Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens

Zhang, Ying; Su, Woyu; Zhang, Bo; Yao, Ling; Kim, Woo Kyun

doi:10.1186/s40104-021-00582-2

Cited by 10 publications

(9 citation statements)

References 60 publications

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“…Studies have shown that high-altitude hypoxic environments have an important impact on energy metabolism in animals ( 15 , 20 , 21 ). Similarly, we found many differentially expressed genes and signaling pathways related to glucose and lipid metabolism.…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep

Yuan

et al. 2022

Front. Vet. Sci.

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Tibetan sheep have lived on the Qinghai-Tibet Plateau for a long time, and after long-term natural selection, they have shown stable genetic adaptability to high-altitude environments. However, little is known about the molecular mechanisms of the long non-coding (lnc)RNAs involved in the adaptation of Tibetan sheep to hypoxia. Here, we collected lung tissues from high-altitude Tibetan sheep and low-altitude Hu sheep for RNA sequencing to study the regulatory mechanisms of the lncRNAs and mRNAs in the adaptation of Tibetan sheep to hypoxia. We identified 254 differentially expressed lncRNAs and 1,502 differentially expressed mRNAs. We found 20 pairs of cis-regulatory relationships between 15 differentially expressed lncRNAs and 14 protein-coding genes and two pairs of trans-regulatory relationships between two differentially expressed lncRNAs and two protein-coding genes. These differentially expressed mRNAs and lncRNA target genes were mainly enriched in pathways related to lipid metabolism and immune function. Interaction network analysis showed that 17 differentially expressed lncRNAs and 15 differentially expressed mRNAs had an interactive relationship. Additionally, we used six differentially expressed lncRNAs and mRNAs to verify the accuracy of the sequencing data via qRT-PCR. Our results provide a comprehensive overview of the expression patterns of the lncRNAs and mRNAs involved in the adaptation of Tibetan sheep to hypoxia, laying a foundation for further analysis of the adaptations of plateau animals.

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Section: Discussionmentioning

confidence: 99%

“…LncRNA may also play an important role in the adaptability of domestic animals to plateaus. Recent studies have shown that lncRNA is involved in the adaptability of Tibetan chickens and yaks to plateaus; however, the regulatory mechanisms of this lncRNA remain largely unknown ( 15 , 16 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep

Yuan

et al. 2022

Front. Vet. Sci.

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“…Amongst avians, chicken has been extensively researched. Studies utilizing sequencing technologies have focused on the roles ncRNAs play in embryogenesis [ 230 ], environmental adaptation [ 231 ], and tissue specific expression [ 232 , 233 ]. Chicken diseases have also received attention with the expression profiles of lncRNAs being studied in avian infectious bronchitis coronavirus (IBV) infected chicken macrophages [ 234 ].…”

Section: Exploring the Ncrna Landscape Beyond Humansmentioning

confidence: 99%

Advances in Non-Coding RNA Sequencing

Micheel

Safrastyan

Wollny

2021

ncRNA

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Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.

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“…Tropomyosin and titin levels were downregulated in yak compared with the three cattle strains, which might facilitate the muscle contraction, since tropomyosin and titin plays an opposite role during the process of muscle contraction [91]. Whole-transcriptome analysis of yak and cattle heart tissues predicted several miRNAs/lncRNAs that are significantly enriched in high-altitude adaptation targeting T cell receptor signaling, VEGF signaling, and cAMP signaling [92] In Tibetan chickens, several key candidate Competing endogenous RNAs (ceRNAs) (DE lncRNAs-DE miRNAs-DE genes), which may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism, were identified [93]. A study which aimed to identify DE genes and novel lncRNAs of yaks for plateau adaptation and their underlying co-expression and regulatory network found a valuable sub-network comprising eight hub genes, one known lncRNA and five novel lncRNAs in the major module.…”

Section: Epigenetic Adaptation Of Animals To High Altitudementioning

confidence: 99%

Exposomes to Exosomes: Exosomes as Tools to Study Epigenetic Adaptive Mechanisms in High-Altitude Humans

Padmasekar

Savai

Seeger

et al. 2021

IJERPH

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Humans on earth inhabit a wide range of environmental conditions and some environments are more challenging for human survival than others. However, many living beings, including humans, have developed adaptive mechanisms to live in such inhospitable, harsh environments. Among different difficult environments, high-altitude living is especially demanding because of diminished partial pressure of oxygen and resulting chronic hypobaric hypoxia. This results in poor blood oxygenation and reduces aerobic oxidative respiration in the mitochondria, leading to increased reactive oxygen species generation and activation of hypoxia-inducible gene expression. Genetic mechanisms in the adaptation to high altitude is well-studied, but there are only limited studies regarding the role of epigenetic mechanisms. The purpose of this review is to understand the epigenetic mechanisms behind high-altitude adaptive and maladaptive phenotypes. Hypobaric hypoxia is a form of cellular hypoxia, which is similar to the one suffered by critically-ill hypoxemia patients. Thus, understanding the adaptive epigenetic signals operating in in high-altitude adjusted indigenous populations may help in therapeutically modulating signaling pathways in hypoxemia patients by copying the most successful epigenotype. In addition, we have summarized the current information about exosomes in hypoxia research and prospects to use them as diagnostic tools to study the epigenome of high-altitude adapted healthy or maladapted individuals.

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Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens

Cited by 10 publications

References 60 publications

Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep

Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep

Advances in Non-Coding RNA Sequencing

Exposomes to Exosomes: Exosomes as Tools to Study Epigenetic Adaptive Mechanisms in High-Altitude Humans

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