Manuscript accepted on :06-06-2024
Published online on: 24-06-2024
Plagiarism Check: Yes
Reviewed by: Dr. Randa Salah Gomaa and Dr. Nadhim M. H
Second Review by: Dr. Alaa Saadi Abbood
Final Approval by: Dr. Mariia Shanaida
1Cell and Molecular Biology, University of Arkansas at Fayetteville, Fayetteville, AR, USA
2Department of Biology, Wasit University, Kut, Iraq,
Corresponding Author E-mail: mu.raheemn@gmail.com
DOI : https://dx.doi.org/10.13005/bpj/2899
Abstract
In bilaterian animals, axon guidance decisions are regulated by many transmembrane receptor proteins called Roundabout (Robo) family members. During the developmental stages of fruit flies (Drosophila melanogaster), three Robo family members play unique roles in the central nervous system. Robo3 is revolutionarily conserved among taxa and studies show that Robo3 regulates mediolateral axonal navigation. Recent studies suggest that Robo3 guides longitudinal axons in a manner independent of its ligand (slit). The expression patterns of Robo3 are controlled by transcription factors (TFs) that play a significant role in gene regulation, and it is not a fully understood mechanism. Knowing the transcription factor binding sites (TFBS) of Robo3 would help to predict TFs that regulate Robo3. In this study, bioinformatics tools MEME Suite, TOMTOM, and MAST were utilized to analyze the Robo3 DNA sequence to identify putative TFs that assist as docking regions for TFs involved in the regulation of Robo3 gene expression. We found seven putative TFs: Btd, Opa, Mad, Odd, Twi, CF2, and h. Mapping these TF motifs against the Robo3 sequence showed that these motifs are located in many regions of the Robo3 gene. Understanding the roles of these TFs in Robo3 gene regulation would help to implement novel strategies to control and overcome disorders related to the Robo3 gene. This study aims to identify the unknown TFs that may play a critical role in Robo3 gene expression.
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References
- Blockus, H. & Chédotal, A. Slit-robo signaling. Development (Cambridge) 143, 3037–3044 (2016). https://doi.org/10.1242/dev.132829
CrossRef - Dickson, B. J. & Gilestro, G. F. Regulation of commissural axon pathfinding by Slit and its Robo receptors. Annu Rev Cell Dev Biol 22, 651–675 (2006).
CrossRef - Carranza, A., Howard, L. J., Brown, H. E., Selom Ametepe, A. & Evans, T. A. Slit-independent guidance of longitudinal axons by Drosophila Robo3. bioRxiv [Preprint] 1–23 (2023). doi: 10.1101/2023.05.08.539901.
CrossRef - Kidd T, Brose K, Mitchell KJ, Fetter RD, Tessier-Lavigne M, Goodman CS, Tear G.. Roundabout controls axon crossing of the CNS midline and defines a novel subfamily of evolutionarily conserved guidance receptors. Cell 92, 205–215 (1998). doi: 10.1016/s0092-8674(00)80915-0.
CrossRef - Kidd, T., Bland, K. S. & Goodman, C. S. Slit is the midline repellent for the Robo receptor in Drosophila. Cell 96, 785–794 (1999). doi: 10.1016/s0092-8674(00)80589-9.
CrossRef - Brose K, Bland KS, Wang KH, Arnott D, Henzel W, Goodman CS, Tessier-Lavigne M, Kidd T. Slit proteins bind robo receptors and have an evolutionarily conserved role in repulsive axon guidance. Cell 96, 795–806 (1999). doi: 10.1016/s0092-8674(00)80590-5.
CrossRef - Long H, Sabatier C, Ma L, Plump A, Yuan W, Ornitz DM, Tamada A, Murakami F, Goodman CS, Tessier-Lavigne M. Conserved roles for Slit and Robo proteins in midline commissural axon guidance. Neuron 42, 213–223 (2004). doi: 10.1016/s0896-6273(04)00179-5.
