Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle

Genomics, Год журнала: 2021, Номер 113(6), С. 3827 - 3841

Опубликована: Сен. 20, 2021

Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose skeletal muscle, two tissues contrasting metabolic functions. While promoter correlated RNA expression, integration of datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized intergenic intron regions. DARs were mapped expressed (DE) genes enriched distinct biological processes each tissue. Randomly selected DE validated by qPCR. Top motifs predicted binding sites for transcription factors (TFs) showing up-regulation. The correlation between differential chromatin at given TF motif expression target further supported functional relevance motif. Our study likely play major role regulation muscle.

Язык: Английский

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Molecular Mechanisms and Current Treatment Options for Cancer Cachexia

Cancers, Год журнала: 2022, Номер 14(9), С. 2107 - 2107

Опубликована: Апрель 23, 2022

Cancer cachexia is a condition marked by functional, metabolic, and immunological dysfunctions associated with skeletal muscle (SM) atrophy, adipose tissue loss, fat reduction, systemic inflammation, anorexia. Generally, the caused variety of mediators produced cancer cells in tumor microenvironments. Myostatin activin signaling, IGF-1/PI3K/AKT JAK-STAT signaling are known to play roles cachexia, thus, these pathways considered potential therapeutic targets. This review discusses current state knowledge molecular mechanisms underlying available options was undertaken increase understanding various factors/pathways/mediators involved identify treatment options.

Язык: Английский

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Transcriptome-wide analysis of RNA m6A methylation regulation of muscle development in Queshan Black pigs

BMC Genomics, Год журнала: 2023, Номер 24(1)

Опубликована: Май 4, 2023

Abstract Background N 6 -methyladenosine (m A) refers to the methylation modification of position RNA adenine, a dynamic reversible epigenetic that plays an important regulatory role in variety life processes. In this study, we used MeRIP-Seq and RNA-Seq longissimus dorsi (LD) muscle adult (QA) newborn (QN) Queshan Black pigs screen key genes with m A involved growth by bioinformatics analysis. Results total 23,445 25,465 peaks were found whole genomes QA QN, respectively. Among them, 613 significantly different (DMPs) 579 defined as differentially methylated (DMGs). Compared QN group, there 1,874 expressed (DEGs) including 620 up-regulated 1,254 down-regulated genes. order investigate relationship between mRNA expression at periods, combined analysis showed 88 both levels. Gene Ontology Kyoto Encyclopedia Genes Genomes results DEGs DMGs mainly skeletal tissue development, FoxO signaling pathway, MAPK insulin PI3K–Akt Wnt pathway. Four ( IGF1R , CCND2 MYOD1 FOS ) four PHKB BIN1 FUT2 ), which are closely related selected candidate for verification, consistent sequencing results, indicated reliability results. Conclusions These lay foundation understanding specific mechanisms pigs, provide theoretical references further research on development breed optimization selection.

Язык: Английский

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Axis “microbiota - muscle”

Experimental and Clinical Gastroenterology, Год журнала: 2023, Номер 11, С. 60 - 69

Опубликована: Янв. 23, 2023

The luminal intestinal microflora affects the state of muscular system experimental animals and humans. role nutrition in development skeletal muscles is considered. metabolically active substances secreted by microbiota cachexia, sarcopenia, kwashiorkor effect exercise on gut microbiome was assessed. Possible variants influence probiotics its functional activity experiment humans are presented.

Язык: Английский

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Transcriptomic regulatory analysis of skeletal muscle development in landrace pigs

Gene, Год журнала: 2024, Номер 915, С. 148407 - 148407

Опубликована: Март 24, 2024

Язык: Английский

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