RNA Regulatory Elements Research Articles

Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs.

The high genetic heterogeneity and environmental effects of subfertility in livestock species make the elucidation of the genetic mechanisms associated with reproductive efficiency a difficult task. Network and co-expression network meta-analyses were applied alongside genetic variant calling and long non-coding RNA (lncRNA) characterization to identify functionally relevant target genes and regulatory subnetworks associated with fertility in dairy cattle. In total, 505 lncRNAs (441 previously annotated in the bovine reference genome ARS-UCD 1.2 and 64 novel lncRNAs) were identified. Seven differentially expressed genes between high-fertile (HF) and sub-fertile (SF) Holstein cows were identified in the network meta-analysis (CA5A, ENSBTAG00000051149, ENSBTAG00000003272, DEFB7, DIO2, TRPV3, and COL4A4). Additionally, seven functional candidate differentially co-expressed (DcoExp) modules with a differential regulatory pattern (|z-score|>2) were identified between HF and SF cows. The functional candidate genes and DcoExp modules identified were associated with fertility relevant processes such as the regulation of embryonic implantation and proliferation, interaction and molecule transfer between the fetus and the cow, and the immune system. These results help to better understand the genetic mechanisms associated with reproductive efficiency in dairy cattle through the identification of potential biomarkers and genetic variants associated with differentially expressed regulatory gene and lncRNAs regulatory element networks.

Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts

Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure–function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed collective variables and metadynamics efforts, to establish a simple metadynamics protocol, which utilizes only one collective variable, based on multiple tertiary contacts, to characterize the underlying free energy landscape of any RNA molecule. We develop a modified collective variable, the tertiary contacts distance (QTC), which can probe the formation and breakage of all or selectively chosen tertiary contacts of the RNA. The SAM-I riboswitch in the presence of three ionic and substrate conditions was investigated and validated against the structure ensemble previously generated using SAXS experiments. This efficient and easy to implement all-atom MD simulation based approach incorporating metadynamics to study RNA conformational dynamics can also be transferred to any other type of biomolecule.

Gene rppA co-regulated by LRR, SigA, and CcpA mediates antibiotic resistance in Bacillus thuringiensis.

Antibiotic resistance genes are usually tightly controlled by transcription factors and RNA regulatory elements including sRNAs, riboswitches, and attenuators, and their expression is activated to respond to antibiotic exposure. In previous work, we revealed that the rppA gene is regulated by attenuator LRR and two mistranslation products in Bacillus thuringiensis BMB171. However, its function and promoter regulation is still not precise. In this study, we demonstrated that the encoding product of the rppA gene acts as an ARE1 ABC-F protein and confers resistance to antibiotics virginiamycin M1 and lincomycin when overexpressed. Besides the reported attenuator LRR, the expression of the rppA gene is controlled by the sigma factor SigA and a global transcription factor CcpA. Consequently, its promoter activity is mainly maintained at the stationary phase of cell growth and inhibited in the presence of glucose. Our study revealed the function and regulation of the rppA gene in detail. KEY POINTS: • The RppA protein acts as an ARE1 ABC-F protein • The rppA gene confers resistance to antibiotics virginiamycin M1 and lincomycin when overexpressed • The expression of the rppA gene is regulated by the sigma factor SigA and the pleiotropic regulator CcpA.

The Role of Transposable Elements in Sexual Development.

Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

BackgroundGenome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity.ResultsCOMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity.ConclusionsThe relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

Abstract 869: Post-transcriptional control of androgen receptor expression

Abstract The Androgen Receptor (AR) is a ligand-dependent transcription factor that modulates the expression of androgen-regulated genes involved in the proliferation and differentiation of normal prostate epithelial cells. However, in Prostate Cancer (PCa), these cellular events are dysregulated upon significant changes in AR, such as AR overexpression, leading to uncontrolled cell growth and proliferation. To elucidate the molecular mechanisms by which AR expression and function are controlled, we have explored the post-transcriptional regulatory RNA elements of AR, particularly the 3’ untranslated region (UTR). The AR 3’UTR is 6.8 Kilobases (Kb) long, which indicates that this region is likely a site for multitudinous levels of post-transcriptional regulation. We found that the length of AR 3’UTR negatively correlates with AR expression, with the full length 3’UTR leading to the most downregulation of expression. Currently, we are exploring cis-acting noncoding RNAs and RNA binding proteins (RBPs) predicted to interact with the AR 3’UTR. Citation Format: Eviania Likos, Girish C. Shukla. Post-transcriptional control of androgen receptor expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 869.

Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action.

T-box riboswitches (T-boxes) are essential RNA regulatory elements with a remarkable structural diversity, especially among bacterial pathogens. In staphylococci, all glyS T-boxes synchronize glycine supply during synthesis of nascent polypeptides and cell wall formation and are characterized by a conserved and unique insertion in their antiterminator/terminator domain, termed stem Sa. Interestingly, in Staphylococcus aureus the stem Sa can accommodate binding of specific antibiotics, which in turn induce robust and diverse effects on T-box-mediated transcription. In the present study, domain swap mutagenesis and probing analysis were performed to decipher the role of stem Sa. Deletion of stem Sa significantly reduces both the S. aureus glyS T-box-mediated transcription readthrough levels and the ability to discriminate among tRNAGly isoacceptors, both in vitro and in vivo. Moreover, the deletion inverted the previously reported stimulatory effects of specific antibiotics. Interestingly, stem Sa insertion in the terminator/antiterminator domain of Geobacillus kaustophilus glyS T-box, which lacks this domain, resulted in elevated transcription in the presence of tigecycline and facilitated discrimination among proteinogenic and nonproteinogenic tRNAGly isoacceptors. Overall, stem Sa represents a lineage-specific structural feature required for efficient staphylococcal glyS T-box-mediated transcription and it could serve as a species-selective druggable target through its ability to modulate antibiotic binding.

Design of a Toolbox of RNA Thermometers.

RNA thermometers are RNA regulatory elements that convert temperature into a functional biological response through a temperature-induced conformational change. These regulatory elements have been investigated in numerous natural contexts and have been designed for synthetic biology as well. A basic challenge has been the design of an RNA thermometer whose final activity in response to temperature matches a prespecified response, in terms of its sensitivity, threshold, and leakiness. This chapter provides a methodology for the design of a toolbox of RNA thermometers. We describe considerations for the conceptual design, a computational assessment, and strategies for experimental synthesis and measurement.

Characterization of Structure and Dynamics of the Guanidine-II Riboswitch from Escherichia coli by NMR Spectroscopy and Small-Angle X-ray Scattering (SAXS).

Riboswitches are regulatory RNA elements that undergo functionally important allosteric conformational switching upon binding of specific ligands. The here investigated guanidine‐II riboswitch binds the small cation, guanidinium, and forms a kissing loop‐loop interaction between its P1 and P2 hairpins. We investigated the structural changes to support previous studies regarding the binding mechanism. Using NMR spectroscopy, we confirmed the structure as observed in crystal structures and we characterized the kissing loop interaction upon addition of Mg2+ and ligand for the riboswitch aptamer from Escherichia coli. We further investigated closely related mutant constructs providing further insight into functional differences between the two (different) hairpins P1 and P2. Formation of intermolecular interactions were probed by small‐angle X‐ray scattering (SAXS) and NMR DOSY data. All data are consistent and show the formation of oligomeric states of the riboswitch induced by Mg2+ and ligand binding.

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

AbstractSARS‐CoV‐2 contains a positive single‐stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS‐CoV and SARS‐CoV‐2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex‐vivo structural probing experiments. These elements contain non‐base‐paired regions that potentially harbor ligand‐binding pockets. Here, we performed an NMR‐based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1H‐based 1D NMR binding assays. The screening identified common as well as RNA‐element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS‐CoV‐2.

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome.

SARS‐CoV‐2 contains a positive single‐stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS‐CoV and SARS‐CoV‐2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex‐vivo structural probing experiments. These elements contain non‐base‐paired regions that potentially harbor ligand‐binding pockets. Here, we performed an NMR‐based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1H‐based 1D NMR binding assays. The screening identified common as well as RNA‐element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS‐CoV‐2.

RNA-Protein Interaction Analysis of SARS-CoV-2 5' and 3' Untranslated Regions Reveals a Role of Lysosome-Associated Membrane Protein-2a during Viral Infection.

