See the published version of this article at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chickens during late postnatal development
Guoxi Li
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-8442-8861
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, to investigate the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens.
Results: A total of 1,252 new lncRNAs and 1,376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Moreover, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Additionally, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks contained the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. We also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11.
Conclusions: This study revealed, for the first time, the dynamic changes in lncRNA expression in Gushi chicken breast muscle at different periods and revealed that the MAPK signaling pathway plays a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating posttranscriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.
Keywords
chicken, breast muscle, lncRNAs, regulatory network, ceRNA
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
This is a list of supplementary files associated with this preprint. Click to download.
- ARRIVEChecklist.pdf
- FigureS1.tif
Figure S1. Heatmap showing DE-lncRNAs from different stages.
- FigureS2.tif
Figure S2. The chromosome distribution of DE-lncRNAs from different stages.
- FigureS3.tif
Figure S3. The enriched GO terms of the DE-lncRNA. (A-B) Cis-target genes in the W14 vs. W6 and W30 vs. W22 comparison groups. (C-D) Trans-target genes in the W14 vs. W6 and W30 vs. W22 comparison groups.
- FigureS4.tif
Figure S4. The enriched KEGG pathways of the DE-lncRNA. (A-C) Cis-target genes in the W14 vs. W6, W22 vs. W14, and W30 vs. W22 comparison groups. (D) Trans-target genes in the W14 vs. W6 comparison groups.
- FigureS5.tif
Figure S5. The lncRNA-miRNA-mRNA ceRNA networks. (A) W14 vs. W6 comparison group; (B) W22 vs. W14 comparison group; (C) W30 vs. W22 comparison group.
- TableS1.docx
Table S1. Summary of draft reads of 12 cDNA libraries, determined by RNA sequencing. Abbreviations: W6_1, sample 1 of 6 weeks; W6_2, sample 2 of 6 weeks; W6_3, sample 3 of 6 weeks; W14_1, sample 1 of 14 weeks; W14_2, sample 2 of 14 weeks; W14_3, sample 3 of 14 weeks; W22_1, sample 1 of 22 weeks; W22_2, sample 2 of 22 weeks; W22_3, sample 3 of 22 weeks; W30_1, sample 1 of 30 weeks; W30_2, sample 2 of 30 weeks; W30_3, sample 3 of 30 weeks.
- TableS2.xls
Table S2. Cis-regulatory interactions between DE-lncRNAs and DE-mRNAs.
- TableS3.xls
Table S3. Trans-regulatory interactions between DE-lncRNAs and DE-mRNAs.
- TableS4.xls
Table S4. The interaction between DE-lncRNAs and DE-miRNAs.
- TableS5.docx
Table S5. Details on the novel miRNAs identified in this study. Abbreviations: W6, W14, W22, and W30 represent small RNA libraries obtained using samples from chickens aged 6, 14, 22, and 30 weeks, respectively.
- TableS6.docx
Table S6. qRT-PCR primers. Abbreviation: AT refers to the annealing temperature; F and R refer to the forward and reverse primers, respectively.
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 09 Jan, 2021
No comments provided
Editorial decision: Minor revision
On 15 Dec, 2020
Review #1 received
Received 14 Dec, 2020
Reviewer #1 agreed
On 22 Nov, 2020
Editor assigned
On 27 Jul, 2020
Reviewers invited
Invitations sent on 27 Jul, 2020
Editor invited
On 26 Jul, 2020
Submission checks complete
On 23 Jul, 2020
No comments provided
Editorial decision: Minor revision
On 19 Jul, 2020
Review #2 received
Received 13 Jul, 2020
Reviewer #2 agreed
On 26 May, 2020
Review #1 received
Received 05 Apr, 2020
Reviewer #1 agreed
On 20 Mar, 2020
Reviewers invited
Invitations sent on 17 Mar, 2020
Editor assigned
On 24 Feb, 2020
Submission checks complete
On 23 Feb, 2020
Editor invited
On 23 Feb, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Learn more about our company.
This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chickens during late postnatal development
Guoxi Li
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-8442-8861
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 09 Jan, 2021
No comments provided
Editorial decision: Minor revision
On 15 Dec, 2020
Review #1 received
Received 14 Dec, 2020
Reviewer #1 agreed
On 22 Nov, 2020
Editor assigned
On 27 Jul, 2020
Reviewers invited
Invitations sent on 27 Jul, 2020
Editor invited
On 26 Jul, 2020
Submission checks complete
On 23 Jul, 2020
No comments provided
Editorial decision: Minor revision
On 19 Jul, 2020
Review #2 received
Received 13 Jul, 2020
Reviewer #2 agreed
On 26 May, 2020
Review #1 received
Received 05 Apr, 2020
Reviewer #1 agreed
On 20 Mar, 2020
Reviewers invited
Invitations sent on 17 Mar, 2020
Editor assigned
On 24 Feb, 2020
Submission checks complete
On 23 Feb, 2020
Editor invited
On 23 Feb, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, to investigate the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens.
Results: A total of 1,252 new lncRNAs and 1,376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Moreover, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Additionally, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks contained the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. We also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11.
Conclusions: This study revealed, for the first time, the dynamic changes in lncRNA expression in Gushi chicken breast muscle at different periods and revealed that the MAPK signaling pathway plays a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating posttranscriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10