In Silico Promoter Motif Analysis of Human Fertility-Related Genes
Abstract
1. Introduction
2. Materials and Methods
2.1. Gene Selection
2.2. Research Objective at the Gene Level
- To define promoter regions and accurately localize transcription start sites (TSS) for each gene.
- To discover conserved and novel cis-regulatory motifs using computational tools.
- To identify assumed transcription factor binding sites through motif comparison with known databases.
- To analyze motif distribution and enrichment patterns, especially in proximity to the TSS.
- To assess potential functional associations of the motifs using Gene Ontology.
- To evaluate CpG island density and distribution as indicators of epigenetic regulation within promoter sequences.
2.3. Data Retrieval and Sequence Preparation
2.4. Software Tools and Parameters Used
- NNPP (Neural Network Promoter Prediction) [33]
- MEME-ChIP (Motif discovery) [34]
- STREME (Sensitive motif finder) [35]
- Tomtom (Motif comparison tool) [36]
- FIMO (Find Individual Motif Occurrences) [37]
- CentriMo (Motif centrality analysis) [38]
- GOMo (Gene Ontology for Motifs) [39]
- MethPrimer (CpG island prediction) [40]
2.5. Data Analysis Strategy
- Promoter prediction using NNPP.
- Motif discovery using MEME-ChIP and STREME.
- Motif annotation using Tomtom (TF binding site inference).
- Motif positioning via FIMO and CentriMo.
- Functional annotation using GOMo.
- CpG island identification using MethPrimer.
3. Results
3.1. Promoter Prediction Using NNPP
3.2. Identification of Significant Motifs—STREME Analysis
3.3. Motif Validation with Tomtom: Projection onto Known Transcription Factors
3.4. Functional Annotation of Motifs Using GOMo
3.5. Motif Occurrence Scanning with FIMO
3.6. Epigenetic Context—MethPrimer CpG Analysis
4. Discussion
4.1. Functional Landscape of Identified Motifs
4.2. Gene-Specific Regulatory Insights
- FOXL2 showed multiple motif occurrences within the −1000 to −1 bp promoter window (Table S2) and contained CpG islands within this region (Table 6; Figure 5). Together with the positional enrichment patterns reported for selected motifs (Figure 3), these features prioritize FOXL2 for targeted promoter-level validation in ovarian cell models.
- FSHR exhibited recurrent motif occurrences in the promoter window, including significant FIMO hits for enriched motifs (Table S2), supporting follow-up testing of motif-driven promoter activity under variable transcription factor contexts.
- ESR1 displayed CpG islands and motif occurrences within the analyzed promoter window (Table 6 and Table S2; Figure 5). Given prior reports of altered methylation patterns affecting ESR1 regulation in reproductive contexts, these promoter features may be useful targets for future validation rather than diagnostic conclusions.
- GDF9 and BMP15 showed fewer motif occurrences overall in the scanned promoter window (Table S2) but included motif instances that warrant prioritization in oocyte-related follow-up assays, particularly in the context of oocyte–cumulus signaling pathways.