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus. The viral genome is capped at the 5′ end, followed by an untranslated region (UTR). There is a poly(A) tail at the 3′ end, preceded by a UTR. The self-interaction between the RNA regulatory elements present within the 5′ and 3′ UTRs and their interaction with host/virus-encoded proteins mediate the function of the 5′ and 3′ UTRs. Using an RNA-protein interaction detection (RaPID) assay coupled to liquid chromatography with tandem mass spectrometry, we identified host interaction partners of SARS-CoV-2 5′ and 3′ UTRs and generated an RNA-protein interaction network. By combining these data with the previously known protein-protein interaction data proposed to be involved in virus replication, we generated the RNA-protein-protein interaction (RPPI) network, likely to be essential for controlling SARS-CoV-2 replication. Notably, bioinformatics analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism. Lysosome-associated membrane protein-2a (Lamp2a), the receptor for chaperone-mediated autophagy, is one of the host proteins that interact with the 5′ UTR. Further studies showed that the Lamp2 level is upregulated in SARS-CoV-2-infected cells and that the absence of the Lamp2a isoform enhanced the viral RNA level whereas its overexpression significantly reduced the viral RNA level. Lamp2a and viral RNA colocalize in the infected cells, and there is an increased autophagic flux in infected cells, although there is no change in the formation of autophagolysosomes. In summary, our study provides a useful resource of SARS-CoV-2 5′ and 3′ UTR binding proteins and reveals the role of Lamp2a protein during SARS-CoV-2 infection.IMPORTANCE Replication of a positive-strand RNA virus involves an RNA-protein complex consisting of viral genomic RNA, host RNA(s), virus-encoded proteins, and host proteins. Dissecting out individual components of the replication complex will help decode the mechanism of viral replication. 5′ and 3′ UTRs in positive-strand RNA viruses play essential regulatory roles in virus replication. Here, we identified the host proteins that associate with the UTRs of SARS-CoV-2, combined those data with the previously known protein-protein interaction data (expected to be involved in virus replication), and generated the RNA-protein-protein interaction (RPPI) network. Analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism, which are important for virus replication. Analysis of one of the interaction partners of the 5′-UTR (Lamp2a) demonstrated its role in reducing the viral RNA level in SARS-CoV-2-infected cells. Collectively, our study provides a resource of SARS-CoV-2 UTR-binding proteins and identifies an important role for host Lamp2a protein during viral infection.

Elevated Expression of Toxin TisB Protects Persister Cells against Ciprofloxacin but Enhances Susceptibility to Mitomycin C.

Bacterial chromosomes harbor toxin-antitoxin (TA) systems, some of which are implicated in the formation of multidrug-tolerant persister cells. In Escherichia coli, toxin TisB from the tisB/istR-1 TA system depolarizes the inner membrane and causes ATP depletion, which presumably favors persister formation. Transcription of tisB is induced upon DNA damage due to activation of the SOS response by LexA degradation. Transcriptional activation of tisB is counteracted on the post-transcriptional level by structural features of tisB mRNA and RNA antitoxin IstR-1. Deletion of the regulatory RNA elements (mutant Δ1-41 ΔistR) uncouples TisB expression from LexA-dependent SOS induction and causes a ‘high persistence’ (hip) phenotype upon treatment with different antibiotics. Here, we demonstrate by the use of fluorescent reporters that TisB overexpression in mutant Δ1-41 ΔistR inhibits cellular processes, including the expression of SOS genes. The failure in SOS gene expression does not affect the hip phenotype upon treatment with the fluoroquinolone ciprofloxacin, likely because ATP depletion avoids strong DNA damage. By contrast, Δ1-41 ΔistR cells are highly susceptible to the DNA cross-linker mitomycin C, likely because the expression of SOS-dependent repair systems is impeded. Hence, the hip phenotype of the mutant is conditional and strongly depends on the DNA-damaging agent.

RNA transport and local translation in neurodevelopmental and neurodegenerative disease.

