scholarly journals Effects of Certain cis-Regulatory Elements on Stage-Specific vitellogenin Expression in the Bombyx mori (Lepidoptera: Bombycidae)

2020 ◽  
Vol 20 (3) ◽  
Author(s):  
Guanwang Shen ◽  
Hongling Liu ◽  
Ying Lin ◽  
Dongxu Xing ◽  
Yujing Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factors ◽  
Bombyx Mori ◽  
Regulatory Network ◽  
Theoretical Basis ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Stage Specificity ◽  
E Box

Abstract Bombyx mori vitellogenin (BmVg) is highly upregulated during pupation, and the 20-hydroxyecdysone and amino acids may regulate stage-specific BmVg expression. However, previous studies showed that other factors may also affect stage-specific BmVg expression. Here, we characterized effective BmVg transcription factors by identifying the corresponding cis-regulatory elements (CREs). We prepared transgenic B. mori, in which DsRed was driven by various lengths of BmVg promoter. qRT-PCR analysis showed that DsRed expression driven by a 1.0-kb BmVg promoter (VgP1.0K) was consistent with endogenous BmVg. VgP1.0K specificity was closer to the endogenous BmVg promoter than that of VgP0.8K. These results suggest that CREs affecting stage-specific BmVg expression were localized to the 1.0-kb BmVg promoter. We investigated the effects of certain CREs that could influence the stage specificity of BmVg promoter on BmVg expression in transgenic B. mori. The relative DsRed expression was significantly reduced in transgenic female B. mori and the peak in DsRed expression was delayed after E-box CRE mutation. These results demonstrate that the E-box element enhanced BmVg expression and also affected stage-specific BmVg expression. Moreover, the relative DsRed expression was significantly increased in transgenic female of B. mori after 3×BD CRE mutation in BmVg promoter. However, the stage specificity of the mutated promoter was consistent with that of the endogenous BmVg promoter. The 3×BD element downregulated BmVg but had no effect on stage-specific BmVg expression. The present study promoted the process of elucidating the regulatory network for stage-specific BmVg expression and furnished a theoretical basis for the application of BmVg promoter.

scholarly journals Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network

2021 ◽  
Author(s):  
Valérie Schreiber ◽  
Reuben Mercier ◽  
Sara Jímenez ◽  
Tao Ye ◽  
Emmanuel García-Sánchez ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Beta Cells ◽  
Regulatory Network ◽  
Islet Cell ◽  
Regulatory Elements ◽  
Cell Development ◽  
Bhlh Transcription Factor ◽  
Gene Regulatory ◽  
Endocrine Progenitors

Objective: Mice lacking the bHLH transcription factor (TF) Neurog3 do not form pancreatic islet cells, including insulin secreting beta cells, causing diabetes. In human, homozygous mutations of NEUROG3 manifest with neonatal or childhood diabetes. Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. Methods: We generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. We used the CUT&RUN technique to map NEUROG3 occupancy and epigenetic marks in pancreatic endocrine progenitors (PEP) differentiated from this hiPSC line. We integrated NEUROG3 occupancy data with chromatin status and gene expression in PEPs and their NEUROG3-dependence. In addition, we searched whether NEUROG3 binds type 2 diabetes mellitus (T2DM)-associated variants at the PEP stage. Results: CUT&RUN revealed a total of 863 NEUROG3 binding sites assigned to 1268 unique genes. NEUROG3 occupancy was found at promoters as well as at distant cis-regulatory elements frequently overlapping within PEP active enhancers. De novo motif analyses defined a NEUROG3 consensus binding motif and suggested potential co-regulation of NEUROG3 target genes by FOXA, RFX or PBX transcription factors. Moreover, we found that 22% of the genes downregulated in NEUROG3−/− hESC-derived PEPs are bound by NEUROG3 and thus likely to be directly regulated. NEUROG3 targets include transcription factors known to have important roles in islet cell development or function, such as NEUROD1, PAX4, NKX2-2, SOX4, MLXIPL, LMX1B, RFX3, and NEUROG3 itself. Remarkably, we uncovered that NEUROG3 binds transcriptional regulator genes with enriched expression in human fetal pancreatic alpha (e.g., IRX1, IRX2), beta (e.g., NKX6-1, SMAD9, ISX, TFCP2L1) and delta cells (ERBB4) suggesting that NEUROG3 could control islets subtype programs. Moreover, NEUROG3 targets genes critical for insulin secretion in beta cells (e.g., GCK, ABCC8/KCNJ11, CACNA1A, CHGA, SCG2, SLC30A8 and PCSK1). In addition, we unveiled a panel of ncRNA potentially regulated by NEUROG3. Lastly, we identified several T2DM risk SNPs within NEUROG3 peaks suggesting a possible developmental role of NEUROG3 in T2DM susceptibility. Conclusion: Mapping of NEUROG3 genome occupancy in PEPs uncovers an unexpectedly broad, direct control of the endocrine gene regulatory network (GRN) and raises novel hypotheses on how this master regulator controls islet and beta cell differentiation.

