Conserved non-coding sequences (CNS) play a crucial role in maize gene regulation by interacting with chromatin accessibility and epigenetic modifications, offering potential targets for crop improvement through molecular breeding.

Keywords: Conserved non-coding sequences, Maize, Phenotypic variations, Regulatory Elements

Conserved non-coding sequences (CNS) play a crucial role in gene regulation despite not encoding proteins. This study aimed to identify CNS in maize (Zea mays B73) by comparing its genome with related species, including Zea mays spp. mexicana, sorghum, foxtail millet, and adlay. The analysis conducted by scientists from Sichuan Agricultural University, Sichuan Tianfu New Area Rural Revitalization Research Institute and Chengdu Normal University revealed that 99.09% of CNS are located in intergenic and promoter regions, suggesting their involvement in transcriptional regulation. CNS near transcription start sites (TSS) may function as enhancers or promoters, while those further away may act as long-range regulatory elements. The study also found that CNS overlap with open chromatin regions, transcription factor binding sites, and epigenetic modifications such as H3K9ac, which is associated with transcriptional activation. Additionally, variations in CNS were significantly linked to maize root traits and agronomic characteristics, reinforcing their regulatory potential in plant development and adaptation.

The study further highlights the functional importance of CNS in gene expression and phenotypic variation. Previous research in plants has demonstrated that CNS can serve as enhancers, such as those regulating the KNOX1 gene family in Arabidopsis. In maize, CNS were identified within the flowering-time regulatory region of Vgt1 and upstream of ZmCCT10, both enriched with enhancer-associated histone modifications. These findings suggest CNS could be leveraged in crop molecular breeding to fine-tune gene expression, improving traits like drought tolerance and yield stability. By using technologies such as CRISPR/Cas9, breeders can modify CNS without disrupting protein-coding regions, enabling precise trait enhancements while maintaining genetic stability.

SorghumBase examples: 

The study identified Zm00001d012886, a maize gene encoding a 40S ribosomal protein, as a key target of conserved non-coding sequences (CNS) that regulate its expression. A total of 41 CNS were found within 5 Kb of the gene, with two SNPs (chr5.S_1568608 and chr5.S_1568631) significantly affecting its expression. These CNS variations were linked to important agronomic traits, including ear leaf length, ear height, and ear length, as well as root traits under drought stress. Gene expression analysis revealed that Zm00001d012886 was more active under drought conditions, suggesting a role in stress adaptation. Since sorghum shares evolutionary similarities with maize, a homologous gene in sorghum may also be CNS-regulated, presenting opportunities for crop improvement in drought-prone environments.

Figure 1: A search for Zm00001d012886 in SorghumBase under the Homology tab using the Gene Tree Homologs filter identified its closest homologs in Sorghum bicolor, specifically SORBI_3001G130301 and SORBI_3001G374700. These genes encode 40S ribosomal protein homologs and are related to RPS21C, a gene involved in protein synthesis. The closest annotated homolog in Arabidopsis thaliana is RPS21C, with sequence identities ranging from 32% to 80% across species. SORBI_3001G130301 is labeled as a hypothetical protein but is considered a putative homolog of RPS21C, while SORBI_3001G374700 is also classified as a hypothetical protein, suggesting potential functional conservation with 40S ribosomal proteins in other species. Notably, sorghum and its related grass species have two copies of this gene located on chromosome 1, whereas maize contains only a single copy, indicating a potential duplication event in sorghum’s evolutionary history. Both sorghum genes are likely involved in ribosomal function and protein synthesis, though their exact roles in gene regulation or stress response require further validation. These findings contribute to comparative genomics studies in cereal crops like maize and rice.
Figure 2: The analysis of SORBI_3001G130301, a homolog of Zm00001d012886, in Sorghum bicolor (BTx623) indicates that this gene is located on Chromosome 1 (10,236,348 – 10,239,420). The ATAC-seq data from Lu et al. (2019), which identifies accessible chromatin regions (ACRs) in 7-day-old sorghum leaves, overlapped with this gene. Specifically, the location 1:10237415-10237589 on the forward strand contains an ACR (10237438), suggesting this region is accessible in 7-day-old sorghum leaves. The ACR within the second exon of SORBI_3001G130301, which is atypical for ACRs. This suggests that the second exon may contain regulatory elements influencing gene expression or alternative splicing in young sorghum leaves. The presence of open chromatin here implies active transcription, potentially revealing an exon-mediated regulatory mechanism that warrants further study.

Reference:

Luo Y, Zhai H, Zhong X, Yang B, Xu Y, Liu T, Wang Q, Zhou Y, Mao Y, Liu Y, Tang Q, Lu Y, Wang Y, Xu J. Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize. BMC Genomics. 2025 Jan 20;26(1):46. PMID: 39833673. doi: 10.1186/s12864-025-11221-9. Read more

Conserved Non-Coding Sequences in Maize: Regulatory Roles and Potential for Crop Improvement

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