Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis

Sun, Zhanpeng; Li, Jingjing; Lv, Lili; Gou, Yifei; Wang, Bin; Hao, Tong

doi:10.3389/fmars.2022.900160

Cited by 3 publications

(3 citation statements)

References 44 publications

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“…Genes associated with closed-to-open peaks in ATAC-seq were compared with DEGs upregulated in RNA-seq. Genes associated with open-to-closed peaks in ATAC-seq were compared with DEGs downregulated in RNA-seq [ 76 ]. Genes with changes in both gene expression and chromatin accessibility were shortlisted, followed by Spearman’s correlation analysis.…”

Section: Methodsmentioning

confidence: 99%

Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi

He,

Li,

et al. 2024

IJMS

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Ascidian larvae undergo tail elongation and notochord lumenogenesis, making them an ideal model for investigating tissue morphogenesis in embryogenesis. The cellular and mechanical mechanisms of these processes have been studied; however, the underlying molecular regulatory mechanism remains to be elucidated. In this study, assays for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were applied to investigate potential regulators of the development of ascidian Ciona savignyi larvae. Our results revealed 351 and 138 differentially accessible region genes through comparisons of ATAC-seq data between stages 21 and 24 and between stages 24 and 25, respectively. A joint analysis of RNA-seq and ATAC-seq data revealed a correlation between chromatin accessibility and gene transcription. We further verified the tissue expression patterns of 12 different genes. Among them, Cs-matrix metalloproteinase 24 (MMP24) and Cs-krüppel-like factor 5 (KLF5) were highly expressed in notochord cells. Functional assay results demonstrated that both genes are necessary for notochord lumen formation and expansion. Finally, we performed motif enrichment analysis of the differentially accessible regions in different tailbud stages and summarized the potential roles of these motif-bearing transcription factors in larval development. Overall, our study found a correlation between gene expression and chromatin accessibility and provided a vital resource for understanding the mechanisms of the development of ascidian embryos.

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Section: Methodsmentioning

confidence: 99%

Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi

He,

Li,

et al. 2024

IJMS

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“…Clustering of the index-coded samples was carried out on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina). The libraries were sequenced on an Illumina platform after the cluster generation and 150 bp paired-end reads were produced [59]. The original Illumina high-throughput sequencing image data files were transformed into original sequences after base group recognition using the bcl2fastq software, and were stored in the FASTQ file format.…”

Section: Atac-seqmentioning

confidence: 99%

“…On the Agilent Bioanalyzer 2100 equipment, the library quality was measured. The clustering and sequencing were consistent with the methods used for the ATAC-seq [59]. Original data (raw reads) were accessed and transferred to sequencing data via base calling to obtain clean reads.…”

Section: Rna-seqmentioning

confidence: 99%

An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs

Zhang,

Liu,

Wang

et al. 2023

IJMS

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Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.

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Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light

Chen

Li²,

Chen³

et al. 2023

Front. Microbiol.

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Isochrysis galbana, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in I. galbana, but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in I. galbana under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including IgLHCA1, IgLHCA4, IgPDS, IgZ-ISO, IglcyB, IgZEP, and IgVDE. The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of I. galbana, including IgMYB1, IgMYB2, IgMYB33, IgMYB42, IgMYB98, IgMYB118, and IgMYB119. The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including IgMYB98, IgLHCA1, IgLHCX2, IgLHCB4, and IgLHCB5. This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 (IgphoA, IgPKN1, IgOTC) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in I. galbana through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in I. galbana and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.

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Integration of ATAC-seq and RNA-seq identifies active G-protein coupled receptors functioning in molting process in muscle of Eriocheir sinensis

Cited by 3 publications

References 44 publications

Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi

Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi

An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs

Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light

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