Neurons decentralize protein synthesis from the cell body to support the active metabolism of remote dendritic and axonal compartments. The neuronal RNA transport apparatus, composed of cis-acting RNA regulatory elements, neuronal transport granule proteins, and motor adaptor complexes, drives the long-distance RNA trafficking required for local protein synthesis. Over the past decade, advances in human genetics, subcellular biochemistry, and high-resolution imaging have implicated each member of the apparatus in several neurodegenerative diseases, establishing failed RNA transport and associated processes as a unifying pathomechanism. In this review, we deconstruct the RNA transport apparatus, exploring each constituent's role in RNA localization and illuminating their unique contributions to neurodegeneration.

Towards elucidating the structure, function, and druggability of coronavirus cis-acting RNA motifs

Coronaviruses are the causative agents of mild to severe respiratory and intestinal infections in humans. They are the largest RNA viruses, which genomes and encoded RNAs are known to fold into the highly-order structures that play essential roles in the viral replication and infectivity cycle. The recent outbreaks of new pathogenic coronaviruses steered researchers’ attention into the possibility of targeting their RNAs directly with novel RNA-specific drugs and therapeutic strategies. In this manuscript, we highlight the recent biochemical and biophysical methodological advancements that yielded more in-depth insight into the structural and functional composition of coronaviruses cis-acting RNA motifs. We discuss the complexity of these RNA regulatory elements, their intermolecular interactions, post-transcriptional regulation, and their potential as druggable targets. We also indicate the location and function of unstructured and highly-conserved regions in coronaviruses RNA genomes representing viable aims for antisense oligonucleotide or CRISPR-based antiviral strategies.

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes.

Hepatitis B virus (HBV) is a major human pathogen that causes liver diseases. The main HBV RNAs are unspliced transcripts that encode the key viral proteins. Recent studies have shown that some of the HBV spliced transcript isoforms are predictive of liver cancer, yet the roles of these spliced transcripts remain elusive. Furthermore, there are nine major HBV genotypes common in different regions of the world, these genotypes may express different spliced transcript isoforms. To systematically study the HBV splice variants, we transfected human hepatoma cells, Huh7, with four HBV genotypes (A2, B2, C2 and D3), followed by deep RNA-sequencing. We found that 13–28 % of HBV RNAs were splice variants, which were reproducibly detected across independent biological replicates. These comprised 6 novel and 10 previously identified splice variants. In particular, a novel, singly spliced transcript was detected in genotypes A2 and D3 at high levels. The biological relevance of these splice variants was supported by their identification in HBV-positive liver biopsy and serum samples, and in HBV-infected primary human hepatocytes. Interestingly the levels of HBV splice variants varied across the genotypes, but the spliced pregenomic RNA SP1 and SP9 were the two most abundant splice variants. Counterintuitively, these singly spliced SP1 and SP9 variants had a suboptimal 5′ splice site, supporting the idea that splicing of HBV RNAs is tightly controlled by the viral post-transcriptional regulatory RNA element.

Post‐transcriptional deregulation of the tisB/istR‐1 toxin–antitoxin system promotes SOS‐independent persister formation in Escherichia coli

Bacterial dormancy is a valuable strategy to endure unfavourable conditions. The term 'persister' has been coined for cells that tolerate antibiotic treatments due to reduced cellular activity. The type I toxin-antitoxin system tisB/istR-1 is linked to persistence in Escherichia coli, because toxin TisB depolarizes the inner membrane and causes ATP depletion. Transcription of tisB is induced upon activation of the SOS response by DNA-damaging drugs. However, translation is repressed both by a 5' structure within the tisB mRNA and by RNA antitoxin IstR-1. This tight regulation limits TisB production to SOS conditions. Deletion of both regulatory RNA elements produced a 'high persistence' mutant, which was previously assumed to depend on stochastic SOS induction and concomitant TisB production. Here, we demonstrate that the mutant generates a subpopulation of growth-retarded cells during late stationary phase, likely due to SOS-independent TisB accumulation. Cell sorting experiments revealed that the stationary phase-derived subpopulation contains most of the persister cells. Collectively our data show that deletion of the regulatory RNA elements uncouples the persister formation process from the intended stress situation and enables the formation of TisB-dependent persisters in an SOS-independent manner.

The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia.

