Gene

BackgroundDUXC is a multi-copy transcription factor gene found within a long tandem repeat locus in several Laurasiatherians. It is suggested to be functionally similar to human DUX4 because of its shared C-terminal domain and its close phylogenetic relationship to DUX4. DUX family genes are transiently expressed in preimplantation embryos of placental mammals. However, early embryo-derived cDNA proof for DUXC, which is needed for its further functional characterization, has not been reported so far. ResultsOur study provides a full-length sequence of DUXC mRNA, derived from the 8-cell stage in vitro fertilization (IVF) bovine embryos, containing double homeobox and 9aa transactivation domain (9aaTAD)-encoding sequences. Identified DUXC sequence uncovered a first exon that was not previously annotated. We showed that DUXC mRNA levels are independent of the embryonic transcription at the 2-, 4-, and 8-cell stage, whereas its decline, observed from the 8-cell stage onwards, is minor embryonic genome activation (EGA)-dependent. We also investigated the genomic organisation of the DUXC array in eight different cattle breed assemblies, revealing polymorphic internal repeats flanked by an incomplete distal unit at the telomeric end and a much shorter unit at the proximal end of the DUXC array. Despite the presence of a putative polyadenylation signal downstream the distal unit, we presented evidence for the expression of internal but not distal DUXC in early bovine IVF embryos. ConclusionsDUXC is a potential bovine EGA inducer, supported by its expression at peak levels at pre-EGA stages followed by a decrease with a dependency on minor EGA.

Schistosoma mansoni is a parasitic flatworm that has two, genetically determined, sexes. We used aggregated data of 8 posttranslational histone modifications (ChIP-Seq), chromatin accessibility (ATAC-Seq), transcription (RNA-Seq) and genome feature annotations to decipher the histone code of genes involved in the differentiation of schistosome gonads (i.e. female ovaries and male testes). We show schistosome gonads express at least two classes of protein coding genes: H3K4me3-positive genes that display canonical features of eukaryotic protein-coding genes such as peaks of H3K4me3 at the transcription start sites (TSS) and increases in histone acetylation marks towards the transcription end site (TES), but also a non-canonical H3K9/27me3 plateau just upstream of the TSS. H3K4me3 enrichment at the TSS is highly predictive for transcription strength in these genes compared to a second class of protein coding genes (H3K4me3-negative genes) that do not display this pattern and is characterised by absence of the investigated histone marks at TSS and TES. This is indicative of the existence of hitherto unknown, potentially schistosome-specific histone marks in these genes. The absence of H3K4me3 at the TSS is not associated with inducible or stable gene expression in the gonads. Instead, gene ontology analysis indicates that H3K4me3-positive genes are related to functions which typically govern processes such as metabolism or signal transduction while H3K4me3-negative genes are dedicated to cell communication or immune responses. Second, individual histone modifications and their combinations are associated with functional features of the schistosome genome, known as "chromatin colours". In H3K4me3-positive genes, there is clear co-linearity of 3 colours, which strongly suggests a functional role for histone modifications in the control of transcription pre-initiation, promotor release, and transcription termination. Third, there are striking chromatin structure changes during maturation of the gonads in all genomic features including protein-coding and non-protein coding genes as well as repetitive sequences. The nature of these changes is different in both sexes. H3K36me3 and H3K9me3, as well as H3K23ac and H3K9ac show the strongest variations. Last, we show that pharmacological inhibition of histone demethylation activity by IOX1 leads to a concentration-dependent separation ("divorce") of schistosome couples confirming the importance of H3K36/H3K9 methylation for pairing maintenance and indicating histone demethylases as a potential drug target family. Collectively, our findings offer unprecedented insights into histone codes and chromatin dynamics governing the reproductive development of S. mansoni gonads.

