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Zinc Finger 226

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Gene

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A multiple sequence alignment of human ZNF226 and ortholog species with selected regions highlighted.

The zinc finger protein 226 (ZNF226) is encoded by the ZNF226 gene. It is also known as the Kruppel-associated box protein.[1] Within humans, the ZNF226 gene is found on the plus strand of chromosome19q13, spanning 33,192 nucleotides from 44,165,070 to 44,198,261.[2] There are six identified exon regions in ZNF226.[2]

 
A multiple sequence alignment of human ZNF226 and ortholog species with selected regions highlighted.
 
ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation

Transcript

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Currently, there are around 20 different transcript variants encoding ZNF226.[2] All of them have six or seven identified exon regions within ZNF226.[2] The longest identified transcript, ZNF226 transcript variant x4 spans 2,797 base pairs (bp).[2]

Proteins

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ZNF226 is currently known to have three isoforms within humans: ZNF226 isoform X1, ZNF226 isoform X2, and ZNF226 isoform X3.[2] The ZNF226 isoform X1 protein is the longest known variant, with 803 amino acids.[2] This protein contains the Kruppel associated box A (KRAB-A) domain, which functions as a transcriptional repressor.[3] However, the exact function of the ZNF226 protein is currently unknown. Within this isoform, there are 18 C2H2 zinc finger structural motif (zf-C2H2) domains, which are known to bind either Zn2+ or nucleic acid.[4][5] Within those regions, cysteine and histidine are what bind to zinc ions (Zn2+ ) or nucleic acid. In addition to the KRAB-A domain and zf-C2H2 domains, there are zinc finger double domains which also contain binding sites for ions or nucleic acids.[2]

ZNF226 human and ortholog protein sequences have molecular weights between 89 to 92 kDa.[6] They had isoelectric points (pI) ranging from 8.60 to 9.00.[6] In humans, the zf-C2H2 and zinc finger double domain region of ZNF226 isoform X1 is 59.3 kDa with a theoretical pI of 9.11.[6] With the spacing of cysteine, or C, there is a cysteine every three amino acids. At least one of the amino acids in between the C’s are either aspartic acid (D) or glutamic acid (E).[7] Despite the region’s patterns of aspartic acid, it is still considered to have a lesser amount of the amino acid at 1.9%.[7]There is also repetition within the chemical patterns within humans that is characteristic of ZNF226. These repetitions appear most common within the zf-C2H2 and zinc finger double domains of the protein, notably with cysteine and histidine binding sites.[7] Predicted secondary structures of ZNF226 demonstrate a variable number of alpha helices, beta-stranded bridges, and random coils throughout the protein. Using various programs, such as GOR4 and the Chou and Fasman program, there is overall similarity in the predictions of coiled, stranded, and helix regions throughout the protein.[8][9][10]

 
ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation
 
ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation

Gene Level Regulation

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Using the Genomatix software, GXP_7536741 (1142 bp) was identified as the best promoter of ZNF226.[11] Within the last 500 bp of the promoter, the signal transducer and activator of transcription (V$STAT.01), selenocysteine tRNA activating factor (V$THAP11.01), and cell cycle regulators: cell cycle homology region (V$CHR.01) were conserved among H. sapiens, Macaca mulatta, Pan troglodytes, and Canis lupus familiaris.[11] In addition, the SPI-1 proto-oncogene; hematopoietic TF PU.1 (V$SPI1.02) was also known for binding to a promoter region within the c-fes proto-oncogene which encodes tyrosine kinase.[12] The TF binding site is also found in two regions within the promoter sequence.The signal transducer and activator of transcription binding site was also conserved in two regions, and is known to have a higher binding specificity, indicating an important role in activation of transcription.[13] The selenocysteine tRNA activating factor may play a role in embryonic stem cell regeneration.[14] The cell cycle regulators: cell cycle homology region binding site plays an important role in cell survival, where mutations in the TF can lead to apoptosis.[15]

In terms of gene expression, ZNF226 is generally expressed in most tissues.[2] Microarray data illustrates higher expression of ZNF226 within the ovaries.[16] This is further supported by data which depicts a decrease in ZNF226 expression in granulosa cells within individuals with polycystic ovary syndrome.[17] There was also higher expressions of ZNF226 observed within the thyroid compared to other tissues.[2] Evidence of decreased ZNF226 expression is observed with individuals with papillary thyroid cancer.[18]