4.3. Epigenetic Landscape
4.4. Clinical and Biological Implications
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Cox, C.M.; Thoma, M.E.; Tchangalova, N.; Mburu, G.; Bornstein, M.J.; Johnson, C.L.; Kiarie, J. Infertility prevalence and the methods of estimation from 1990 to 2021: A systematic review and meta-analysis. Hum. Reprod. Open 2022, 2022, hoac051. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- The European IVF Monitoring Consortium (EIM) for the European Society of Human Reproduction and Embryology (ESHRE); Smeenk, J.; Wyns, C.; De Geyter, C.; Kupka, M.; Bergh, C.; Saiz, I.C.; De Neubourg, D.; Rezabek, K.; Tandler-Schneider, A.; et al. ART in Europe, 2019: Results generated from European registries by ESHRE. Hum. Reprod. 2023, 38, 2321–2338. [Google Scholar] [CrossRef] [Scilit]
- Wallace, W.H.B.; Kelsey, T.W. Human ovarian reserve from conception to the menopause. PLoS ONE 2010, 5, e8772. [Google Scholar] [CrossRef] [Scilit]
- Mutlu, M.F.; Erdem, M.; Erdem, A.; Yildiz, S.; Mutlu, I.; Arisoy, O.; Oktem, M. Antral follicle count determines poor ovarian response better than anti-Müllerian hormone but age is the only predictor for live birth in in vitro fertilization cycles. J. Assist. Reprod. Genet. 2013, 30, 657–665. [Google Scholar] [CrossRef] [Scilit]
- Baldini, G.M.; Ferri, D.; Malvasi, A.; Laganà, A.S.; Vimercati, A.; Dellino, M.; Baldini, D.; Trojano, G. Genetic Abnormalities of Oocyte Maturation: Mechanisms and Clinical Implications. Int. J. Mol. Sci. 2024, 25, 13002. [Google Scholar] [CrossRef] [Scilit]
- Simoni, M.; Nieschlag, E.; Gromoll, J. Isoforms and single nucleotide polymorphisms of the FSH receptor gene: Implications for human reproduction. Hum. Reprod. Update 2002, 8, 413–421. [Google Scholar] [CrossRef] [Scilit]
- Polyzos, N.P.; Neves, A.R.; Drakopoulos, P.; Spits, C.; Mercadal, B.A.; Garcia, S.; Ma, P.Q.M.; Le, L.H.; Ho, M.T.; Mertens, J.; et al. The effect of polymorphisms in FSHR and FSHB genes on ovarian response: A prospective multicenter multinational study in Europe and Asia. Hum. Reprod. 2021, 36, 1711–1721. [Google Scholar] [CrossRef] [Scilit]
- Li, N.; Guan, Y.; Ren, B.; Zhang, Y.; Du, Y.; Kong, H.; Zhang, Y.; Lou, H. Effect of blastocyst morphology and developmental rate on euploidy and live birth rates in preimplantation genetic testing for aneuploidy cycles with single-embryo transfer. Front. Endocrinol. 2022, 13, 858042. [Google Scholar] [CrossRef] [Scilit]
- Yan, J.; Qin, Y.; Zhao, H.; Sun, Y.; Gong, F.; Li, R.; Sun, X.; Ling, X.; Li, H.; Hao, C.; et al. Live birth with or without preimplantation genetic testing for aneuploidy. N. Engl. J. Med. 2021, 385, 2047–2058. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Kasaven, L.S.; Marcus, D.; Theodorou, E.; Jones, B.P.; Saso, S.; Naja, R.; Serhal, P.; Ben-Nagi, J. Systematic review and meta-analysis: Does pre-implantation genetic testing for aneuploidy at the blastocyst stage improve live birth rate? J. Assist. Reprod. Genet. 2023, 40, 2297–2316. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Mastenbroek, S.; Twisk, M.; van der Veen, F.; Repping, S. Preimplantation genetic screening: A systematic review and meta-analysis of RCTs. Hum. Reprod. Update 2011, 17, 454–466. [Google Scholar] [CrossRef] [Scilit]
