BMC genomic data最新文献

{"title":"Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots.","authors":"Van Hong Thi Dao, Loan To Nguyen, Khanh Phuong Do, Vinh The Nguyen, Hieu Van Nguyen, Khanh Ngoc Pham, Truong Xuan Nguyen, Son Truong Dinh","doi":"10.1186/s12863-024-01291-1","DOIUrl":"10.1186/s12863-024-01291-1","url":null,"abstract":"<p><strong>Objectives: </strong>This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomonas sp. strain HOU2 will help identify potential genes or pathways that could be involved in the plant growth-promoting effects on in vitro dangshen plants, providing valuable information for future applications.</p><p><strong>Data description: </strong>The genomic DNA of Pseudomonas sp. strain HOU2 was sequenced using Oxford Nanopore's PromethION sequencer with an R10.4.1 flow cell (Table 1, Data file 1). The assembly of the Pseudomonas sp. strain HOU2 genome was conducted using Flye version 2.9, resulting in a single circular chromosome of 6,047,544 bp with a mean coverage of 488 (Table 1, Data file 2). The annotation of genes, proteins, and features of the HOU2 genome were performed by the RAST server (Rapid Annotation using Subsystem Technology) ( https://rast.nmpdr.org/ ) (Table 1, Data file 3, 4, 5) [6, 7]. The Pseudomonas sp. strain HOU2 genome was determined to be most similar to that of Pseudomonas koreensis using the Type Strain Genome Server ( https://tygs.dsmz.de/ , version v391) [8].</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"107"},"PeriodicalIF":1.9,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide phylogenetic analysis and expansion of gene families involved in detoxification in Smittia aterrima (Meigen)and Smittia pratorum (Goetghebuer) (Diptera, Chironomidae).","authors":"Bin Mao, Yue Zheng, Yunli Xiao, Kaixia Yang, Jingru Shangguan, Mi Shen, Hao Sun, Xiangliang Fang, Yue Fu","doi":"10.1186/s12863-024-01289-9","DOIUrl":"10.1186/s12863-024-01289-9","url":null,"abstract":"<p><p>Smittia aterrima (Meigen, 1818) and Smittia pratorum (Goetghebuer, 1927) are important indicator insects for aquatic environments, showing extensive tolerance to the environment. However, the genome-wide phylogenetic relationships and characteristics of the detoxification mechanisms in S. aterrima and S. pratorum remain unclear. Based on the genomes of the two species obtained in our preliminary studies and nine genomes from the NCBI database, we found that chironomids diverged from other mosquitoes approximately 200 million years ago (MYA), and S. aterrima and S. pratorum diverged about 30 MYA according to phylogenetic analysis. Gene family evolution analysis showed significant expansion of 43 and 15 gene families in S. aterrima and S. pratorum, respectively, particularly those related to detoxification pathways. Positive selection analysis reveals that genes under positive selection are crucial for promoting environmental adaptation. Additionally, the detoxification-associated gene families including Cytochrome P450 (CYP), Glutathione S-transferases (GST), ATP-binding cassette (ABC), carboxylesterase (CCE), and UDP-glucuronosyltransferase (UGT) were annotated. Our analysis results show that these five detoxification gene families have significantly expanded in the chironomid genomes. This study highlights the genome evolution of chironomids and their responses to mechanisms of tolerance to environmental challenges.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"106"},"PeriodicalIF":1.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification, characterization and expression profiles of FORMIN gene family in cotton (Gossypium Raimondii L.).","authors":"Pollob Shing, Md Shohel Ul Islam, Mst Sumaiya Khatun, Fatema Tuz Zohra, Naimul Hasan, Shaikh Mizanur Rahman, Md Abdur Rauf Sarkar","doi":"10.1186/s12863-024-01285-z","DOIUrl":"10.1186/s12863-024-01285-z","url":null,"abstract":"<p><strong>Background: </strong>Gossypium raimondii serves as a widely used genomic model cotton species. Its genetic influence to enhance fiber quality and ability to adapt to challenging environments both contribute to increasing cotton production. The formins are a large protein family that predominately consists of FH1 and FH2 domains. The presence of the formin domains highly regulates the actin and microtubule filament in the cytoskeleton dynamics confronting various abiotic stresses such as drought, salinity, and cold temperatures.