Epigenomics of rats' liver and its cross-species functional annotation reveals key regulatory genes underlying short term heat-stress response

Dou, Junling; Luo, Hanpeng; Sammad, Abdul; Lou, Wenqi; Wang, Di; Schenkel, F. S.; Yu, Ying; Fang, Lingzhao; Wang, Yachun

doi:10.1016/j.ygeno.2022.110449

Cited by 6 publications

(6 citation statements)

References 102 publications

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“…In addition, almost 90% of them (121 out of the 134 mRNAs) were found to be regulated by 216 miRNAs. According to the previous studies and the findings of the current work, the expression of several important genes are modified under HS; including HSPA5 12 , 36 , 72 , 75 , 76 , EIF2A 77 – 79 , RBPJ 80 , ABCC9 81 , TAT 82 , 83 , ATP5J2 84 , CD80 85 , EEF2K 86 , EIF4B 87 , FTO 88 , 89 , GLRX 90 , IGF1R 91 , INSR 77 , 92 , VAV3 93 , UBR5 94 , TNIP1 90 , PTPN9 95 , EIF2A 96 , AKR1D1 97 , HSPA13 98 , CYP1A2 99 , and SDF2L1 12 . Additionally, based on our result, other protein-coding genes such as ABCC9, TAT, ATP5J2, CD80, EEF2K, EIF4B, FTO, GLRX, IGF1R, INSR, VAV3, UBR5, TNIP1, RBPJ, and PTPN9, were significantly modified with the heat stress in conjunction with the regulation effect of ENSGALT00000099876, ENSGALT00000106323, and ENSGALT00000107573 lncRNAs.…”

Section: Discussionsupporting

confidence: 69%

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

Hosseinzadeh,

Hasanpur

2024

Sci Rep

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Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.

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Section: Discussionsupporting

confidence: 69%

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

Hosseinzadeh,

Hasanpur

2024

Sci Rep

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“…The nf‐core atacseq pipeline (version 1.2.2) [39] was used to call ATAC‐seq peak data with parameters (—genome mm10—narrow_peak). In brief, Trim Galore (version 0.6.5) [40] was used for adapter trimming. Clean reads were then aligned to mouse reference genome (mm10) with BWA (version 0.7.17) [41] and then filtered with default parameters using SAMtools (version 1.10) [42] and Picard (version 2.23.1) [43].…”

Section: Methodsmentioning

confidence: 99%

Early life vaccination reprograms the metabolism and function of myeloid cells in neonates

Chen,

Li,

Zhou

2024

Immunology

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Vaccination after birth provides protection against pathogen infection and immune related disorders in healthy children. The detailed effects of vaccination on neonatal immunity, however, remain largely unknown. Here, we reported that vaccination using Bacillus Calmette‐Guérin (BCG) diminished the immunosuppressive function of myeloid‐derived suppressor cells in neonatal mice, an immature myeloid population. A combination of single‐cell transcriptome, metabolite profiling, and functional analysis demonstrated that upregulation of mTOR/HIF1a signalling and the enhanced glycolysis explained the effects of BCG on neonatal myeloid cells. Pharmalogical inhibition of glycolysis or mTOR signalling efficiently rescued the effects of BCG on neonatal myeloid cells. These observations suggest that BCG facilitates the maturation of myeloid cells in early life, which may contribute to its beneficial effects against immune disorders later in life.

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“…59 Heat stress can cause heat stroke, heat cramps in humans, 60 and reduced immunity in animals, 61,62 which leads to disease 63 and reduces productivity. 63 Thus, researchers 64,65 have conducted a series of studies in which they found that the BTBD7 gene is involved in heat stress/heat shock and cellular adaptation functions in the presence of stressors. BTBD7 promotes angiogenesis, 16 which causes vasodilation in animals with heat stress, 66 leading to heat shock.…”

Section: Btbd7 Is Involved In the Heat-stress Response And Progress O...mentioning

confidence: 99%

The Role of BTBD7 in Normal Development and Tumor Progression

Liu

Song

et al. 2023

Technol Cancer Res Treat

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BTB/POZ domain-containing protein 7 (BTBD7) has a relative molecular weight of 126KD and contains two conserved BTB/POZ protein sequences. BTBD7 has been shown to play an essential role in normal human development, precancerous lesions, heat-stress response, and tumor progression. BTBD7 promotes branching morphogenesis during development and participates in the salivary gland, lung, and tooth formation. Furthermore, many studies have shown that aberrant expression of BTBD7 promotes heat stress response and the progression of precancerous lesions. BTBD7 has also been found to play an important role in cancer. High expression of BTBD7 affects tumor progression by regulating multiple pathways. Therefore, a complete understanding of BTBD7 is crucial for exploring human development and tumor progression. This paper reviews the research progress of BTBD7, which lays a foundation for the application of BTBD7 in regenerative medicine and as a biomarker for tumor prediction or potential therapeutic target.

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Epigenomics of rats' liver and its cross-species functional annotation reveals key regulatory genes underlying short term heat-stress response

Cited by 6 publications

References 102 publications

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

Early life vaccination reprograms the metabolism and function of myeloid cells in neonates

The Role of BTBD7 in Normal Development and Tumor Progression

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