the Generation of Patient-Specific Pluripotent Stem Cells. Cell Stem Cell. [Online]2007;1(1):39-49.Available from: http://dx.doi.org/10.1016/j.stem.2007.05.012 [Accessed November 6th 2014].
Wei Z et al. Klf4 interacts directly with Oct4 and Sox2 to promote reprogramming. Stem Cells. .[Online]2009; 27(12):2969-78.Available from:  http://www.ncbi.nlm.nih.gov/pubmed/19816951 [Accessed October 25th 2014].
Ying Shi and Walden Ai. Function of KLF4 in Stem Cell Biology. Intech.[Online]2013.Available from:  10.5772/54370 [Accessed October 25th 2014].









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