Simple SummaryAlterations in primary RNA motifs and aberrant expression levels of non-coding RNA molecules have emerged as biomarkers of disease development and progression. Advances in antisense oligonucleotide (ASO) techniques and pharmacologic discoveries in targeting of RNA structures and RNA–protein interactions with small molecules open a new area in RNA therapeutics that may help in developing a next generation of anti-cancer drugs.RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.

Prediction of putative regulatory elements in the subgenomic promoters of cucumber green mottle mosaic virus and their interactions with the RNA dependent RNA polymerase domain.

Characterization of the subgenomic RNA (sgRNA) promoter of many plant viruses is important to understand the expression of downstream genes and also to configure their genome into a suitable virus gene-vector system. Cucumber green mottle mosaic virus (CGMMV, genus Tobamovirus) is one of the RNA viruses, which is extensively being exploited as the suitable gene silencing and protein expression vector. Even though, characters of the sgRNA promoters (SGPs) of CGMMV are yet to be addressed. In the present study, we predicted the SGP for the movement protein (MP) and coat protein (CP) of CGMMV. Further, we identified the key regulatory elements in the SGP regions of MP and CP, and their interactions with the core RNA dependent RNA polymerase (RdRp) domain of CGMMVwas deciphered. The modeled structure of core RdRp contains two palm (1-41 aa, and 63-109 aa), one finger (42-62 aa) subdomains with three conserved RdRp motifs that played important role in binding to the SGP nucleic acids. RdRp strongly preferred the double helix form of the stem region in the stem and loop (SL) structures, and the internal bulge elements. In MP-SGP, a total of six elements was identified; of them, the affinity of binding to - 26nt to - 17nt site (CGCGGAAAAG) was higher through the formation of strong hydrogen bonds with LYS16, TYR17, LYS19, SER20, etc. of the motif A in the palm subdomain of RdRp. Similar strong interactions were noticed in the internal bulge (CAACUUU) located at + 33 to + 39 nt adjacent to the translation start site (TLSS) (+ 1). These could be proposed as the putative core promoter elements in MP-SGP. Likewise, total five elements were predicted within - 114nt to + 144 nt region of CP-SGPwith respect to CP-TLSS. Of them, RdRp preferred to bind at the small hairpin located at - 60 nt to - 43 nt (UUGGAGGUUUAGCCUCCA) in the upstream region, and at the complex duplex structure spanning between + 99 and + 114 nt in the downstream region, thus indicating the distribution of core promoter within - 60 nt to + 114 nt region of CP-SGPwith respect to TLSS (+ 1)of the CP; whereas, the - 114 nt to + 144 nt region of CP-SGP might be necessary for the full activity of the CP-SGP. Ourinsilicoprediction certifies the gravity of these nucleotide stretches as the RNA regulatory elements and identifies their potentiality for binding with of palm and finger sub-domain of RdRp. Identification of such elements will be helpful to anticipate the critical length of the SGPs. Our finding will not only be helpful to delineate the SGPs of CGMMV but also their subsequent application in the efficient construction of virus gene-vector for the expression of foreign protein in plant.

BMP7 is a candidate gene for reproductive traits in Yorkshire sows

Bone morphogenetic protein 7 (BMP7) is of the BMP subfamily, and has effects on female fertility by regulating steroidogenesis, granulosa cell states, and follicular development. In the present study, there was assessment of the combined genotypes formed by the three variants within the 3′-UTR of BMP7 gene as associations with sow reproductive functions. The 3′-UTR of the BMP7 gene of pigs was identified using the 3′ RACE assay, and its full-length sequence was found to be 1538 bp in length. Multiple RNA regulatory elements were detected in this region, luciferase activity assays were performed and results indicated miR-22−3p affects BMP7 by directly binding to the miRNA response element in the 3′-UTR (c.2358–2382). In addition, two novel complete linkage variants, c.2256 G > C and a 7-bp indel (c.2259–2265), were identified within the 3′-UTR of the BMP7 gene of pigs. Importantly, combined genotypes with these two novel variants and c.1569A > G, a variant previously identified in the BMP7 3′-UTR of pigs, were associated with sow reproductive traits, including the total number of piglets born, number of dead piglets at birth, and litter weight in the Yorkshire pig population studies. Results from the present study confirm that BMP7 is a candidate gene for the reproductive traits in Yorkshire sows.