scholarly journals Cloning and expression analysis of GATA1 gene in Carassius auratus red var

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yusu Tian ◽  
Yuandong Sun ◽  
Mi Ou ◽  
Xiaojuan Cui ◽  
Dinggang Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Carassius Auratus ◽  
Cdna Sequence ◽  
Cloning And Expression ◽  
Abnormal Development ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Gene Expression Levels ◽  
Gata Family

AbstractBackgroundGATA1 is a key transcription factor in the GATA family, and promotes the differentiation and maturation of red blood cell, which is essential for normal hematopoiesis.ResultsOur results showed that the cDNA sequence ofGATA1 was 2730 bp long encoding 443 amino acids. qRT-PCR analysis demonstrated thatGATA1 had the highest expression in testis (T), followed by pituitary (P) and spleen (S).GATA1 gene expression inC. auratusred var. embryo from the neuroblast stage (N) to the embryo hatching (H) changes continuously; and the gene expression levels of nonylphenol (NP)-treated and those of control embryos were significantly different. Moreover, Methylation levels ofGATA1gene in NP-treated embryos were higher than those in control embryos, indicating that NP affectedGATA1methylation.ConclusionsOur study provides cues for further studying the roles ofGATA1 gene in fish development, and suggested a potential molecular mechanism by which NP leads to abnormal development of fish embryos.

scholarly journals Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12484
Author(s):  
Zilin Zhao ◽  
Jiaran Shuang ◽  
Zhaoguo Li ◽  
Huimin Xiao ◽  
Yuling Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Qrt Pcr

Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

scholarly journals Genomic Retargeting of Tumor Suppressors p53 and CTCF Promotes Oncogenesis

2019 ◽  
Author(s):  
Michal Schwartz ◽  
Avital Sarusi Portugez ◽  
Bracha Zukerman Attia ◽  
Miriam Tannenbaum ◽  
Olga Loza ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Tumor Suppressors ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Cancer Development ◽  
Chromatin Binding ◽  
Transcriptional Reprogramming ◽  
Major Variation ◽  
Regulatory Landscape

AbstractGene transcription is substantially regulated by distant regulatory elements via combinatorial binding of transcription factors. It is more and more recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional reprogramming associated with this process. Using Hi-C data, we couple between differentially expressed genes and their differentially active regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as major determinants of transcriptional reprogramming at early stages of HRas-induced transformation. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.

scholarly journals Transcriptome-based Discovery of AP2/ERF Transcription Factors Related to Terpene Trilactones Synthesis in Ginkgo biloba

2019 ◽  
Vol 47 (3) ◽  
Author(s):  
Linling LI ◽  
Honghui YUAN ◽  
Sanxing ZHA ◽  
Jie YU ◽  
Xian XIAO ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Ginkgo Biloba ◽  
Target Gene ◽  
Active Pharmaceutical Ingredient ◽  
Regulatory Elements ◽  
Digital Object Identifier ◽  
E Box ◽  
Terpene Trilactones ◽  
Erf Transcription Factors

Ginkgo biloba is a unique tree in China with medicinally and phylogenetically important characteristics. Terpene trilactones (TTL) is a key active pharmaceutical ingredient in Ginkgo, so the content of TTL in Ginkgo has become one of the important indices for evaluating quality of the medicinal materials. By transcriptome sequencing on samples treated by chlormequat, ultraviolet (UV) and drought, totally 59820 contigs and 37564 unigenes were obtained. Furthermore, 18234 unigenes were annotated through COG, KEGG and GO analysis. There were 78 AP2/ERF transcription factors, 23 factors of up-regulation and 66 factors of down-regulation that were related with synthetic pathway of TTL in Ginkgo. Phylogenetic tree clustering analysis indicated that there were 42 AP2s could be clustered into ERF, DREB and RVA subfamilies. EMSA analysis demonstrated that GbERF13, GbERF25 and GbERF27 could bind with regulatory elements, such as E-box, in the upstream of GbMECPs promoter. Expression analysis showed that the expression level of GbERF25 was the highest in root, and GbERF25 and GbERF27 were expressed in relatively high transcription levels in leaf and other tissues. The results of qRT-PCR indicated that CCC treatment could significantly improve expression levels of ERF25 and ERF27, and UV and drought could induce transcription levels of ERF13 and ERF25, respectively. The results implied that ERF25 and ERF27 might involve in the induction and regulation of CCC treatment on synthesis of bilobalide in G. biloba. ERF13 might participate in the regulation of bilobalide synthesis induced by UV, and EFR25 might involve in the regulation of the synthesis induced by drought. During annual cycle of expression, the transcription levels of ERF13, ERF25 and ERF27 had significantly positive correlation with diterpene level with correlation coefficient 0.975. It implied that these transcription factors mainly acted on the MEP pathway that regulated synthesis of bilobalide. The aim of the research was to indicate the mechanism of environment or cultivation measure regulating target gene of TTL metabolic pathway by AP2/ERF, and establish metabolic network of AP2/ERF regulating TTL synthesis.   ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

scholarly journals Transcriptomic analysis reveals key transcription factors associated to drought tolerance in a wild papaya (Carica papaya) genotype