AO_SCPLOWBSTRACTC_SCPLOWThe cellular transcription factor BCL11b (B-cell CLL/lymphoma 11b) interacts with numerous cellular and viral factors to modulate gene expression positively or negatively. Post-translational modifications of BCL11b, such as SUMOylation and phosphorylation, have been documented to switch its transcriptional activity from a repressor to an activator state. In the present study, we investigated the acetylation of BCL11b and we identified the histone acetyltransferase p300 as able to acetylate BCL11b. Subsequently, we observed that the mutation of the lysine K686 residue of BCL11b (BCL11b K686R) influenced its global acetylation. Furthermore, the BCL11b K686R mutation also modulated the transcriptional regulation of BCL11b, including its activity in regulating the p21 and IL-2 promoters. This effect on transcriptional regulation was due to the importance of the lysine K686 residue for BCL11b nuclear localization. Our results underscore the critical role of the lysine K686 residue in BCL11b for its interaction with p300 and its nuclear localization, suggesting a possible function of p300 in the nuclear transport of BCL11b. Collectively, our findings contribute to a better understanding of BCL11b-mediated gene expression and of the interactions of BCL11b with cellular partners.

Short Interrupted Repeats Cassettes (SIRC) are recently discovered eukaryotic DNA elements possessing many traits of satellite DNA and mobile genetic elements, and consisted of short direct repeats interspersed with diverse spacer sequences. The SIRC ensemble of individual species is highly heterogenous and cannot be studied using alignment methods. It was found that number of similar SIRC sequences in a given pair of species is in general correlated with their taxonomic distance, and, at the same time, closely related species can possess very diverged SIRC ensembles, which makes SIRC evolutionary pattern closer to mobile genetic element type. The SIRC sequences make up clusters with comparable sequence patterns, that are likely to demonstrate doublet evolutionary model which strongly supports that the SIRC structure is supported by the evolutionary selection. Several SIRC sequences of Arabidopsis were found to be of ancient origin with traceable evolution history as far as to the moss clade. We carried out unbiased detection of SIRC ensembles in 10 plant genomes and found that, despite very high intraspecies heterogeneity, SIRC sets possess strong interspecies phylogenetic signal. Key messageShort Interrupted Repeats Cassettes are elements of ancient origin, and could potentially be used to trace organism history, and to facilitate syntheny and Hi-C analysis.

Polycystic Ovary Syndrome (PCOS) is known as an endocrine and metabolic disorder; however, emerging molecular evidence suggests a far more complex systems-level pathology. In this study, we performed an integrative transcriptomic and pathway-level analysis of endometrial tissue from women with PCOS to gain a deeper understanding of the underlying mechanism facilitating the disorder. The findings of the study highlighted mitochondrial dysfunction, chronic oxidative stress, and multi-layered immune dysregulation, adding some new insight apart from classical hyperandrogenism and insulin resistance. We identified some novel gene disease associations which involve C15orf48, ODF3B PRR15-DT, LINC01176, and LOC105379193. The upstream regulators such as (NFE2L2, TWNK, ALKBH1, BCOR, SMARCA4) involved in processes including mitochondrial genome, redox balance, and chromatin remodeling provided new insights into regulatory mechanisms. The IPA pathway analysis validated the compromised immune recovery with low grade inflammations and mitochondrial dysfunctionality. The observations emphasize on complex associations discarding its PCOS pure endocrine nature through immunometabolic-mitochondrial dysfunctionalities.

The cockroach Blattella germanica possesses panoistic ovaries, in which oocytes lack nurse cells and therefore need to rely on their own transcriptional activity to support embryogenesis. Ovarian development in this species involves the development of a single basal ovarian follicle (BOF) per gonadotropic cycle, a process strictly regulated by endocrine signals, primarily juvenile hormone and ecdysone, which act at both the transcriptional and translational levels. In addition, transcriptional activity in these ovaries is necessary for both regulating and genome protection, and at this level, PIWI-interacting RNAs (piRNAs) play an essential role. Although insect ovaries are known to be particularly rich in piRNAs, their function in ovary maturation is still not well defined. For this purpose, we characterize the piRNA expression dynamics across seven key developmental and reproductive stages, ranging from late nymphal instars to post-vitellogenic adults. piRNA expression in B. germanica shows coordinated fluctuations. Expression remains stable in previtellogenic ovaries, whereas vitellogenic ovaries show pronounced changes. Moreover, vitellogenic ovaries exhibit reduced piRNA diversity due to strong enrichment of a subset of highly expressed piRNAs. Our data show that although piRNAs predominantly map to transposable elements, particularly LINEs, there is a notable increase in gene-derived piRNAs toward the end of the cycle. Our results suggest regulatory roles of piRNAs in modulating both TEs and mRNAs during BOF maturation, likely related to changes in the follicular cell program.