Within fetuses, there is some level of ZNF226 expression present within all tissues throughout the gestational period of 10 to 20 weeks.[2] However, there is a higher level of ZNF226 expression in the heart at 10 weeks of gestation, and a decreased level of expression within kidneys at 20 weeks gestation.[2]

ZNF226 expression has been observed within epithelial progenitor cells (EPCs) in the peripheral blood (PB) and umbilical cord blood (CB). The gene expression is lower in PB-EPCs when compared to CB-EPCs.[19] PB-EPCs have more tumor suppressor (TP53) expression when compared to CB-EPCs.[19] CB-EPCs have more angiogenic expression, or growth and splitting of vasculature.[19]

 
ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation

Transcript Level Regulation

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Using RNAfold, minimum free energy structures were created based on the extended 5’ UTR and 3’ UTR human sequences. Unconserved amino acids, miRNA, stem-loop formations, and RNA binding proteins (RBPs) are all shown on the diagram. Within the 5’ UTR region, both miR-4700-5p and miR-4667-5p were referenced in an experiment demonstrating that certain miRNAs were expressed consistently in ERBB2+ breast cancer gene.[20] In addition, miR-8089 was referenced in a study showing certain novel miRNAs found within sepsis patients.[21] miR-4271 was shown to have effects on coronary heart disease binding to the 3' UTR region of the APOC3 gene.[22] Literature on miR-7113-5p shows that this miRNA is a mirtron.[23]

Within the 3’ UTR region, miR-3143 is referenced in a study where miRNAs were expressed consistently in ERBB2+ breast cancer gene.[20] miR-152-5p plays a role in inhibiting DNA methylation of genes involved in metabolic and inflammatory pathways.[24] miR-31-3p is overexpressed in esophageal squamous cell carcinoma (ESCC).[25] One miRNA result was shown to be conserved across multiple homologs within the 3’ UTR region more than 3000 bp downstream.[26] The miR-150-5p miRNA plays a role in colorectal cancer (CRC), where a lower expression of the miRNA was associated with a suppression of CRC metastasis.[26]

In terms of some of the RBPs found, PAPBC1 had five binding sites, two of which are highlighted on the 5’ UTR. This protein is known to attach poly-a-tails for proteins that have entered the cytoplasm, preventing them from re-entry into the nucleus. The FUS protein was another one found with a binding site on a predicted stem loop. The gene encodes for a protein which facilitates transportation of the protein into the cytoplasm.[27] Within the 3’ UTR, the RBMY1A1, RBMX, and ACO1 proteins were some of the top scoring RBPs. The RBMY1A1 is a protein known to partake in splicing, and is required for sperm development.[28] The RBMX protein is a homolog of the RBMY protein involved in sperm production.[29] It is also known to promote transcription of a tumor suppressor gene, TXNIP.[29] ACO1 is another RBP found to have a binding site on the 3’ UTR, known to bind with mRNA to regulate iron levels.[30] By binding to iron responsive elements, it can repress translation of ferritin and inhibit degradation of transferring receptor mRNA when iron levels become low.[30]

Protein Level Regulation

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Analysis to predict post-translational modifications of the protein were conducted on. Based on the results of Expasy’s Myristoylator in Homo sapiens, Mirounga leonina, and Fukomys damarensis, it can be concluded that ZNF226 is not myristoylated at the N-terminus.[31] Numerous predicted binding sites for post-translational modifications were also identified among the three species.The phosphorylation region at the C-terminus of the protein was also identified as a match for the protein kinase C phosphorylation binding site.[32][33][34][35] S-nitrosylation was another identified modification at C354 (see conceptual translation). This modification is found in SRG1, a zinc finger protein that plays a role preventing nitric oxide (NO) synthesis.[36] When NO is sustained, s-nitrosylation occurs within the protein, disrupting its transcriptional repression abilities.[36] Acetylation was another modification identifed. In the case of promyelocytic leukemia, a condition resulting in the abundance of blood forming cells in the bone marrow, promyelocytic leukemia zinc finger proteins are known to be activated by histone acetyltransferases, or by acetylation of a C-terminus lysine.[37] Acetylation in other zinc finger proteins, such as GATA1, are known to enhance their ability to interact with other proteins.[38] Arginine dimethylation is another identifed modification within ZNF226. Arginine methylation of cellular nucleic acid binding protein (CNBP), a zinc finger protein, has shown to impede its ability to bind nucleic acids.[39] However, most literature supports the methylation of zinc finger proteins within their promoter regions.[40]