CrossRef - Evans, T. A. & Bashaw, G. J. Functional Diversity of Robo Receptor Immunoglobulin Domains Promotes Distinct Axon Guidance Decisions. Current Biology 20, 567–572 (2010). doi: 10.1016/j.cub.2010.02.021.
CrossRef - Jaworski, A., Long, H. & Tessier-Lavigne, M. Collaborative and specialized functions of Robo1 and Robo2 in spinal commissural axon guidance. Journal of Neuroscience 30, 9445–9453 (2010). doi: 10.1523/JNEUROSCI.6290-09.2010.
CrossRef - Sabatier C, Plump AS, Le Ma, Brose K, Tamada A, Murakami F, Lee EY, Tessier-Lavigne M. The Divergent Robo Family Protein Rig-1/Robo3 Is a Negative Regulator of Slit Responsiveness Required for Midline Crossing by Commissural Axons. Cell 117(2):157-69. (2004). doi: 10.1016/s0092-8674(04)00303-4.
CrossRef - Hauptman, G., Reichert, M. C., Abdal Rhida, M. A. & Evans, T. A. Characterization of enhancer fragments in Drosophila robo2. Fly (Austin) 16, 312–346 (2022). doi: 10.1080/19336934.2022.2126259.
CrossRef - Evans TA, Santiago C, Arbeille E, Bashaw GJ. Robo2 acts in trans to inhibit Slit-Robo1 repulsion in pre-crossing commissural axons. doi:10.7554/eLife.08407.001
CrossRef - Gorla M, Bashaw GJ. Molecular mechanisms regulating axon responsiveness at the midline. Dev Biol. 2020;466(1-2):12-21. doi:10.1016/j.ydbio.2020.08.006
CrossRef - Brown HE, Evans TA. Minimal structural elements required for midline repulsive signaling and regulation of Drosophila Robo1. PLoS One. 2020;15(10 October). doi:10.1371/journal.pone.0241150
CrossRef - Friocourt F, Kozulin P, Belle M, et al. Shared and differential features of Robo3 expression pattern in amniotes. Journal of Comparative Neurology. 2019;527(12):2009-2029. doi:10.1002/cne.24648
CrossRef - Schweitzer, J., Löhr, H., Bonkowsky, J. L., Hübscher, K. & Driever, W. Sim1a and Arnt2 contribute to hypothalamo-spinal axon guidance by regulating Robo2 activity via a Robo3- dependent mechanism. Development (Cambridge) 140, 93–106 (2013). doi: 10.1242/dev.087825.
CrossRef - Transcription Factors – an overview | ScienceDirect Topics. Accessed February 23, 2024. https://www.sciencedirect.com/ topics/neuroscience/transcription-factors
- Karin M. Too many transcription factors: positive and negative interactions. New Biol. 1990;2(2):126-131. http://europepmc.org/abstract/MED/2128034
- He H, Yang M, Li S, et al. Mechanisms and biotechnological applications of transcription factors. Synth Syst Biotechnol. 2023;8(4):565-577. doi:10.1016/j.synbio.2023.08.006
CrossRef - Ritter, D. I., Dong, Z., Guo, S. & Chuang, J. H. Transcriptional enhancers in protein-coding exons of vertebrate developmental genes. PLoS One 7(5):e35202., (2012). doi: 10.1371/journal.pone.0035202.
CrossRef - Prerna J, Yasha H. In-silico Approach to Map Transcription Factor Binding Motifs onto Drosophila Cardiac Genes. Austin Journal of Biotechnology & Bioengineering. 2014;1(1):1-8.
- Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. Elife. 2023;12. doi:10.7554/eLife.88187
CrossRef - Hellman, L. M. & Fried, M. G. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2, 1849–1861 (2007). doi: 10.1038/nprot.2007.249.