</p><p><strong>Results: </strong>In this study, 26 formin genes were analyzed and characterized in G. raimondii and mostly were found in the nucleus and chloroplast. According to the evolutionary phylogenetic relationship, GrFH were dispersed and classified into seven different groups and shared an ancestry relationship with MtFH. The GrFH gene structure prediction revealed diverse intron-exon arrangements between groups. The FH2 conserved domain was found in all the GrFH distributed on 12 different chromosomes. Moreover, 11 pairs of GrFH transpired segmental duplication. Among them, GrFH4-GrFH7 evolved 35 million years ago (MYA) according to the evolutionary divergence time. Besides, 57 cis-acting regulatory elements (CAREs) motifs were found to play a potential role in plant growth, development, and in response to various abiotic stresses, including cold stress. The GrFH genes mostly exhibited biological processes resulting in the regulation of actin polymerization. The ERF, GATA, MYB, and LBD, major transcription factors (TFs) families in GrFH, regulated expression in abiotic stress specifically salt as well as defense against certain pathogens. The microRNA of GrFH unveiled the regulatory mechanism to regulate their gene expression in abiotic stresses such as salt and cold. One of the most economic aspects of cotton (G.raimondii) is the production of lint due to its use in manufacturing fabrics and other industrial applications. The expression profiles of GrFH in different tissues particularly during the conversion from ovule to fiber (lint), and the increased levels (up-regulation) of GrFH4, GrFH6, GrFH12, GrFH14, and GrFH26 under cold conditions, along with GrFH19 and GrFH26 in response to salt stress, indicated their potential involvement in combating these environmental challenges. Moreover, these stress-tolerant GrFH linked to cytoskeleton dynamics are essential in producing high-quality lint.</p><p><strong>Conclusions: </strong>The findings from this study can contribute to elucidating the evolutionary and functional characterizations of formin genes and deciphering their potential role in abiotic stress such as cold and salt as well as in the future implications in wet lab.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"105"},"PeriodicalIF":1.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pre-pandemic artificial MERS analog of polyfunctional SARS-CoV-2 S1/S2 furin cleavage site domain is unique among spike proteins of genus Betacoronavirus.","authors":"Andreas Martin Lisewski","doi":"10.1186/s12863-024-01290-2","DOIUrl":"10.1186/s12863-024-01290-2","url":null,"abstract":"<p><strong>Objectives: </strong>SARS-CoV-2 spike (S) glycoprotein furin cleavage site is a key determinant of SARS-CoV-2 virulence and COVID-19 pathogencity. Located at the S1/S2 junction, it is unique among sarbecoviruses but frequently found among betacoronaviruses. Recent evidence suggests that this site includes two additional functional motifs: a pat7 nuclear localization signal and two flanking O-glycosites. However, a systematic genus and subgenus analysis of spike protein sequences bearing this polyfunctional sequence domain has been missing.</p><p><strong>Data description: </strong>Here we report comprehensive sequence data to demonstrate that among spike proteins of genus Betacoronavirus and outside of the SARS-CoV-2 clade a fully analogous S1/S2 domain was found in only one other virus: the artificial MERS infectious clone MERS-MA30, described already in 2017, which was rationally selected from serial passage in genetically humanized mice. As the evolutionarily closest betacoronaviruses outside of the SARS-CoV-2 clade lack all its three functional motifs, these data extend-beyond natural evolution and zoonosis-the current view on SARS-CoV-2 pre-pandemic origins by presenting the analogous S1/S2 MERS-MA30 sequence domain as a precise molecular blueprint for SARS-CoV-2.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"104"},"PeriodicalIF":1.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pharmacogenomic insights into tuberculosis treatment shows the NAT2 genetic variants linked to hepatotoxicity risk: a systematic review and meta-analysis.","authors":"Rashmi Mahajan, Anuj Kumar Tyagi","doi":"10.1186/s12863-024-01286-y","DOIUrl":"10.1186/s12863-024-01286-y","url":null,"abstract":"<p><strong>Background: </strong>Tuberculosis (TB) patients undergoing anti-tuberculosis treatment often face serious adverse drug reactions, such as hepatotoxicity. Genetic variants of the N-acetyltransferase 2 (NAT2) gene have been linked to an increased risk of these toxic events.</p><p><strong>Objective: </strong>This study aims to provide a comprehensive evaluation of the evidence linking NAT2 genetic variants to anti-tuberculosis drug-related hepatotoxicity (ATDH).