Translation is a crucial regulatory mechanism involved in several diseases, including cancer, where pro-inflammatory conditions within the microenvironment have been shown to modulate the translation of specific mRNAs. In the present study, we focused on the regulation of insulin growth factor-like family member 1 (IGFL1) in MCF7 breast cancer cells in response to pro-inflammatory IL-1{beta} and observed an induction of both transcription and translation. We characterized the 3 untranslated region as regulatory hub for the post-transcriptional regulation and identified a distinct G-rich region to confer the IL-1{beta}-dependent translational increase. Our study therefore provides new insights into the translation regulation of IGFL1 in the context of an inflammatory tumor microenvironment.

Sockeye salmon (Oncorhynchus nerka) is a traditional object of fishery in the northern Pacific, but its island populations now face emerging threats from territories development and escalating risks of unregulated fishing. The present study aims to assess the current status of Kuril island populations associated with the biogeographical processes in the past. We analyzed diversity distribution of the D-loop sequence and three mtSNPs localized in the Cytb and COI genes in sockeye salmon populations across the North Pacific. mtDNA variants were grouped into two distinct lineages: haplogroups 10T and 13T. Their distribution suggests an Asian origin for the 10T lineage and a North American origin for the 13T haplogroup. Testing the biogeographical scenarios support recurrent postglacial expansions of North American strains into the southernmost territories of the Asian range during the last two glacial cycles. Concurrently, during the Holocene transgression, there were two centers of sockeye salmon radiation in Asia associated with the refugium in the Kamchatka River basin and a minor cryptic refugium in the Hokkaido region. We also propose an island bridge hypothesis to explain dispersal of 10T-lineage from the Kamchatka River basin into Cook Inlet and Alaska Peninsula watersheds via the Aleutian Islands.

The X chromosome (chrX) is the eighth largest human chromosome, harbouring an estimated total of 839 protein-coding genes. Historically, the chrX has been described as enriched for genes related to brain development, sexual differentiation and reproduction, earning the epithet of "smart and sexy chromosome". Many studies have confirmed that the chrX is indeed "smart", including a recent systematic analysis of human chrX genes which found an enrichment in genes relevant to brain functions. However, it is less clear whether the chrX being "sexy" still holds true. Here we reviewed the origins of this idea and we evaluated human X-linked genes in terms of their expression across several tissues, their annotated functions and their association with monogenic disorders related to sexual differentiation and reproduction (SDR). We found that sex-specific tissues show higher expression levels from chrX genes than from autosomal genes except in testis, but that X-linked genes are significantly enriched among the most highly expressed genes in testis, specifically within spermatogonia and Sertoli cells. Yet, we found no evidence for an enrichment of genes on the X with annotated functions related to male or female SDR. When analysing SDR-related monogenic disorders, we found a significant enrichment of genes on chrX associated with clinical terms related to male SDR but not with clinical terms related to female or general SDR. Overall, our results support the notion of a somewhat "sexy" X chromosome, shaped by X-linked expression patterns and clinical associations rather than current annotated gene functions.

Cancer-related genomic instability (GI) may cause genetic alterations in spermatozoa, implying health issues not only in cancer survivors, but also in their children [1, 2]. We therefore studied Loss of Y chromosome (LOY), considered as hallmark of GI [3-15], in spermatozoa and blood from survivors of childhood and testicular cancer (CC, TC), and controls (CTRL). We found that LOY was statistically significantly more frequent in spermatozoa from cancer survivors than in controls (Odds Ratio [OR]=2.2 for CC vs. CTRL and OR=2.4 for TC vs. CTRL). Furthermore, LOY was about an order of magnitude more prevalent in spermatozoa than in blood among 18-53-year-old males within all cohorts. Our findings suggest that LOY in spermatozoa might be a clinically useful marker of GI, reduced fertility and disease predisposition in males. Introducing LOY in spermatozoa as a biomarker opens a new research avenue into disease prevention and the causes and consequences of LOY.