CrossRef - Brand, L. H., Kirchler, T., Hummel, S., Chaban, C. & Wanke, D. DPI-ELISA: A fast and versatile method to specify the binding of plant transcription factors to DNA in vitro. Plant Methods 6:25., (2010). doi: 10.1186/1746-4811-6-25.
CrossRef - He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z. De novo ChIP-seq analysis. Genome Biol 16(1):205. (2015). doi: 10.1186/s13059-015-0756-4.
CrossRef - Santiago C, Bashaw J. Transcription factors and effectors that regulate neuronal morphology. Development (Cambridge). 2014;141(24):4667-4680. doi:10.1242/dev.110817
CrossRef - Drysdale R; FlyBase Consortium. FlyBase : a database for the Drosophila research community. Methods Mol Biol. 2008;420:45-59. doi: 10.1007/978-1-59745-583-1_3.
CrossRef - Nystrom SL, McKay DJ. Memes: A motif analysis environment in R using tools from the MEME Suite. PLoS Comput Biol. 2021;17(9):1-14. doi:10.1371/JOURNAL.PCBI.1008991
CrossRef - Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36.
- Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L. & Noble, W. S. Quantifying similarity between motifs. Genome Biol 8(2):R24. (2007). doi: 10.1186/gb-2007-8-2-r24.
CrossRef - Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 1998;14(1):48-54. doi: 10.1093/bioinformatics/14.1.48.
CrossRef - Hashim FA, Mabrouk MS, Al-Atabany W. Review of Different Sequence Motif Finding Algorithms. Avicenna J Med Biotechnol. 2019 Apr-Jun;11(2):130-148. PMID: 31057715
- Bailey, T. L., Elkan, C., Hunter, L., Searls, D. & Shavlik, J. Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Mach Learn 21, 51–80 (1995). https://doi.org/ 10.1007/BF0099337926.
CrossRef - Mathelier, A. & Wasserman, W. W. The Next Generation of Transcription Factor Binding Site Prediction. PLoS Comput Biol 9(9):e1003214. (2013). doi: 10.1371/journal.pcbi.1003214.
CrossRef - Bagni, C., Bray, S., Gogos, J. A., Kafatos, F. C. & Hsu, T. The Drosophila Zinc Finger Transcription Factor CF2 Is a Myogenic Marker Downstream of MEF2 during Muscle Development. Mech Dev. 117(1-2):265-8. (2002). doi: 10.1016/s0925-4773(02)00176-4.
CrossRef - Gajewski, K. M. & Schulz, R. A. CF2 represses actin 88F gene expression and maintains filament balance during indirect flight muscle development in drosophila. PLoS One 5(5):e10713., (2010). doi: 10.1371/journal.pone.0010713.
CrossRef - Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with zelda to control gene expression in embryos. Elife 9:e59610. (2020). doi: 10.7554/eLife.59610.
CrossRef - Quéva C, Hurlin PJ, Foley KP, Eisenman RN. Sequential expression of the MAD family of transcriptional repressors during differentiation and development. Oncogene. 1998 Feb 26;16(8):967-77. doi: 10.1038/sj.onc.1201611.
CrossRef - Scho, F., Sauer, F. & Purnell, B. A. Drosophila Head Segmentation Factor Buttonhead Interacts with the Same TATA Box-Binding Protein-Associated Factors and in Vivo DNA Targets as Human Sp1 but Executes a Different Biological Program. Developmental Biology 96(9):5061-5. (1999). doi: 10.1073/pnas.96.9.5061.
CrossRef - He JG, Zhou HY, Xue SG, et al. Transcription Factor TWIST1 Integrates Dendritic Remodeling and Chronic Stress to Promote Depressive-like Behaviors. Biol Psychiatry. 2021;89(6):615-626. doi:10.1016/j.biopsych. 2020.09.003
CrossRef - Baylies, M. K. & Bate, M. Twist: A Myogenic Switch in Drosophila. Science. 272(5267):1481-4. (1996) doi: 10.1126/science.272.5267.1481.
CrossRef