- Fu, W.; Cui, Q.; Bu, Z.; Shi, H.; Yang, Q.; Hu, L. Elevated sperm DNA fragmentation is correlated with an increased chromosomal aneuploidy rate of miscarried conceptus in women of advanced age undergoing fresh embryo transfer cycle. Front. Endocrinol. 2024, 15, 1289763. [Google Scholar] [CrossRef] [Scilit]
- Ye, L.; Dimitriadis, E. Endometrial Receptivity–Lessons from “Omics”. Biomolecules 2025, 15, 106. [Google Scholar] [CrossRef] [Scilit]
- Rocha-Junior, C.V.; Da Broi, M.G.; Miranda-Furtado, C.L.; Navarro, P.A.; Ferriani, R.A.; Meola, J. Progesterone receptor B (PGR-B) is partially methylated in eutopic endometrium from infertile women with endometriosis. Reprod. Sci. 2019, 26, 1568–1574. [Google Scholar] [CrossRef] [Scilit]
- Kanhere, A.; Bansal, M. Structural properties of promoters: Similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res. 2005, 33, 3165–3175. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Bucher, P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 1990, 212, 563–578. [Google Scholar] [CrossRef] [Scilit]
- Pirtea, P.; de Ziegler, D.; Marin, D.; Sun, L.; Tao, X.; Ayoubi, J.M.; Franasiak, J.; Scott, R.T., Jr. Gonadotropin receptor polymorphisms (FSHR N680S and LHCGR N312S) are not predictive of clinical outcome and live birth in assisted reproductive technology. Fertil. Steril. 2022, 118, 494–503. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Schmidt, D.; Ovitt, C.E.; Anlag, K.; Fehsenfeld, S.; Gredsted, L.; Treier, A.C.; Treier, M. The murine winged-helix transcription factor Foxl2 is required for granulosa cell differentiation and ovary maintenance. Development 2004, 131, 933–942. [Google Scholar] [CrossRef] [Scilit]
- Quaynor, S.D.; Stradtman, E.W., Jr.; Kim, H.G.; Shen, Y.; Chorich, L.P.; Schreihofer, D.A.; Layman, L.C. Delayed puberty and estrogen resistance in a woman with estrogen receptor α variant. N. Engl. J. Med. 2013, 369, 164–171. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Lledó, B.; Llácer, J.; Turienzo, A.; Ortiz, J.A.; Guerrero, J.; Morales, R.; Ten, J.; Bernabeu, R. Androgen receptor CAG repeat length is associated with ovarian reserve but not with ovarian response. Reprod. Biomed. Online 2014, 29, 509–515. [Google Scholar] [CrossRef] [Scilit]
- Chand, A.L.; Ooi, G.T.; Harrison, C.A.; Shelling, A.N.; Robertson, D.M. Functional analysis of the human inhibin α subunit variant A257T and its potential role in premature ovarian failure. Hum. Reprod. 2007, 22, 3241–3248. [Google Scholar] [CrossRef] [Scilit]
- Albarel, F.; Perrin, J.; Jegaden, M.; Roucher-Boulez, F.; Reynaud, R.; Brue, T.; Courbiere, B. Successful IVF pregnancy despite inadequate ovarian steroidogenesis due to congenital lipoid adrenal hyperplasia (CLAH): A case report. Hum. Reprod. 2016, 31, 2609–2612. [Google Scholar] [CrossRef] [Scilit]
- Rigon, C.; Andrisani, A.; Forzan, M.; D’Antona, D.; Bruson, A.; Cosmi, E.; Ambrosini, G.; Tiboni, G.M.; Clementi, M. Association study of AMH and AMHRII polymorphisms with unexplained infertility. Fertil. Steril. 2010, 94, 1244–1248. [Google Scholar] [CrossRef] [Scilit]
