RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat &amp; rat

Gao, Xiaoxiao; Ye, Jing; Yang, Chen; Luo, Lei; Liu, Ya; Ding, Jianping; Zhang, Yunhai; Ling, Yinghui; Huang, Weiping; Zhang, Xiaorong; Zhang, Kaifa; Li, Xiumei; Zhou, Jie; Fang, Fugui; Cao, Zubing

doi:10.1186/s12863-018-0608-9

Cited by 24 publications

(25 citation statements)

References 61 publications

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“…Increasingly numerous studies have opened the door to our understanding of noncoding small RNA molecules, however, lncRNA research is in its infancy, and the functions of most lncRNAs have not been determined. With the development of high-throughput sequencing technology, an increasing number of lncRNAs have been identified, and their functions have also become increasingly detailed [19,20].…”

Section: Discussionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

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Section: Discussionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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“…Detailed information on the GO functions and the genes involved are summarized in ( S5 Table ). In the identification and characterization of the late embryogenesis abundant proteins (LEA) in cotton, Magwanga et al [ 1 ], found that integral to membrane (GO: 0016021), was detected for over 95% of the LEA genes, and this he postulated to have a functional role in maintaining the cell membrane integrity. Moreover, in the analysis of the genes which could been introgressed into the backcross population, BC 2 F 2 developed from G .…”

Section: Resultsmentioning

confidence: 99%

“…The two parental lines flowers were tagged and samples harvested at 0, 5, 25 and 30 DPA for real time quantitative polymerase chain reaction (RT-qPCR). The RT-qPCR analysis was carried out as outlined by Magwanga et al [ 1 ], cotton GrActin with forward sequence “ ” and reverse sequence “ ” was used as the reference gene…”

Section: Methodsmentioning

confidence: 99%

“…is the most important fiber crop and one of the sources for animal feeds and edible oil. However cotton growing has significantly been threatened by various abiotic and biotic stresses, this condition has been worsened by intensive selection and inbreeding resulting into the narrow genetic base [ 1 ]. Improving cotton yield and fiber quality is important for the survival of the cotton industry [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

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SSR-Linkage map of interspecific populations derived from Gossypium trilobum and Gossypium thurberi and determination of genes harbored within the segregating distortion regions

Kirungu

et al. 2018

PLoS ONE

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Wild cotton species have significant agronomic traits that can be introgressed into elite cultivated varieties. The use of a genetic map is important in exploring, identification and mining genes which carry significant traits. In this study, 188 F2mapping individuals were developed from Gossypium thurberi (female) and Gossypium trilobum (male), and were genotyped by using simple sequence repeat (SSR) markers. A total of 12,560 simple sequence repeat (SSR) markers, developed by Southwest University, thus coded SWU were screened out of which only 994 were found to be polymorphic, and 849 markers were linked in all the 13 chromosomes. The map had a length of 1,012.458 cM with an average marker distance of 1.193 cM. Segregation distortion regions (SDRs) were observed on Chr01, Chr02, Chr06, Chr07 Chr09, Chr10 and Chr11 with a large proportion of the SDR regions segregating towards the heterozygous allele. There was good syntenic block formation that revealed good collinearity between the genetic and physical map of G. raimondii, compared to the Dt_sub genome of the G. hirsutum and G. barbadense. A total of 2,496 genes were mined within the SSR related regions. The proteins encoding the mined genes within the SDR had varied physiochemical properties; their molecular weights ranged from 6.586 to 252.737 kDa, charge range of -39.5 to 52, grand hydropathy value (GRAVY) of -1.177 to 0.936 and isoelectric (pI) value of 4.087 to 12.206. The low GRAVY values detected showed that the proteins encoding these genes were hydrophilic in nature, a property common among the stress responsive genes. The RNA sequence analysis revealed more of the genes were highly upregulated in various stages of fiber development for instance; Gorai.002G241300 was highly up regulated at 5, 10, 20 and 25 day post anthesis (DPA). Validation through RT-qPCR further revealed that these genes mined within the SDR regions might be playing a significant role under fiber development stages, therefore we infer that Gorai.007G347600 (TFCA), Gorai.012G141600 (FOLB1), Gorai.006G024500 (NMD3), Gorai.002G229900 (LST8) and Gorai.002G235200 (NSA2) are significantly important in fiber development and in turn the quality, and further researches needed to be done to elucidate their exact roles in the fiber development process. The construction of the genetic map between the two wild species paves away for the mapping of quantitative trait loci (QTLs) since the average distance between the markers is small, and mining of genes on the SSR regions will provide an insight in identifying key genes that can be introgressed into the cultivated cotton cultivars.

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“…Some research has investigated the role of lncRNA on growth development in muscles [41], heart [42], brain [43], spinal cord neuron [44] and cancer cells [45]. In addition, hypothalamic-pituitary-gonadal (HPG) axis plays an important role in reproduction, and there are many studies focus on hypothalamus [46,47], testis [48] and ovary [49] during different development stages. The pituitary gland is essential for mammalian reproduction and growth development owing to its function of GH, FSH, LH, and PRL hormone secretion.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

Yang

Wang

et al. 2020

Genes

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Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction.

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RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat

Cited by 24 publications

References 61 publications

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

SSR-Linkage map of interspecific populations derived from Gossypium trilobum and Gossypium thurberi and determination of genes harbored within the segregating distortion regions

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

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