It is predicted that ZNF226 localizes within the nucleus, which aligns with its known functions as a transcription factor.[41] It has also been predicted to localize within the mitochondria.[41]

Homology/Evolution

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The ZNF226 evolutionary rate in comparison to the cytochrome c and fibrinogen alpha chain proteins

Although there is little information available on the ZNF226 gene, homologs of the gene have been found across eukaryotes and bacteria species. Strict orthologs were only found within mammals. The ZNF226 gene is also closely related to the ZNF234 gene and the Zfp111 gene within mice.[2][3] Across the various species in which ZNF226 orthologs and homologs that were identified, conservation of the C2H2 binding sites is apparent.[42] In human ZNF226 paralogs, there is also conservation of the C2H2 binding sites, as well as nucleic acid binding sites.[2]

Slow rate evolution is apparent for the ZNF226 protein. It evolves in a manner similar to the cytochrome c protein instead of the fibrinogen alpha chain protein.

Interacting Proteins

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Two interactions detected via the two hybrid method occurred with SSBP3 and ATF4. These two proteins presented dectected interactions via the two hybrid method, and they are both transcription factors. ZNF226 is known to be expressed at greater levels within human stem cells, making it certainly possible for it to interact with SSBP3.[43]

Interacting Molecule/Protein Interaction Type Interaction Detection Method Role Function/Significance
H2BC10/ H2B.1A/H2BC8/ H2BC4 Physical Association Proximity Labelling Bait Analysis of histone interaction partners.  Also known as HIST1H2BG, it encodes replication-dependent histones in H2B family.[44][45]
RNF123 Physical Association Affinity Chromatography Bait RING finger containing E3 ubiquitin ligase was studied for its interactions, and was found to target lamin B1, which is involved in nuclear stability.[46]
MRPL58 Physical Association Cross-linking Neutral Analyzing protein interactions within histones in the nucleus. The mitochondrial ribosome protein L58 acts as a ribosome release factor to translate mitochondrial genes.[47][48]
ATF4/CREB-2 Direct Interaction Two Hybrid Bait Analysis of TF interactions. ATF4 is a transcription factor which may bind to the long terminal repeat of the human T-cell leukemia type 1 virus (HTLV-1). It can be an activator of HTLV-1.[49][50][51]
SSBP3/CSDP Physical Association Two Hybrid Prey Analysis of TF interactions. Found in mice embryonic stem cells to develop into trophoblasts (provide nutrients to embryo).[49][52]
H2BC8 Physical Association Unspecified Bait Analysis of histone interaction partners. Also known as HIST1H2BG, it encodes replication-dependent histone in H2B family.[44][45]
BRD1 Association ChIP assay Bait Bromodomain containing 1 gene is known to play a role in brain development, and the BRD1 network can lead to an increased risk in schizophrenia.[53] Localizes within the nucleus, and is a part of the MOZ/MORF acetyltransferase complex. This plays a role in acetylation of histone H3 and H4.[54]
H2BC4 Physical Association Bioid - Analysis of histone interaction partners.  Also known as HIST1H2BG, it encodes replication-dependent histone in H2B family.[44][45]

Function/Biochemistry

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With ZNF226 being a transcription factor, playing a role in transcriptional repression, the 18 zf-C2H2 binding domains are predicted to bind to the DNA sequence shown in the sequence logo.

 
Sequence logo of ZNF226 zf-C2H2 structural domain DNA binding sites

Clinical Significance

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A mutation within ZNF226 gene has been positively correlated with the presence of hepatocellular carcinoma (HCC).[55] A particular SNP also correlated with an increased expression of ZNF226 in brain frontal cortical tissue and peripheral mononuclear cells, such as T cells and B cells.[56] The promoter region of ZNF226 was found to be hypomethylated in those who were exposed to the Chinese famine.[57] The hypomethylated region in ZNF226 was shown to have a correlation of methylation in the blood and the prefrontal cortex, although the exact function of the protein in the famine is not understood.[57] ZNF226 gene was listed among many other genes with a copy number variation (CNV) that was associated with single common variable immunodeficiency (CVID).[58] ZNF225, ZNF234, and ZNF233 are also genes listed with a CNV, indicating the region of duplication.[58]

