In silico analysis of the promoter region of prolactin gene in cattle to understand its gene regulation

Abstract

Prolactin (PRL) is a key endocrine regulator of lactation, mammary gland growth, and systemic metabolic homeostasis in cattle. The transcriptional architecture of bovine PRL regulation remains incompletely characterized, despite its physiological importance. In this study we used an in silico TSS, CpG island, and TFBS profiling approach to analyze the ~5 kb upstream regulatory region of the Bos taurus PRL gene. By employing Neural Network Promoter Prediction under stringent criteria, we identified three highly reliable TSSs located at -4478, -2123, and -517 base pairs relative to the translational start codon, indicating a multi-TSS promoter complex that facilitates alternative transcript initiation. Canonical CpG islands were absent, consistent with tissue-specific, fine-tuned transcriptional control. TFBS analysis revealed a densely populated, hierarchically organized promoter enriched for pituitary-specific POU1F1 motifs, hormone-responsive ESRRA and RARA elements, signal-dependent STAT5 and AP-1 sites, and developmental transcription factors such as NANOG, HOXD9, and FOXI3. High-affinity TFBS clusters, including cis-regulatory modules of activators and repressors (like PRDM1) suggest combinatorial control and dynamic transcriptional responsiveness. These findings give mechanistic insights into the transcriptional complexity of bovine PRL locus and built an essential resource base on functional genomics studies to enhance efficiency of lactation and endocrine resilience in cattle.