Photoperiod sensitivity (PS) is a key biological response in plants as they adapt to specific environments. Rice (Oryza sativa L.) exhibits a clear PS, as it implements critical phase transition decisions based on PS signals. In this study, we identified a novel PS gene, JMJ706, that is expected to deliver photoperiod-related signals to the flowering-time regulatory network in a day-length-dependent manner. The JMJ706 mutants exhibit early flowering under LD and later flowering under SD compared to WT plants. The gene encodes an H3K9me2 demethylase, and under long-day (LD) conditions, its demethylase activity facilitates the expression of Grain number, Plant height, and Heading-date7 (Ghd7). Since Ghd7 is a floral repressor in LD, it promotes the vegetative phase by delaying flowering. Under short-day conditions (SD), H3K9me2 demethylase activity facilitates Early heading-date 1 (Ehd1) expression, and it acts as a floral accelerator by inducing Heading date 3 (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Furthermore, we propose that the daylength-dependent promotion of target genes (Ghd7 and Ehd1) occurs through demethylation of specific promoter regions at a crucial time window. In addition, JMJ706 may play an important role in regulating plant architecture, including plant height. The natural variation in JMJ706 alleles shows high frequencies across major rice subpopulations, suggesting that JMJ706 could play an important role in the geographical distribution and adaptation of rice cultivars. Our results may add a new layer to the rice flowering-time regulatory pathway, supporting regional adaptation and potential for future breeding.

Infertility is a complex condition affecting both the male and female population. Influenced by multiple factors, it remains a constant challenge due to limited understanding of endometrial abnormalities. With this study we aim to investigate the molecular basis of infertility using transcriptomic analysis of endometrial tissue from the NCBI GEO dataset GSE92324. We performed exploratory data analysis using Principal Component Analysis (PCA) to find samples variance followed by differential gene expression (DGE) analysis using DESeq2 package where we identified 168 significant genes with adjusted p-value < 0.05 and |log2FC| > 2. Upregulated genes included GPX3, CXCL14, and PPARGC1A and downregulated genes included WNK4, GJB2, and TRPM6. Functional enrichment using KEGG and GO showed that differentially expressed genes (DEGs) are involved in immune-inflammatory pathways, lipid metabolism and steroid biosynthesis pathways. Through Ingenuity Pathway Analysis (IPA) we identified affected canonical pathways such as increased innate immune responses, altered lipid metabolism and inhibition of mitochondrial dysfunction. Upstream regulator analysis highlighted PTEN, PRKAA1, HDAC4, IL10RA, and RAD51, which were impacting metabolic pathways and anti-inflammatory signalling. Further, through Weighted Gene Co-expression Network Analysis (WGCNA) we found a Turquoise module that had very strong and highly significant negative correlation (cor = - 0.84, respectively and P < 0.0001) with traits of interest. This led to the discovery of C7orf50 as a novel insight involved in cholesterol metabolism linked to infertility. This integrative approach reveals crucial genes, co-expression modules, and underlying pathways involved in female infertility. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/701467v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@4418a6org.highwire.dtl.DTLVardef@ae7900org.highwire.dtl.DTLVardef@89f581org.highwire.dtl.DTLVardef@154f1a9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIFrom the dataset GSE92324 total of 168 significant DEGs associated with unexplained infertility were identified using adjusted p-value < 0.05 and |log2FC| > and < 2. C_LIO_LIIn comparison with the CTD list we identified five genes C1orf106, C15orf59, LINC00461, C15orf48, and C10orf99 previously unknown as having direct evidence of involvement in infertility. C_LIO_LIWGCNA analysis highlighted the turquoise module as highly associated and gave the novel gene C7orf50 associated with cholesterol metabolism. C_LIO_LIIPA revealed PTEN, PRKAA1, IL10RA, and RAD51 as potential upstream regulators and inflammatory pathways, mitochondrial dysfunction as canonical pathways. C_LIO_LIThe study highlights a novel link between GI inflammation and endometrial receptivity. C_LI

Hydroxycarboxylic acid receptors (HCARs) are class A G-protein-coupled receptors that function as metabolic sensors. This receptor family includes three members (HCAR1, HCAR2, and HCAR3) expressed in metabolically active tissues and immune cells, where they link cellular metabolic status to physiological responses. This study aims to elucidate the evolutionary history of the most recently originated members of the HCAR gene family, namely HCAR2 and HCAR3, in primates. According to our phylogenetic analyses, the duplicative history of these genes involved multiple independent duplication events during ape evolution. Thus, most ape lineages possess independently originated duplicated copies, while non-ape primates retain the ancestral condition of a single-copy gene (HCAR2/3). Our analyses further indicate that this single-copy gene in non-ape primates is functionally equivalent to HCAR2, suggesting that the primary functional innovation in apes is associated with the physiological roles of HCAR3. Finally, gene expression analyses reveal that major divergence in tissue expression occurred after the initial duplication event that generated HCAR1 and the HCAR2/3 lineage, whereas HCAR2 and HCAR3 exhibit substantial overlap in their expression profiles. Thus, the more refined and context-dependent regulation of lipid metabolism that provides the HCAR3 receptor seems to have originated multiple times during the evolutionary history of apes.