References

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  1. ^ "GeneCards entry on ZNF226". 2020.{{cite web}}: CS1 maint: url-status (link)
  2. ^ a b c d e f g h i j k l m n "ZNF226 zinc finger protein 226 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-10-20.
  3. ^ a b Shannon, Mark; Hamilton, Aaron T.; Gordon, Laurie; Branscomb, Elbert; Stubbs, Lisa (2003-06-01). "Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters". Genome Research. 13 (6a): 1097–1110. doi:10.1101/gr.963903. ISSN 1088-9051. PMC 403638. PMID 12743021.{{cite journal}}: CS1 maint: PMC format (link)
  4. ^ Persikov, Anton V.; Rowland, Elizabeth F.; Oakes, Benjamin L.; Singh, Mona; Noyes, Marcus B. (2014-02-01). "Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets". Nucleic Acids Research. 42 (3): 1497–1508. doi:10.1093/nar/gkt1034. ISSN 0305-1048. PMC 3919609. PMID 24214968.{{cite journal}}: CS1 maint: PMC format (link)
  5. ^ Persikov, Anton V.; Wetzel, Joshua L.; Rowland, Elizabeth F.; Oakes, Benjamin L.; Xu, Denise J.; Singh, Mona; Noyes, Marcus B. (2015-02-18). "A systematic survey of the Cys2His2 zinc finger DNA-binding landscape". Nucleic Acids Research. 43 (3): 1965–1984. doi:10.1093/nar/gku1395. ISSN 0305-1048. PMC 4330361. PMID 25593323.{{cite journal}}: CS1 maint: PMC format (link)
  6. ^ a b c "Expasy Compute pI/MW tool".{{cite web}}: CS1 maint: url-status (link)
  7. ^ a b c Madeira, Fábio; Park, Young mi; Lee, Joon; Buso, Nicola; Gur, Tamer; Madhusoodanan, Nandana; Basutkar, Prasad; Tivey, Adrian R. N.; Potter, Simon C.; Finn, Robert D.; Lopez, Rodrigo (2019-07-02). "The EMBL-EBI search and sequence analysis tools APIs in 2019". Nucleic Acids Research. 47 (W1): W636–W641. doi:10.1093/nar/gkz268. ISSN 0305-1048. PMC 6602479. PMID 30976793.{{cite journal}}: CS1 maint: PMC format (link)
  8. ^ Combet, C; Blanchet, C; Geourjon, C; Deléage, G (2000-03-01). "NPS@: Network Protein Sequence Analysis". Trends in Biochemical Sciences. 25 (3): 147–150. doi:10.1016/s0968-0004(99)01540-6. ISSN 0968-0004.
  9. ^ Yang, Jianyi; Zhang, Yang (2015-07-01). "I-TASSER server: new development for protein structure and function predictions". Nucleic Acids Research. 43 (W1): W174–W181. doi:10.1093/nar/gkv342. ISSN 0305-1048. PMC 4489253. PMID 25883148.{{cite journal}}: CS1 maint: PMC format (link)
  10. ^ Zhang, Chengxin; Freddolino, Peter L.; Zhang, Yang (2017-07-03). "COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information". Nucleic Acids Research. 45 (W1): W291–W299. doi:10.1093/nar/gkx366. ISSN 0305-1048. PMC 5793808. PMID 28472402.{{cite journal}}: CS1 maint: PMC format (link)
  11. ^ a b "Genomatix Website".
  12. ^ Ray-Gallet, D.; Mao, C.; Tavitian, A.; Moreau-Gachelin, F. (1995-07-20). "DNA binding specificities of Spi-1/PU.1 and Spi-B transcription factors and identification of a Spi-1/Spi-B binding site in the c-fes/c-fps promoter". Oncogene. 11 (2): 303–313. ISSN 0950-9232. PMID 7624145.
  13. ^ Horvath, C. M.; Wen, Z.; Darnell, J. E. (1995-04-15). "A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain". Genes & Development. 9 (8): 984–994. doi:10.1101/gad.9.8.984. ISSN 0890-9369. PMID 7774815.