</p><p><strong>Method: </strong>A comprehensive review and meta-analysis was performed by accessing databases such as PubMed, Scopus, and Web of Science. A total of 24 articles were incorporated into the dataset. Meta-analyses were conducted to gather estimates of the association between the slow acetlylators (SA) genotype and ATDH. The studies were stratified by ethnicity, regimen, genotyping methods, criteria for liver toxicity, and dosage. Also, meta-analysis for the specific SA type that was most likely responsible for the ATDH was also conducted.</p><p><strong>Results: </strong>The included studies showed individuals with a slow NAT2 acetylator had a significantly greater risk of experiencing hepatotoxicity ATDH (odds ratio [OR] 2.52 (95% CI: 1.95-3.27; p value < 0.001) compared to individuals with other types of acetylator (i.e., rapid and immediate). Among individuals with slow acetylator NAT2*5/7, NAT2*5/6, and NAT2*6/6 genotypes, there is a greater likelihood of association compared to other variations.</p><p><strong>Conclusion: </strong>Our meta-analysis confirms a significant association between slow NAT2 acetylator and increased hepatotoxicity risk. The findings from the present underscore the potential of pharmacogenomic testing to improve TB treatment outcomes. By identifying patients with the slow acetylator NAT2 genotype, healthcare providers can predict an increased risk of anti-tuberculosis drug-induced hepatotoxicity. This allows for personalized treatment strategies, such as adjusting drug dosages or selecting alternative therapies, to minimize adverse effects and optimize efficacy.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"103"},"PeriodicalIF":1.9,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PALS1-dependent modulations of mRNA profiles in MDCK II cells grown in non-confluent monolayers and three-dimensional cysts.","authors":"Klaus Schughart, Annika Möller-Kerutt, Verena Höffken, Pavel Nedvetsky, Ann-Christin Groh, Daniela Anne Braun, Hermann Pavenstädt, Thomas Weide","doi":"10.1186/s12863-024-01284-0","DOIUrl":"10.1186/s12863-024-01284-0","url":null,"abstract":"<p><p>In epithelia, apicobasal cell polarization is closely linked to cell-cell contact formation, both controlled by the conserved Crumbs (CRB) complex, which includes the transmembrane protein Crumbs (CRB3a) and adapter proteins PALS1, PATJ, and LIN7c. In MDCK II cells, a model for cell polarization, depletion of PALS1 - which binds to all CRB components - leads to defective cell polarization and improper distribution of tight junction proteins, resulting in severe epithelial barrier defects in 3D cyst models. This study investigated whether this phenotype is associated with transcriptional changes by analyzing wildtype (WT) and PALS1 knockout (KO) MDCK II cell lines grown under non-confluent conditions and in 3D cyst cultures. Our results indicate that the transition from non-confluent cells to 3D cysts involves numerous differentially expressed genes (DEGs) in both WT and KO cells. Importantly, the analyses revealed significant overlaps between WT and KO cells in their maturation processes, suggesting that most identified DEGs are linked to differentiation from non-confluent to polarized MDCK cells and likely not a result of PALS1 deficiency. Gene Ontology (GO) enrichment and over-representation analyses using REACTOME and KEGG databases confirmed these similarities. In contrast, the direct comparison of WT and KO cells at the two stages showed fewer DEGs and overlaps in associated biological processes and signaling pathways. DEGs associated with the 3D stage, in which the phenotype manifests, contain DEGs and pathways that were predominantly linked to cell cycle linked processes, centromere assembly, or DNA replication. Furthermore, the transcription of genes encoding key junction proteins, additional polarity proteins, and cell-substrate interaction proteins is less affected by the loss of PALS1, indicating that PALS1 influences the transcriptional profiles in epithelial cells as a modulating factor.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"102"},"PeriodicalIF":1.9,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11607895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PIWIL genes in hepatocellular carcinoma: a multi-omics approach uncovering dysregulated expression and ceRNA networks in mice.","authors":"Hailing Huang, Ruiqun Lu, Shenni Peng, Shi Huang, Yinyin Mo, Genliang Li","doi":"10.1186/s12863-024-01283-1","DOIUrl":"10.1186/s12863-024-01283-1","url":null,"abstract":"&lt;p&gt;&lt;p&gt;This multi-omics study delves into the expression patterns of PIWIL genes and their correlation with hepatocellular carcinoma (HCC) progression, utilizing whole transcriptome sequencing, bioinformatics, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) in mice. We identified differential expression levels of PIWIL genes between HCC and