- Rossetti, R.; Di Pasquale, E.; Marozzi, A.; Bione, S.; Toniolo, D.; Grammatico, P.; Nelson, L.M.; Beck-Peccoz, P.; Persani, L. BMP15 mutations associated with primary ovarian insufficiency cause a defective production of bioactive protein. Hum. Mutat. 2009, 30, 804–810. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Kovanci, E.; Rohozinski, J.; Simpson, J.L.; Heard, M.J.; Bishop, C.E.; Carson, S.A. Growth differentiating factor-9 mutations may be associated with premature ovarian failure. Fertil. Steril. 2007, 87, 143–146. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Tu, Y.A.; Lin, S.J.; Chen, P.L.; Chou, C.H.; Huang, C.C.; Ho, H.N.; Chen, M.J. HSD3B1 gene polymorphism and female pattern hair loss in women with polycystic ovary syndrome. J. Formos. Med. Assoc. 2019, 118, 1225–1231. [Google Scholar] [CrossRef] [Scilit]
- Zhou, Z.; Ni, C.; Wu, L.; Chen, B.; Xu, Y.; Zhang, Z.; Mu, J.; Li, B.; Yan, Z.; Fu, J.; et al. Novel mutations in ZP1, ZP2, and ZP3 cause female infertility due to abnormal zona pellucida formation. Hum. Genet. 2019, 138, 327–337. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Altmäe, S.; Haller, K.; Peters, M.; Saare, M.; Hovatta, O.; Stavreus-Evers, A.; Velthut, A.; Karro, H.; Metspalu, A.; Salumets, A. Aromatase gene (CYP19A1) variants, female infertility and ovarian stimulation outcome: A preliminary report. Reprod. Biomed. Online 2009, 18, 651–657. [Google Scholar] [CrossRef] [Scilit]
- Lang-Muritano, M.; Sproll, P.; Wyss, S.; Kolly, A.; Hürlimann, R.; Konrad, D.; Biason-Lauber, A. Early-onset complete ovarian failure and lack of puberty in a woman with mutated estrogen receptor β (ESR2). J. Clin. Endocrinol. Metab. 2018, 103, 3748–3756. [Google Scholar] [CrossRef] [Scilit]
- Lourenço, D.; Brauner, R.; Lin, L.; De Perdigo, A.; Weryha, G.; Muresan, M.; Boudjenah, R.; Guerra-Junior, G.; Maciel-Guerra, A.T.; Bashamboo, A. Mutations in NR5A1 associated with ovarian insufficiency. N. Engl. J. Med. 2009, 360, 1200–1210. [Google Scholar] [CrossRef] [Scilit]
- Yang, J.Y.; Zhou, Y.; Yu, Z.G.; Anh, V.; Zhou, L.Q. Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides. BMC Bioinform. 2008, 9, 113. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Gangal, R.; Sharma, P. Human pol II promoter prediction: Time series descriptors and machine learning. Nucleic Acids Res. 2005, 33, 1332–1336. [Google Scholar] [CrossRef] [Scilit]
- Reese, M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 2001, 26, 51–56. [Google Scholar] [CrossRef] [Scilit]
- Machanick, P.; Bailey, T.L. MEME-ChIP: Motif analysis of large DNA datasets. Bioinformatics 2011, 27, 1696–1697. [Google Scholar] [CrossRef] [Scilit]
- Bailey, T.L. STREME: Accurate and versatile sequence motif discovery. Bioinformatics 2021, 37, 2834–2840. [Google Scholar] [CrossRef] [Scilit]
- Gupta, S.; Stamatoyannopoulos, J.A.; Bailey, T.L.; Noble, W.S. Quantifying similarity between motifs. Genome Biol. 2007, 8, R24. [Google Scholar] [CrossRef] [Scilit]
- Grant, C.E.; Bailey, T.L.; Noble, W.S. FIMO: Scanning for occurrences of a given motif. Bioinformatics 2011, 27, 1017–1018. [Google Scholar] [CrossRef] [Scilit]
- Bailey, T.L.; Machanick, P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 2012, 40, e128. [Google Scholar] [CrossRef] [Scilit]