  14. ^ Dejosez, Marion; Levine, Stuart S.; Frampton, Garrett M.; Whyte, Warren A.; Stratton, Sabrina A.; Barton, Michelle C.; Gunaratne, Preethi H.; Young, Richard A.; Zwaka, Thomas P. (2010-07-15). "Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells". Genes & Development. 24 (14): 1479–1484. doi:10.1101/gad.1935210. ISSN 0890-9369. PMC 2904937. PMID 20581084.{{cite journal}}: CS1 maint: PMC format (link)
  15. ^ Otaki, Masayuki; Hatano, Masahiko; Kobayashi, Koichi; Ogasawara, Takeshi; Kuriyama, Takayuki; Tokuhisa, Takeshi (2000-09-07). "Cell cycle-dependent regulation of TIAP/m-survivin expression". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1493 (1): 188–194. doi:10.1016/S0167-4781(00)00142-1. ISSN 0167-4781.
  16. ^ Dezső, Zoltán; Nikolsky, Yuri; Sviridov, Evgeny; Shi, Weiwei; Serebriyskaya, Tatiana; Dosymbekov, Damir; Bugrim, Andrej; Rakhmatulin, Eugene; Brennan, Richard J.; Guryanov, Alexey; Li, Kelly (2008-11-12). "A comprehensive functional analysis of tissue specificity of human gene expression". BMC Biology. 6 (1): 49. doi:10.1186/1741-7007-6-49. ISSN 1741-7007. PMC 2645369. PMID 19014478.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  17. ^ Kaur, Surleen; Archer, Kellie J.; Devi, M. Gouri; Kriplani, Alka; Strauss, Jerome F.; Singh, Rita (2012-10-01). "Differential Gene Expression in Granulosa Cells from Polycystic Ovary Syndrome Patients with and without Insulin Resistance: Identification of Susceptibility Gene Sets through Network Analysis". The Journal of Clinical Endocrinology & Metabolism. 97 (10): E2016–E2021. doi:10.1210/jc.2011-3441. ISSN 0021-972X. PMC 3674289. PMID 22904171.{{cite journal}}: CS1 maint: PMC format (link)
  18. ^ "GEO Profiles entry on ZNF226 Papillary Thyroid Cancer".{{cite web}}: CS1 maint: url-status (link)
  19. ^ a b c Cheng, Cheng-Chung; Lo, Hung-Hao; Huang, Tse-Shun; Cheng, Yi-Chieh; Chang, Shi-Ting; Chang, Shing-Jyh; Wang, Hsei-Wei (2012-09-03). "Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations". BMC Genomics. 13 (1): 447. doi:10.1186/1471-2164-13-447. ISSN 1471-2164. PMC 3443421. PMID 22943456.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  20. ^ a b Persson, Helena; Kvist, Anders; Rego, Natalia; Staaf, Johan; Vallon-Christersson, Johan; Luts, Lena; Loman, Niklas; Jonsson, Goran; Naya, Hugo; Hoglund, Mattias; Borg, Ake (2011-01-01). "Identification of New MicroRNAs in Paired Normal and Tumor Breast Tissue Suggests a Dual Role for the ERBB2/Her2 Gene". Cancer Research. 71 (1): 78–86. doi:10.1158/0008-5472.CAN-10-1869. ISSN 0008-5472. PMID 21199797.
  21. ^ Wang, Hui-juan; Zhang, Peng-jun; Chen, Wei-jun; Jie, Deng; Dan, Feng; Jia, Yan-hong; Xie, Li-xin (2013-06-01). "Characterization and Identification of Novel Serum MicroRNAs in Sepsis Patients With Different Outcomes". Shock. 39 (6): 480–487. doi:10.1097/SHK.0b013e3182940cb8. ISSN 1073-2322.
  22. ^ Hu, Sen-Lin; Cui, Guang-Lin; Huang, Jin; Jiang, Jian-Gang; Wang, Dao-Wen (2016-09-14). "An APOC3 3′UTR variant associated with plasma triglycerides levels and coronary heart disease by creating a functional miR-4271 binding site". Scientific Reports. 6 (1): 32700. doi:10.1038/srep32700. ISSN 2045-2322. PMC 5021972. PMID 27624799.{{cite journal}}: CS1 maint: PMC format (link)