control tissues and analyzed their roles within the competing endogenous RNA (ceRNA) network related to regulatory non-coding RNA-mediated gene silencing (RNGS). Our findings showed that Piwil1 and Piwil4 were overexpressed while Piwil2 is underexpressed. As ceRNAs, specific lncRNAs, including Pvt1, Gas5, and BGIGI10090_38749, might sponge up miR-351-5p and miR-31-5p, promoting Piwil1 and Piwil4 expression, while miR-133b-3p, lacking ceRNA sponge absorption, continues to inhibit Piwil2. Through their interactions with PPI proteins encoded by RNGS genes, especially Dhx9, Drosha, Mov10, and Tdrd1, PIWI family members might play a multifaceted role in regulating gene expression and metabolic processes, thereby involving the development and progression of HCC. These interactions within the PPI network could influence the stability and activity of PIWIL proteins and contribute to the overall regulation of gene expression and HCC progression. In the RNGS, a diverse array of miRNAs, genes, lncRNAs, circRNAs, and pseudogenes have been observed, which are suggested to intricately interplay, potentially weaving a complex ceRNA regulatory network. Abnormally expressed miRNA-targeted genes in RNGS are associated with key biological processes, such as lipid metabolism and immune responses, crucial for tumor cell survival, and processes supporting tumor growth and invasion, like translation and cytoskeleton organization. This regulation is reflected in distinct KEGG pathways for downregulated and upregulated targets, highlighting the dualistic role of PIWIL genes in modulating HCC progression. The study concludes that PIWI family members have a correlation with HCC progression and play divergent roles in the pathogenesis, with overexpression of the Piwil1 and Piwil4 potentially promoting HCC progression and underexpression of Piwil2 likely suppressing tumor development. The ceRNA mechanism and PPI network are crucial in regulating the expression and function of PIWIL genes, respectively. The intricate ceRNA network potentially regulates the expression of miRNA-targeted genes in RNGS, which might be crucial for tumor survival and promotion, with impacts on immune responses and cell growth based on enriching results of dysregulated miRNA-targeted genes in HCC. By shedding light on the molecular intricacies of HCC, this multi-omics study underscores the pivotal roles of epigenetic regulations, especially the influence of PIWI family genes with other genes and ncRNAs in the RNGS process in HCC pathology. The findings offer valuable insights into the molecular mechanisms underpinning HCC, which may info","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"101"},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico splicing analysis of the PMS2 gene: exploring alternative molecular mechanisms in PMS2-associated Lynch syndrome.","authors":"Cătălin Vasile Munteanu, Cătălin Marian, Adela Chiriță-Emandi, Maria Puiu, Adrian Pavel Trifa","doi":"10.1186/s12863-024-01281-3","DOIUrl":"10.1186/s12863-024-01281-3","url":null,"abstract":"<p><p>Lynch syndrome (LS) is one of the most common hereditary cancer syndrome in human populations, associated with germline variants in MLH1, MSH2/EPCAM, MSH6 and PMS2 genes. The advent of next generation sequencing has proven a significant impact in germline variant detection in the causative genes; however, a large proportion of patients with clinical criteria still receive uncertain or negative results. PMS2 is the least frequent reported gene, associated with up to 15% of LS cases with late-onset disease and low penetrance phenotype; however, the proportion of PMS2-LS cases is considered to be highly underestimated. In this context, our analysis aimed to improve the current diagnostic yield by focusing on missense and intronic PMS2 variants available in public clinical databases (ClinVar, LOVD). We performed an in silico assessment of the wild-type DNA sequence and the reported genetic variants, employing splicing bioinformatics tools known for their effectiveness in other genes. Splicing variants were predicted in silico and using GTEx short-read RNA expression data. Out of the 2384 missense variants discovered, 90% were classified with uncertain significance (VUS). 