- Li, L.C.; Dahiya, R. MethPrimer: Designing primers for methylation PCRs. Bioinformatics 2002, 18, 1427–1431. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Daei-Farshbaf, N.; Aflatoonian, R.; Amjadi, F.S.; Taleahmad, S.; Ashrafi, M.; Bakhtiyari, M. Expression pattern of olfactory receptor genes in human cumulus cells as an indicator for competent oocyte selection. Turk. J. Biol. 2020, 44, 371–380. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Shen, L.; Hong, X.; Liu, Y.; Zhou, W.; Zhang, Y. The miR-25-3p/Sp1 pathway is dysregulated in ovarian endometriosis. J. Int. Med. Res. 2020, 48, 0300060520918437. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Anjali, G.; Kaur, S.; Lakra, R.; Taneja, J.; Kalsey, G.S.; Nagendra, A.; Shrivastav, T.; Devi, M.G.; Malhotra, N.; Kriplani, A.; et al. FSH stimulates IRS-2 expression in human granulosa cells through cAMP/SP1, an inoperative FSH action in PCOS patients. Cell. Signal. 2015, 27, 2452–2466. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Deng, Y.; Lou, T.; Kong, L.; Liu, C. Prohibitin2/PHB2, transcriptionally regulated by GABPA, inhibits cell growth via PRKN/Parkin-dependent mitophagy in endometriosis. Reprod. Sci. 2023, 30, 3629–3640. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Huang, Y.; Wang, Y.; Li, R.; Liu, Y.; Yang, Y. miR-450b-5p promotes development of endometriosis by inhibiting the GABPA/HOXD10 axis. iScience 2024, 27, 111487. [Google Scholar] [CrossRef] [Scilit]
- Kalantari, S.; Varnosfaderani, A.S.; Ramezanali, F.; Amirchaghmaghi, E.; Shahhoseini, M. Dynamic regulation of CYP19A1 promoter region under control of CREB family members in endometrial tissues of women with endometriosis: A case-control study. Int. J. Fertil. Steril. 2025, 19, 151. [Google Scholar]
- Huang, C.C.; Chen, M.J.; Lan, C.W.; Wu, C.E.; Huang, M.C.; Kuo, H.C.; Ho, H.N. Hyperactive CREB signaling pathway involved in the pathogenesis of polycystic ovarian syndrome revealed by patient-specific induced pluripotent stem cell modeling. Fertil. Steril. 2019, 112, 594–607. [Google Scholar] [CrossRef] [Scilit]
- Di, F.; Liu, J.; Li, S.; Yao, G.; Hong, Y.; Chen, Z.J.; Li, W.; Du, Y. ATF4 contributes to ovulation via regulating COX2/PGE2 expression: A potential role of ATF4 in PCOS. Front. Endocrinol. 2018, 9, 669. [Google Scholar] [CrossRef] [Scilit]
- Wang, Z.; Liu, Y.; Liu, J.; Kong, N.; Jiang, Y.; Jiang, R.; Zhen, X.; Zhou, J.; Li, C.; Sun, H.; et al. ATF3 deficiency impairs the proliferative–secretory phase transition and decidualization in RIF patients. Cell Death Dis. 2021, 12, 387. [Google Scholar] [CrossRef] [Scilit]
- Cheng, X.; Liu, J.; Shan, H.; Sun, L.; Huang, C.; Yan, Q.; Jiang, R.; Ding, L.; Jiang, Y.; Zhou, J.; et al. Activating transcription factor 3 promotes embryo attachment via up-regulation of leukemia inhibitory factor in vitro. Reprod. Biol. Endocrinol. 2017, 15, 42. [Google Scholar] [CrossRef] [Scilit]
- Ma, X.; Han, X.; Wang, W.; Zhang, Q.; Tang, H. β-Catenin regulates ovarian granulosa cell cycle and proliferation in laying hens by interacting with TCF4. Poult. Sci. 2024, 103, 103377. [Google Scholar] [CrossRef] [Scilit]
- Fischer, C.P.; Kayisili, U.; Taylor, H.S. HOXA10 expression is decreased in endometrium of women with adenomyosis. Fertil. Steril. 2011, 95, 1133–1136. [Google Scholar] [CrossRef] [Scilit]
- Fambrini, M.; Sorbi, F.; Bussani, C.; Cioni, R.; Sisti, G.; Andersson, K.L. Hypermethylation of HOXA 10 gene in mid-luteal endometrium from women with ovarian endometriomas. Acta Obstet. Et Gynecol. Scand. 2013, 92, 1331–1334. [Google Scholar] [CrossRef] [Scilit]