Insulin resistance, excessive and ectopic fat accumulation, chronic low-grade inflammation, and pancreatic beta-cell failure are pathological features of type 2 diabetes mellitus.MiR-130a has been demonstrated to suppress the mRNA levels of PPAR{gamma}, NF-{kappa}B, and TNF- in vitro. PPAR{gamma} is a master regulator of systemic fat and glucose metabolism. NF-{kappa}B and TNF- are pivotal modulators of inflammation. Therefore, we aimed to examine the systemic effect of miR130a on fat metabolism, glucose/insulin homeostasis, and inflammation in mice. We found that mirR130a-deficient mice exhibited larger white fat mass with hypertrophic adipocytes, increased lipogenic gene expression in fat, and elevated serum leptin levels than controls. The white fat pads of mirR130a-deficient mice showed significant macrophage infiltration with enhanced expression of pro-inflammatory genes. In addition, mirR130a-deficient mice had more severe hepatic steatosis and higher hepatic triglycerides content than controls. Similarly, mirR130a-deficient mice had increased macrophage infiltration and lipogenic and inflammatory gene expression in the liver. Consistently, we found that Lepob/ob mice expressed markedly decreased miR130a expression in the liver and white fat compared to controls. Importantly, mirR130a-deficient mice displayed impaired glucose tolerance and worsened insulin resistance, accompanied with reduced serum adiponectin levels. Furthermore, insulin secretion is reduced in mirR130a-deficient mice compared to controls. In conclusion, knockout of miR130a in mice results in fat hypertrophy, hepatic steatosis, increased macrophage infiltration in liver and fat, glucose intolerance, and insulin resistance. These data indicate miR130a exert systemic anti-diabetic effects.

Sirtuin 6 (SIRT6) is an important regulator of DNA repair, metabolism, chromatin maintenance and longevity. SIRT6 Serine 10 phosphorylation controls SIRT6 recruitment to the sites of DNA damage. To explore the effect of SIRT6 Serine 10 phosphorylation on lifespan, we generated two SIRT6 mutant mouse strains: phospho-null S10A and phosphomimetic S10E. The S10E mutant mice demonstrated enhanced DNA repair capacity, elevated LINE1 expression and reduced lifespan in male mice compared to the wild-type and S10A mice. This result suggests that SIRT6 S10E mutation enhances DNA repair capacity at the expense of reduced LINE1 silencing leading to shorter lifespan. While both SIRT6 functions in DNA repair and chromatin maintenance are important for longevity, our results suggest that when the balance between these functions is shifted, diminished of LINE1 control has a stronger impact on lifespan than enhanced DNA repair.

Linkage disequilibrium (LD) and haplotype block structure govern the resolution and utility of genomic selection, marker-assisted selection, and genome-wide association studies (GWAS) in livestock. We performed a comprehensive genome-wide characterization of LD decay, haplotype block architecture, and population diversity across all 24 autosomes in Nili-Ravi buffalo (Bubalus bubalis; n = 85), using 43,543 post-quality-control SNPs. Mean genome-wide r2 was 0.124 (median 0.074) and mean D was 0.540 (median 0.481), with LD half-decay at {approx}70 kb. A total of 133 haplotype blocks encompassing 721 SNPs were identified (Gabriel et al., 2002). Haploview analysis of nine chromosomes harbouring bTB resistance candidate genes revealed contrasting selection signatures: directional selection at innate immune loci (IFNG, TLR1; H < 0.55) versus balancing selection at adaptive immune loci (BoLA-DRB3, SP110; H > 1.0). Critically, BBU15 Block 3 (28.6 kb; OR52E5/NCR1 locus, 47.16 Mb) showed a genome-wide significant integrated haplotype score (iHS; -log1 0 p = 5.408), directly co-localising with the published bTB susceptibility QTL (Bermingham et al., 2014). The TAA haplotype (frequency 53.3%) at this block represents a candidate resistance-associated haplotype for marker-assisted selection. These findings provide essential parameters for SNP panel design and bTB resistance breeding in South Asian buffalo.