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245855
Author(s):  
Humberto Estrella-Maldonado ◽  
Amaranta Girón Ramírez ◽  
Gabriela Fuentes Ortiz ◽  
Santy Peraza-Echeverría ◽  
Octavio Martínez-de la Vega ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Water Deficit ◽  
Carica Papaya ◽  
Differential Expression Analysis ◽  
Transcriptomic Analysis ◽  
Cdna Libraries ◽  
Pcr Analysis ◽  
Water Deficit Stress ◽  
Wild Genotype ◽  
Qrt Pcr

Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown in Mexico. In the present study, plants from a wild Carica papaya genotype and a commercial genotype were subjected to water deficit stress (WDS), and their response was characterized in physiological and molecular terms. The physiological parameters measured (water potential, photosynthesis, Fv/Fm and electrolyte leakage) confirmed that the papaya wild genotype showed better physiological responses than the commercial one when exposed to WDS. Subsequently, RNA-Seq was performed for 4 cDNA libraries in both genotypes (susceptible and tolerant) under well-watered conditions, and when they were subjected to WDS for 14 days. Consistently, differential expression analysis revealed that after 14 days of WDS, the wild tolerant genotype had a higher number of up-regulated genes, and a higher number of transcription factors (TF) that were differentially expressed in response to WDS, than the commercial genotype. Thus, six TF genes (CpHSF, CpMYB, CpNAC, CpNFY-A, CpERF and CpWRKY) were selected for further qRT-PCR analysis as they were highly expressed in response to WDS in the wild papaya genotype. qRT-PCR results confirmed that the wild genotype had higher expression levels (REL) in all 6 TF genes than the commercial genotype. Our transcriptomic analysis should help to unravel candidate genes that may be useful in the development of new drought-tolerant cultivars of this important tropical crop.

scholarly journals The long non-coding RNA MEG3 plays critical roles in the pathogenesis of cholesterol gallstone

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10803
Author(s):  
Changlin Qian ◽  
Weiqing Qiu ◽  
Jie Zhang ◽  
Zhiyong Shen ◽  
Hua Liu ◽  
...  
Keyword(s):  
Normal Control ◽  
Regulatory Network ◽  
Cholesterol Gallstone ◽  
Normal Control Group ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Control Group ◽  
Ppi Network ◽  
Model Group ◽  
Qrt Pcr

Background Cholesterol gallstone (CG) is the most common gallstone disease, which is induced by biliary cholesterol supersaturation. The purpose of this study is to investigate the pathogenesis of CG. Methods Sixteen mice were equally and randomly divided into model group and normal control group. The model group was fed with lithogenic diets to induce CG, and then gallbladder bile lipid analysis was performed. After RNA-seq library was constructed, differentially expressed mRNAs (DE-mRNAs) and differentially expressed lncRNAs (DE-lncRNAs) between model group and normal control group were analyzed by DESeq2 package. Using the cluster Profiler package, enrichment analysis for the DE-mRNAs was carried out. Based on Cytoscape software, the protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were built. Using quantitative real-time reverse transcription-PCR (qRT-PCR) analysis, the key RNAs were validated. Results The mouse model of CG was suc cessfully established, and then 181 DE-mRNAs and 33 DE-lncRNAs between model and normal groups were obtained. Moreover, KDM4A was selected as a hub node in the PPI network, and lncRNA MEG3 was considered as a key lncRNA in the regulatory network. Additionally, the miR-107-5p/miR-149-3p/miR-346-3-MEG3 regulatory pairs and MEG3-PABPC4/CEP131/NUMB1 co-expression pairs existed in the regulatory network. The qRT-PCR analysis showed that KDM4A expression was increased, and the expressions of MEG3, PABPC4, CEP131, and NUMB1 were downregulated. Conclusion These RNAs might be related to the pathogenesis of CG.

scholarly journals Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yang Wang ◽  
Peng Yuan ◽  
Zhiqiang Yan ◽  
Ming Yang ◽  
Ying Huo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Single Cell ◽  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Cell Mass ◽  
Regulatory Elements ◽  
Epigenetic Reprogramming ◽  
Genome Wide ◽  
Early Embryos

AbstractExtensive epigenetic reprogramming occurs during preimplantation embryo development. However, it remains largely unclear how the drastic epigenetic reprogramming contributes to transcriptional regulatory network during this period. Here, we develop a single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell. We apply this method to depict a single-cell multiomics map of mouse preimplantation development. We find that genome-wide DNA methylation remodeling facilitates the reconstruction of genetic lineages in early embryos. Further, we construct a zygotic genome activation (ZGA)-associated regulatory network and reveal coordination among multiple epigenetic layers, transcription factors and repeat elements that instruct proper ZGA. Cell fates associated cis-regulatory elements are activated stepwise in post-ZGA stages. Trophectoderm (TE)-specific transcription factors play dual roles in promoting the TE program while repressing the inner cell mass (ICM) program during the ICM/TE separation.

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