- Muharam, R.; Harzif, A.K.; Catherine; Asmarinah; Wiweko, B. A preliminary communication: Ongoing study on HOXA10 methylation profile of endometriosis patients with infertility. J. Endometr. Pelvic Pain Disord. 2016, 8, 106–110. [Google Scholar] [CrossRef] [Scilit]
- Mirabutalebi, S.H.; Karami, N.; Montazeri, F.; Fesahat, F.; Sheikhha, M.H.; Hajimaqsoodi, E.; Zarchi, M.K.; Kalantar, S.M. The relationship between the expression levels of miR-135a and HOXA10 gene in the eutopic and ectopic endometrium. Int. J. Reprod. Biomed. 2018, 16, 501. [Google Scholar] [CrossRef] [Scilit]
- Obermair, A.; Baxter, E.; Brennan, D.J.; McAlpine, J.N.; Muellerer, J.J.; Amant, F.; van Gent, M.D.J.M.; Coleman, R.L.; Westin, S.N.; Yates, M.S.; et al. Fertility-sparing treatment in early endometrial cancer: Current state and future strategies. Obstet. Gynecol. Sci. 2020, 63, 417–431. [Google Scholar] [CrossRef] [Scilit]
- Centini, G.; Colombi, I.; Ianes, I.; Perelli, F.; Ginetti, A.; Cannoni, A.; Habib, N.; Negre, R.R.; Martire, F.G.; Raimondo, D.; et al. Fertility Sparing in Endometrial Cancer: Where Are We Now? Cancers 2025, 17, 112. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Hsu, Y.T.; Hsu, H.C.; Lee, C.Y.; Hung, W.T.; Chen, C.H. Long-term outcomes of fertility-sparing treatment in endometrial carcinoma and endometrial intraepithelial neoplasia: Recurrence risk factors over a 9-year follow-up. Acta Obstet. Et Gynecol. Scand. 2025, 104, 1994–2005. [Google Scholar] [CrossRef] [Scilit]
- Chae, S.H.; Shim, S.H.; Lee, S.J.; Lee, J.Y.; Kim, S.N.; Kang, S.B. Pregnancy and oncologic outcomes after fertility-sparing management for early stage endometrioid endometrial cancer. Int. J. Gynecol. Cancer 2019, 29, 77–85. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Yu, J.; Zhang, Y.; Yang, H.; Xu, Y. Reproductive advance of fertility preservation in patients with early endometrial carcinoma or endometrial atypical hyperplasia. Gynecol. Obstet. Clin. Med. 2022, 2, 186–190. [Google Scholar] [CrossRef] [Scilit]
- Geng, R.; Zheng, Y.; Zhou, D.; Li, Q.; Li, R.; Guo, X. ZBTB7A, a potential biomarker for prognosis and immune infiltrates, inhibits progression of endometrial cancer based on bioinformatics analysis and experiments. Cancer Cell Int. 2020, 20, 542. [Google Scholar] [CrossRef] [Scilit]
- Boroń, D.; Zmarzły, N.; Wierzbik-Strońska, M.; Rosińczuk, J.; Mieszczański, P.; Grabarek, B.O. Recent multiomics approaches in endometrial cancer. Int. J. Mol. Sci. 2022, 23, 1237. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Flegel, C.; Manteniotis, S.; Osthold, S.; Hatt, H.; Gisselmann, G. Expression profile of ectopic olfactory receptors determined by deep sequencing. PLoS ONE 2013, 8, e55368. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Maßberg, D.; Hatt, H. Human olfactory receptors: Novel cellular functions outside of the nose. Physiol. Rev. 2018, 98, 1739–1763. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Zhang, Q.; Madden, N.E.; Wong, A.S.T.; Chow, B.K.C.; Lee, L.T.O. The role of endocrine G protein-coupled receptors in ovarian cancer progression. Front. Endocrinol. 2017, 8, 66. [Google Scholar] [CrossRef] [Scilit]





| Gene | Name | Function | Comment | References |