  23. ^ Ladewig, Erik; Okamura, Katsutomo; Flynt, Alex S.; Westholm, Jakub O.; Lai, Eric C. (2012-09-01). "Discovery of hundreds of mirtrons in mouse and human small RNA data". Genome Research. 22 (9): 1634–1645. doi:10.1101/gr.133553.111. ISSN 1088-9051. PMC 3431481. PMID 22955976.{{cite journal}}: CS1 maint: PMC format (link)
  24. ^ Frazier, Sonya; McBride, Martin W.; Mulvana, Helen; Graham, Delyth (2020-04-30). "From animal models to patients: the role of placental microRNAs, miR-210, miR-126, and miR-148a/152 in preeclampsia". Clinical Science. 134 (8): 1001–1025. doi:10.1042/CS20200023. ISSN 0143-5221. PMC 7239341. PMID 32337535.{{cite journal}}: CS1 maint: PMC format (link)
  25. ^ Fong, Louise Y.; Taccioli, Cristian; Palamarchuk, Alexey; Tagliazucchi, Guidantonio Malagoli; Jing, Ruiyan; Smalley, Karl J.; Fan, Sili; Altemus, Joseph; Fiehn, Oliver; Huebner, Kay; Farber, John L. (2020-03-17). "Abrogation of esophageal carcinoma development in miR-31 knockout rats". Proceedings of the National Academy of Sciences. 117 (11): 6075–6085. doi:10.1073/pnas.1920333117. ISSN 0027-8424. PMC 7084137. PMID 32123074.{{cite journal}}: CS1 maint: PMC format (link)
  26. ^ a b Wang, Wei-Hua; Chen, Jie; Zhao, Feng; Zhang, Bu-Rong; Yu, Hong-Sheng; Jin, Hai-Ying; Dai, Jin-Hua (2014). "MiR-150-5p Suppresses Colorectal Cancer Cell Migration and Invasion through Targeting MUC4". Asian Pacific Journal of Cancer Prevention. 15 (15): 6269–6273. doi:10.7314/APJCP.2014.15.15.6269. ISSN 1513-7368.
  27. ^ "GeneCards entry on FUS".{{cite web}}: CS1 maint: url-status (link)
  28. ^ "GeneCards entry on RBMY1A1".{{cite web}}: CS1 maint: url-status (link)
  29. ^ a b "GeneCards entry on RBMX".{{cite web}}: CS1 maint: url-status (link)
  30. ^ a b "GeneCards entry on ACO1".{{cite web}}: CS1 maint: url-status (link)
  31. ^ "Expasy Myristoylator tool".{{cite web}}: CS1 maint: url-status (link)
  32. ^ Xue, Yu; Liu, Zexian; Cao, Jun; Ma, Qian; Gao, Xinjiao; Wang, Qingqi; Jin, Changjiang; Zhou, Yanhong; Wen, Longping; Ren, Jian (2011-03-01). "GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection". Protein Engineering, Design and Selection. 24 (3): 255–260. doi:10.1093/protein/gzq094. ISSN 1741-0126.
  33. ^ Xue, Yu; Ren, Jian; Gao, Xinjiao; Jin, Changjiang; Wen, Longping; Yao, Xuebiao (2008-09-01). "GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy". Molecular & Cellular Proteomics. 7 (9): 1598–1608. doi:10.1074/mcp.M700574-MCP200. ISSN 1535-9476. PMC 2528073. PMID 18463090.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  34. ^ Xue, Yu; Zhou, Fengfeng; Zhu, Minjie; Ahmed, Kashif; Chen, Guoliang; Yao, Xuebiao (2005-07-01). "GPS: a comprehensive www server for phosphorylation sites prediction". Nucleic Acids Research. 33 (suppl_2): W184–W187. doi:10.1093/nar/gki393. ISSN 0305-1048. PMC 1160154. PMID 15980451.{{cite journal}}: CS1 maint: PMC format (link)
  35. ^ "Motif Scan tool".{{cite web}}: CS1 maint: url-status (link)
  36. ^ a b Cui, Beimi; Pan, Qiaona; Clarke, David; Villarreal, Marisol Ochoa; Umbreen, Saima; Yuan, Bo; Shan, Weixing; Jiang, Jihong; Loake, Gary J. (2018-10-12). "S -nitrosylation of the zinc finger protein SRG1 regulates plant immunity". Nature Communications. 9 (1): 4226. doi:10.1038/s41467-018-06578-3. ISSN 2041-1723. PMC 6185907. PMID 30315167.{{cite journal}}: CS1 maint: PMC format (link)