4.9% of missense variants were shown to have a potential splicing consequence (DS > 0.2) using SpliceAI. As described in the original publication, SpliceAI-visual was proven effective in annotation of short intronic variants (< 50 bp). Four short intronic variants were identified using SpliceAI-visual as potentially splicing disturbing, in spite of using a lower threshold (DS > 0.1). Exons 2, 3, 4, 5, 6, 7, 8, 11, 12 and 14 were consistently predicted in at least three out of eight software with weak canonical splice sites. Additionally, we noted that both Exonic Splicing Enhancers (ESEs) and Exonic Splicing Silencers (ESSs) contribute significantly to alternative splicing and exonic selection in PMS2 gene. Specifically, ESE motifs were consistently more abundant in highly expressed exons 5, 11 and 14, while ESS motifs played a fundamental role in exons 6, 7 and 10. Computational analysis performed in our study serves as a valuable filtering step for guiding further RNA experiments. Additional functional data is necessary to validate our findings.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"100"},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic data of peach varieties with different chilling requirement levels.","authors":"Weihan Zhang, Yayun Sun, Haiyan Li, Yuepeng Han, Baoxiong Wan, Liao Liao","doi":"10.1186/s12863-024-01279-x","DOIUrl":"10.1186/s12863-024-01279-x","url":null,"abstract":"<p><strong>Objectives: </strong>Peach is a deciduous tree widely cultivated in temperate and subtropical regions that requires a process of bud endodormancy to produce normal flowering and fruiting. This release requires a certain accumulation of cold, named chilling requirement (CR). CR is genotype dependent and with varies levels among different species and accessions. Thus, we collected the bud transcriptomic data of two peaches with different CR levels and conduct a series standard basic analysis. The peach bud transcriptomic data we gathered provides a valuable dataset for exploring the relationships between gene expression and peach CR levels.</p><p><strong>Data description: </strong>We extracted and sequenced the RNA of different CR peach buds at the same status in three endodormancy stages. Each stages have three biological replicates. A total of 18 RNA-seq libraries were obtained and mapped to the reference genome after quality control. The gene expression level was normalized by two methods (TPM and FPKM). Differentially expressed genes (DEGs) analysis revealed that a total of 2,481 unique genes with an absolute value of log2 fold change (FC) greater than 1.0. Homologous functional annotation of these DEGs were conducted which provided further information for CR potential related genes identified and functional genomics studies.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"99"},"PeriodicalIF":1.9,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The amniote-conserved DNA-binding domain of CGGBP1 restricts cytosine methylation of transcription factor binding sites in proximal promoters to regulate gene expression.","authors":"Ishani Morbia, Praveen Kumar, Aditi Lakshmi Satish, Akanksha Mudgal, Subhamoy Datta, Umashankar Singh","doi":"10.1186/s12863-024-01282-2","DOIUrl":"10.1186/s12863-024-01282-2","url":null,"abstract":"<p><p>CGGBP1 is a GC-rich DNA-binding protein which is important for genomic integrity, gene expression and epigenome maintenance through regulation of CTCF occupancy and cytosine methylation. It has remained unclear how CGGBP1 integrates multiple diverse functions with its simple architecture of only a DNA-binding domain tethered to a C-terminal tail with low structural rigidity. We have used truncated forms of CGGBP1 with or without the DNA-binding domain (DBD) to assay cytosine methylation and global gene expression. Proximal promoters of CGGBP1-repressed genes, although significantly GC-poor, contain GC-rich transcription factor binding motifs and exhibit base compositions indicative of low C-T transition rates due to prevention of cytosine methylation. Genome-wide analyses of cytosine methylation and binding of CGGBP1 DBD show that CGGBP1 restricts cytosine methylation in a manner that depends on its DBD and its DNA-binding. The CGGBP1-repressed genes show an increase in promoter cytosine methylation alongside a decrease in transcript abundance when the DBD-deficient CGGBP1 is expressed. Our findings suggest that CGGBP1 protects transcription factor binding sites (TFBS) from cytosine methylation-associated loss and thereby regulates gene expression. By analysing orthologous promoter sequences we show that restriction of cytosine methylation is a function of CGGBP1 progressively acquired during vertebrate evolution. A superimposition of our results and evolution of CGGBP1 suggests that mitigation of cytosine methylation is majorly achieved by its N-terminal DBD. Our results position CGGBP1 DNA-binding as a major evolutionarily acquired mechanism through which it keeps cytosine methylation under check and regulates TFBS retention and gene activity.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"98"},"PeriodicalIF":1.9,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}