|---|---|---|---|---|
| FSHR ID: 2492 | follicle-stimulating hormone receptor | Receptor for FSH, GPCR | Important for follicle development | [6,7] |
| PGR ID: 5241 | progesterone receptor (PR, NR3C3) | Nuclear receptor for progesterone | Important for implantation and pregnancy support; has two promoters/isoforms | [14] |
| LHCGR ID: 3973 | luteinizing hormone/choriogonadotropin receptor | Receptor for LH and hCG, GPCR | Activates G-protein/adenylate cyclase, key in ovulation and testosterone production | [17] |
| FOXL2 ID: 668 | forkhead box L2 | Transcription factor for ovarian function | Regulator of PGR, ESR2, CYP19A1 | [18] |
| ESR1 ID: 2099 | estrogen receptor 1 (ERα) | Nuclear estrogen receptor | Regulator of development, metabolism, and reproduction; functions as a homodimer/heterodimer with ERβ | [19] |
| AR ID: 367 | androgen receptor (NR3C4) | Nuclear receptor for testosterone/DHT | Regulator of male development; localized in the nucleus, activates transcription | [20] |
| INHA ID: 3623 | inhibin alpha | Inhibin α-subunit regulates FSH | Expression in granulosa cells | [21] |
| STAR ID: 6770 | steroidogenic acute regulatory protein | Transport of cholesterol into mitochondria | Activated by CREB, GATA4, SF-1 | [22] |
| AMH ID: 268 | anti-Müllerian hormone | Follicle regulator | Targeted by FOXL2 and GATA | [23] |
| BMP15 ID: 9210 | bone morphogenetic protein 15 | Oocyte-secreted growth factor | Cross-regulation with FSHR | [24] |
| GDF9 ID: 2661 | growth differentiation factor 9 | Similar to BMP15 | Helps in oocyte–granulosa communication | [25] |
| HSD3B1 ID: 111785 | 3-beta-hydroxysteroid dehydrogenase 1 | Key enzyme in steroidogenesis | Regulated by the same signaling as STAR | [26] |
| ZP3 ID: 7784 | zona pellucida glycoprotein 3 | Zona pellucida protein | Important for sperm–egg interaction | [27] |
| CYP19A1 * ID: 1588 | cytochrome P450 family 19 subfamily A member 1 | An enzyme that converts androgens to estrogens | Subject to regulation by FSH and LH | [28] |
| ESR2 * ID: 2100 | estrogen receptor 2 (ERβ) | Nuclear estrogen receptor | Nuclear regulator of ovarian function, follicular maturity, and estrogen signaling; functions as a homodimer/heterodimer with ERα estrogen receptor | [29] |
| NR5A1 * (SF-1) ID: 2516 | nuclear receptor subfamily 5 group A member 1 | Transcription factor for gonadal expression | Regulator of LHCGR, STAR, INHA | [30] |
| Gene | #Promoters (Score ≥ 0.80) | Promoter with the Highest Prediction Score (Start–End *) | Score | Location in Our ** 1 kb Sequence |
|---|---|---|---|---|
| AR | 1 | 108–158 | 1.00 | −892 → −842 |
| LHCGR | 4 | 641–691 | 0.91 | −359 → −309 |
| FSHR | 1 | 106–156 | 0.80 | −894 → −844 |
| ESR1 | 2 | 180–230 | 0.83 | −820 → −770 |
| PGR | 2 (overlap) | 591–641 | 0.90 | −409 → −359 |
| INHA | 2 | 450–500 | 0.86 | −550 → −500 |
| STAR | 2 | 826–876 | 0.82 | −174 → −124 |
| FOXL2 | 1 | 938–988 | 0.82 | −62 → −12 |
| AMH | 1 | 295–345 | 0.92 | −705 → −655 |
| BMP15 | 2 | 2–52 | 1.00 | −998 → −948 |
| GDF9 | 1 | 202–252 | 0.84 | −798 → −748 |
| HSD3B1 | 1 | 837–887 | 1.00 | −163 → −113 |
| ZP3 | 3 | 948–998 | 1.00 | −52 → −2 |
| Motif ID | Consensus | Width | Train Pos Count | Train p-Value | Train Log p-Value | E-Value | Total Sites |