  37. ^ Guidez, Fabien; Howell, Louise; Isalan, Mark; Cebrat, Marek; Alani, Rhoda M.; Ivins, Sarah; Hormaeche, Itsaso; McConnell, Melanie J.; Pierce, Sarah; Cole, Philip A.; Licht, Jonathan (2005-07-01). "Histone Acetyltransferase Activity of p300 Is Required for Transcriptional Repression by the Promyelocytic Leukemia Zinc Finger Protein". Molecular and Cellular Biology. 25 (13): 5552–5566. doi:10.1128/MCB.25.13.5552-5566.2005. ISSN 0270-7306. PMC 1156991. PMID 15964811.{{cite journal}}: CS1 maint: PMC format (link)
  38. ^ Jen, Jayu; Wang, Yi-Ching (2016-07-13). "Zinc finger proteins in cancer progression". Journal of Biomedical Science. 23 (1): 53. doi:10.1186/s12929-016-0269-9. ISSN 1423-0127. PMC 4944467. PMID 27411336.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  39. ^ Wei, Hung-Ming; Hu, Huan-Hsuan; Chang, Gia-Yun; Lee, Yu-Jen; Li, Yi-Chen; Chang, Hong-How; Li, Chuan (2014). "Arginine methylation of the cellular nucleic acid binding protein does not affect its subcellular localization but impedes RNA binding". FEBS Letters. 588 (9): 1542–1548. doi:10.1016/j.febslet.2014.03.052. ISSN 1873-3468.
  40. ^ Jen, Jayu; Wang, Yi-Ching (2016-07-13). "Zinc finger proteins in cancer progression". Journal of Biomedical Science. 23 (1): 53. doi:10.1186/s12929-016-0269-9. ISSN 1423-0127. PMC 4944467. PMID 27411336.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  41. ^ a b "PSORT II tool".{{cite web}}: CS1 maint: url-status (link)
  42. ^ Madeira, Fábio; Park, Young mi; Lee, Joon; Buso, Nicola; Gur, Tamer; Madhusoodanan, Nandana; Basutkar, Prasad; Tivey, Adrian R N; Potter, Simon C; Finn, Robert D; Lopez, Rodrigo (2019-07-02). "The EMBL-EBI search and sequence analysis tools APIs in 2019". Nucleic Acids Research. 47 (W1): W636–W641. doi:10.1093/nar/gkz268. ISSN 0305-1048.
  43. ^ Cheng, Cheng-Chung; Lo, Hung-Hao; Huang, Tse-Shun; Cheng, Yi-Chieh; Chang, Shi-Ting; Chang, Shing-Jyh; Wang, Hsei-Wei (2012-09-03). "Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations". BMC Genomics. 13 (1): 447. doi:10.1186/1471-2164-13-447. ISSN 1471-2164. PMC 3443421. PMID 22943456.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  44. ^ a b c Lambert, Jean-Philippe; Tucholska, Monika; Go, Christopher; Knight, James D. R.; Gingras, Anne-Claude (2015-04-06). "Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes". Journal of Proteomics. Protein dynamics in health and disease. 118: 81–94. doi:10.1016/j.jprot.2014.09.011. ISSN 1874-3919. PMC 4383713. PMID 25281560.{{cite journal}}: CS1 maint: PMC format (link)
  45. ^ a b c "GeneCards entry on H2BC10".{{cite web}}: CS1 maint: url-status (link)
  46. ^ Khanna, Richa; Krishnamoorthy, Vidhya; Parnaik, Veena K. (2018). "E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins". The FEBS Journal. 285 (12): 2243–2262. doi:10.1111/febs.14477. ISSN 1742-4658.
  47. ^ Fasci, Domenico; Ingen, Hugo van; Scheltema, Richard A.; Heck, Albert J. R. (2018-10-01). "Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei". Molecular & Cellular Proteomics. 17 (10): 2018–2033. doi:10.1074/mcp.RA118.000924. ISSN 1535-9476. PMC 6166682. PMID 30021884.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  48. ^ "GeneCards entry on MRPL58".{{cite web}}: CS1 maint: url-status (link)