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesize that the putative wheat TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examine the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversions tracts between these two genes and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appears to have diverged from a common ancestor, acquiring distinct structural organizations and biological functions.

Following our laboratorys earlier observations on systemic damage inflicted by sev-Gal4 driven activated Ras (sev>RasV12) over-expression in Drosophila larval eye discs, we now show that sev>RasV12 expressing males suffer enhanced eye roughening and pupal death than female sibs because the former have significantly greater Ras levels in ommatidial cells than in female counterpart. In normally developing ommatidial cells, TBPH/TDP-43 was more abundant in cytoplasm in male than in female eye discs. The sev>RasV12 expression reduced nuclear TBPH in female eye discs but caused no apparent change in males. Caz/Fus, an interacting partner of TBPH, was significantly downregulated in sev>RasV12 eye discs, more so in males. Significant reduction in the microtubule binding protein Futsch in eye discs of sev>RasV12 larvae of either sexes but female-specific elevation of Fas2 appears to be due to the above normal developmental differences in TBPH and Caz in female and male ommatidial cells and because Sxl, the master regulator of sex-determination, is present only in females. In view of known auto-regulatory loop between Fas2 and Ras, we suggest that elevated levels of Fas2 cause levels of Ras to be much less elevated in sev>RasV12 female eye discs than in male sibs. This results in greater local and systemic damage in males. These findings have general and clinical relevance since perturbed Ras signaling is a major factor in several diseases, including cancer.

BackgroundConventional models of human ribosomal DNA (rDNA) array organization have historically depended on transcription-centric boundaries, partitioning the unit into a [~]13 kb rDNA transcription region and a monolithic [~]31 kb intergenic spacer (IGS). While our previous identification of Duplication Segment Units (DSUs) mapped these arrays based on an intuitive analysis of the microsatellite density landscape of the complete reference human genome, our present deep mining of this landscape has revealed a more accurate rDNA Gene Unit Pattern. Methods & ResultsIn this study, we conducted a deep mining analysis of our previously established microsatellite density landscape of the T2T-CHM13 assembly, focusing specifically on nucleolar organizing regions (NORs). We suggest a more accurate rDNA Gene Unit Pattern containing a (CTTT)n microsatellite aggregation ahead of the rDNA gene and a (CT)n microsatellite aggregation behind the gene, rather than a pattern featuring an IGS region inserted between two rDNA genes. ConclusionsA correct rDNA gene pattern of the human genome probably includes a (CTTT)n microsatellite aggregation ahead of the gene and a (CT)n microsatellite aggregation behind it, which possibly constitute cis- and trans-regulating regions; the (CTTT)n and (CT)n microsatellite aggregations may provide two different local stable DNA structures for regulatory protein binding.

MicroRNAs (miRNAs) play essential roles in the posttranscriptional regulation of gene expression in organisms. In the process of synthesizing mature miRNAs from miRNA precursors, the miRNA precursors are cleaved via Dicer at their loop structure, after which the miRNA precursors become mature and regulate transcription. However, the consequences of altering the loop sequence are not fully understood. The silkworm Bombyx mori is a lepidopteran insect with many genetic strains. We identified a mutant of the miRNA miR-3260 whose the part of the loop structure was lacking in a silkworm strain with translucent larval skin. Here, we aimed to analyze the role of wild-type miR-3260 and the influence of the mutation of the loop structure in B. mori. First, we identified the genomic region responsible for the translucent larval skin phenotype and determined that the mutated miR-3260 nucleotide sequences. Then, we predicted the binding partners of wild-type miR-3260 using the RNA hybrid tool and found two juvenile hormone (JH)-related genes as targets of wild-type miR-3260. Next, we assessed the relationships between miR-3260 and JH and found that miR-3260 was highly expressed in the Corpora allata and its expression responded to JH treatment. Meanwhile, miR-3260 mimic and inhibitor did not induce the typical phenotypes associated with JH in B. mori. Then, we compared the dicing products from wild-type and mutant miR-3260 precursors and observed that neither form underwent Dicer-mediated cleavage when the loop structure was altered. These results suggest that loop mutations in the miR-3260 precursor may not influence dicing activity, consistent with the lack of observable phenotypic effects.