|---|---|---|---|---|---|---|---|
| STREME-1 | GWGGATC | 7 | 10 | 5.40 × 10−5 | −4.26887 | 5.00 × 100 | 10 |
| STREME-2 | CGACCAGCCY | 10 | 8 | 8.20 × 10−4 | −3.08418 | 5.00 × 100 | 8 |
| STREME-3 | TRCHAAAARTV | 11 | 8 | 8.20 × 10−4 | −3.08418 | 5.00 × 100 | 8 |
| STREME-4 | GGAAGGCMKGM | 11 | 6 | 7.50 × 10−3 | −2.12764 | 5.00 × 100 | 6 |
| STREME-5 | AYTAGTCAG | 9 | 5 | 2.00 × 10−2 | −1.70852 | 5.00 × 100 | 5 |
| Query Motif * | PWM-ID (Base) | SuggestedTF ** | Consensus of PWM | E-Value | q-Value | Total Matching | Significance *** |
|---|---|---|---|---|---|---|---|
| STREME-1 (GWGGATC) | MA0130.1 | Sp1 | GTGGAT | 2.08 | 1.00 | 2 | No significance |
| STREME-2 (CGACCAGCCY) | MA1655.2 | ZBT7A | GAACAGCC | 0.51 | 0.71 | 11 | No significance |
| STREME-3 (TRCHAAAARTV) | MA1715.1 | Homeobox/ZnF | GTACCAGGAGTGGGG | 5.20 | 1.00 | 10 | No significance |
| STREME-4 (GGAAGGCMKGM) | MA0149.1 | GABPA (ETS) | GGAAGGAAGGAAGGAAGG | 0.14 | 0.28 | 6 | No significance |
| STREME-5 (AYTAGTCAG) | MA0489.3 | CREB/ATF | ATGAGTCA | 3.18 | 1.00 | 13 | No significance |
| MEME-2 (MRCMCCAGNNWGTK) | TCF4_DBD | TCF4/E-box | CGCACCTGCT | 2.96 | 0.87 | 9 | No significance |
| Motif | Total GO Terms | Main p-Value | Main q-Value | Main Score | Main Specificity (%) | Most Likely Related Process |
|---|---|---|---|---|---|---|
| STREME-1 | 7 | 5.34 × 10−6 | 0.013 | 0.00827 | 67.43 | negative regulation of endocytosis |
| STREME-2 | 229 | 2.63 × 10−4 | 0.015 | 0.017 | 12.57 | protein assembly, mitochondrial function, TGF-β signaling |
| STREME-3 | 9 | 1.64 × 10−7 | 0.000218 | 0.847 | 26.11 | olfactory receptor/GPCR signaling |
| STREME-4 | 133 | 1.82 × 10−4 | 0.0202 | 0.0181 | 15.66 | growth factor signaling, ECM remodeling |
| STREME-5 | 23 | 5.26 × 10−6 | 0.00286 | 0.00347 | 19.78 | GPCR signaling, SERPIN inhibition |
| MEME-2 | 5 | 4.03 × 10−6 | 0.0165 | 0.00847 | 1.4 | general regulation |
| Gene | Number of CpG Islands * | Length (bp) | Start/End ** |
|---|---|---|---|
| AR | Island 1 | 263 | −792/−593 |
| Island 2 | 102 | −211/−110 | |
| LHCGR | no | ||
| FSHR | no | ||
| ESR1 | Island 1 | 256 | −625/−370 |
| island 2 | 214 | −269/−56 | |
| PGR | Island 1 | 155 | −685/−531 |
| Island 2 | 276 | −463/−188 | |
| INHA | No | ||
| STAR | No | ||
| FOXL2 | Island 1 | 619 | −883/−265 |
| Island 2 | 123 | −177/−55 | |
| AMH | No | ||
| BMP15 | No | ||
| GDF9 | No | ||
| HSD3B1 | No | ||
| ZP3 | No |
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© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
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Hristov, D.; Stojanov, D. In Silico Promoter Motif Analysis of Human Fertility-Related Genes. Appl. Biosci. 2026, 5, 14. https://doi.org/10.3390/applbiosci5010014
Hristov D, Stojanov D. In Silico Promoter Motif Analysis of Human Fertility-Related Genes. Applied Biosciences. 2026; 5(1):14. https://doi.org/10.3390/applbiosci5010014
Chicago/Turabian StyleHristov, Daniela, and Done Stojanov. 2026. "In Silico Promoter Motif Analysis of Human Fertility-Related Genes" Applied Biosciences 5, no. 1: 14. https://doi.org/10.3390/applbiosci5010014
APA StyleHristov, D., & Stojanov, D. (2026). In Silico Promoter Motif Analysis of Human Fertility-Related Genes. Applied Biosciences, 5(1), 14. https://doi.org/10.3390/applbiosci5010014