  49. ^ a b Ravasi, Timothy; Suzuki, Harukazu; Cannistraci, Carlo Vittorio; Katayama, Shintaro; Bajic, Vladimir B.; Tan, Kai; Akalin, Altuna; Schmeier, Sebastian; Kanamori-Katayama, Mutsumi; Bertin, Nicolas; Carninci, Piero (2010-03-05). "An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man". Cell. 140 (5): 744–752. doi:10.1016/j.cell.2010.01.044. ISSN 0092-8674. PMC 2836267. PMID 20211142.{{cite journal}}: CS1 maint: PMC format (link)
  50. ^ "NCBI entry on ATF4".{{cite web}}: CS1 maint: url-status (link)
  51. ^ Gachon, Frederic; Peleraux, Annick; Thebault, Sabine; Dick, Joelle; Lemasson, Isabelle; Devaux, Christian; Mesnard, Jean-Michel (1998-10-01). "CREB-2, a Cellular CRE-Dependent Transcription Repressor, Functions in Association with Tax as an Activator of the Human T-Cell Leukemia Virus Type 1 Promoter". Journal of Virology. 72 (10): 8332–8337. doi:10.1128/JVI.72.10.8332-8337.1998. ISSN 0022-538X. PMID 9733879.
  52. ^ Liu, Jifeng; Luo, Xinlong; Xu, Yanli; Gu, Junjie; Tang, Fan; Jin, Ying; Li, Hui (2016-05-28). "Single-stranded DNA binding protein Ssbp3 induces differentiation of mouse embryonic stem cells into trophoblast-like cells". Stem Cell Research & Therapy. 7 (1): 79. doi:10.1186/s13287-016-0340-1. ISSN 1757-6512. PMC 4884356. PMID 27236334.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  53. ^ Fryland, Tue; Christensen, Jane H.; Pallesen, Jonatan; Mattheisen, Manuel; Palmfeldt, Johan; Bak, Mads; Grove, Jakob; Demontis, Ditte; Blechingberg, Jenny; Ooi, Hong Sain; Nyegaard, Mette (2016-05-03). "Identification of the BRD1 interaction network and its impact on mental disorder risk". Genome Medicine. 8 (1): 53. doi:10.1186/s13073-016-0308-x. ISSN 1756-994X. PMC 4855718. PMID 27142060.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  54. ^ "GeneCards entry on BRD1".{{cite web}}: CS1 maint: url-status (link)
  55. ^ Fujimoto, Akihiro; Totoki, Yasushi; Abe, Tetsuo; Boroevich, Keith A.; Hosoda, Fumie; Nguyen, Ha Hai; Aoki, Masayuki; Hosono, Naoya; Kubo, Michiaki; Miya, Fuyuki; Arai, Yasuhito (2012-05-12). "Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators". Nature Genetics. 44 (7): 760–764. doi:10.1038/ng.2291. ISSN 1546-1718.
  56. ^ Rao, Shuquan; Ghani, Mahdi; Guo, Zhiyun; Deming, Yuetiva; Wang, Kesheng; Sims, Rebecca; Mao, Canquan; Yao, Yao; Cruchaga, Carlos; Stephan, Dietrich A.; Rogaeva, Ekaterina (2018-06-01). "An APOE-independent cis-eSNP on chromosome 19q13.32 influences tau levels and late-onset Alzheimer's disease risk". Neurobiology of Aging. 66: 178.e1–178.e8. doi:10.1016/j.neurobiolaging.2017.12.027. ISSN 0197-4580. PMC 7050280. PMID 29395286.{{cite journal}}: CS1 maint: PMC format (link)
  57. ^ a b He, Yujie; de Witte, Lot D.; Houtepen, Lotte C.; Nispeling, Danny M.; Xu, Zhida; Yu, Qiong; Yu, Yaqin; Hol, Elly M.; Kahn, René S.; Boks, Marco P. (2019-05-16). "DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data". Clinical Epigenetics. 11 (1): 80. doi:10.1186/s13148-019-0680-7. ISSN 1868-7083. PMC 6524251. PMID 31097004.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  58. ^ a b [http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=znf226&OS=znf226&RS= znf226 "US Trademark and Patent Office entry on ZNF226 in CVID Study"]. {{cite web}}: Check |url= value (help); line feed character in |url= at position 161 (help)CS1 maint: url-status (link)
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