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Cheng Y, Zhang Z, Zhang G, Chen L, Zeng C, Liu X, Feng Y. The Male-Biased Expression of miR-2954 Is Involved in the Male Pathway of Chicken Sex Differentiation. Cells 2022; 12:cells12010004. [PMID: 36611798 PMCID: PMC9818168 DOI: 10.3390/cells12010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/26/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Many expression data showed miRNAs have a potential function on regulating gonadal differentiation in animals, but their function is rarely studied in vivo, especially in chickens. Using the comprehensive expression profiles analysis, the specific male-biased miR-2954, which is significantly higher expressed in male embryos and gonads at all detected stages, was firstly screened during the early stages of chicken embryogenesis and gonadogenesis. In sex-reversed female gonads treated with aromatase inhibitors, the expression of miR-2954 was increased, which was consistent with the up-regulation of DMRT1 and SOX9. The injection of vivo-morpholino of miR-2954 significantly inhibited the expression of miR-2954 in chicken embryos, and the down-regulation of miR-2954 decreased the expression of testis-associated genes DMRT1 and SOX9, while the expression of ovary-associated genes and the gonadal morphology did not change obviously. These results confirm that miR-2954 coincides with testicular differentiation in chicken embryos, but whether it might be an upstream cell autonomous factor to sex development in birds still need to be further determined.
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2
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Friedrich SR, Nevue AA, Andrade ALP, Velho TAF, Mello CV. Emergence of sex-specific transcriptomes in a sexually dimorphic brain nucleus. Cell Rep 2022; 40:111152. [PMID: 35926465 PMCID: PMC9385264 DOI: 10.1016/j.celrep.2022.111152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/26/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
We present the transcriptomic changes underlying the development of an extreme neuroanatomical sex difference. The robust nucleus of the arcopallium (RA) is a key component of the songbird vocal motor system. In zebra finch, the RA is initially monomorphic and then atrophies in females but grows up to 7-fold larger in males. Mirroring this divergence, we show here that sex-differential gene expression in the RA expands from hundreds of predominantly sex chromosome Z genes in early development to thousands of predominantly autosomal genes by the time sexual dimorphism asymptotes. Male-specific developmental processes include cell and axonal growth, synapse assembly and activity, and energy metabolism; female-specific processes include cell polarity and differentiation, transcriptional repression, and steroid hormone and immune signaling. Transcription factor binding site analyses support female-biased activation of pro-apoptotic regulatory networks. The extensive and sex-specific transcriptomic reorganization of RA provides insights into potential drivers of sexually dimorphic neurodevelopment. Friedrich et al. demonstrate extensive transcriptomic sex differences underlying the sexually dimorphic development of vocal nucleus RA in the songbird brain. They find sex-specific gene regulation linked to distinct biological processes, developmental shifts in the relative signal from sex chromosome to autosomal genes, and evidence of female-biased pro-apoptotic regulatory networks.
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Affiliation(s)
- Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
| | - Alexander A Nevue
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
| | - Abraão L P Andrade
- Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil
| | - Tarciso A F Velho
- Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA.
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3
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Zhou KZ, Wu PF, Zhang XC, Ling XZ, Zhang J, Zhang L, Li PF, Zhang T, Wei QY, Zhang GX. Comparative Analysis of miRNA Expression Profiles in Skeletal Muscle of Bian Chickens at Different Embryonic Ages. Animals (Basel) 2022; 12:1003. [PMID: 35454249 PMCID: PMC9025512 DOI: 10.3390/ani12081003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 01/09/2023] Open
Abstract
MicroRNAs (miRNAs) are widely involved in the growth and development of skeletal muscle through the negative regulation of target genes. In order to screen out the differentially expressed miRNAs (DEMs) associated with skeletal muscle development of Bian chickens at different embryonic ages, we used the leg muscles of fast-growing and slow-growing Bian chickens at the 14th and 20th embryonic ages (F14, F20, S14 and S20) for RNA-seq. A total of 836 known miRNAs were identified, and 121 novel miRNAs were predicted. In the F14 vs. F20 comparison group, 127 DEMs were screened, targeting a total of 2871 genes, with 61 miRNAs significantly upregulated and 66 miRNAs significantly downregulated. In the S14 vs. S20 comparison group, 131 DEMs were screened, targeting a total of 3236 genes, with 60 miRNAs significantly upregulated and 71 miRNAs significantly downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the predicted target genes were significantly enriched in 706 GO terms and 6 KEGG pathways in the F14 vs. F20 group and 677 GO terms and 5 KEGG pathways in the S14 vs. S20 group. According to the interaction network analysis, we screened five coexpressed DEMs (gga-miR-146a-3p, gga-miR-2954, gga-miR-34a-5p, gga-miR-1625-5p and gga-miR-18b-3p) with the highest connectivity degree with predicted target genes between the two comparison groups, and five hub genes (HSPA5, PKM2, Notch1, Notch2 and RBPJ) related to muscle development were obtained as well. Subsequently, we further identified nine DEMs (gga-let-7g-3p, gga-miR-490-3p, gga-miR-6660-3p, gga-miR-12223-5p, novel-miR-327, gga-miR-18a-5p, gga-miR-18b-5p, gga-miR-34a-5p and gga-miR-1677-3p) with a targeting relationship to the hub genes, suggesting that they may play important roles in the muscle development of Bian chickens. This study reveals the miRNA differences in skeletal muscle development between 14- and 20-day embryos of Bian chickens from fast- and slow-growing groups and provides a miRNA database for further studies on the molecular mechanisms of the skeletal muscle development in Bian chickens.
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Affiliation(s)
- Kai-Zhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Peng-Fei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Xin-Chao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Xuan-Ze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Li Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan 030032, China; (L.Z.); (P.-F.L.); (Q.-Y.W.)
| | - Pei-Feng Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan 030032, China; (L.Z.); (P.-F.L.); (Q.-Y.W.)
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
| | - Qing-Yu Wei
- College of Animal Science, Shanxi Agricultural University, Taiyuan 030032, China; (L.Z.); (P.-F.L.); (Q.-Y.W.)
| | - Gen-Xi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (K.-Z.Z.); (P.-F.W.); (X.-C.Z.); (X.-Z.L.); (J.Z.); (T.Z.)
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4
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Biegler MT, Fedrigo O, Collier P, Mountcastle J, Haase B, Tilgner HU, Jarvis ED. Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Sci Rep 2022; 12:4369. [PMID: 35288582 PMCID: PMC8921232 DOI: 10.1038/s41598-022-07434-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line, designated CFS414, from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we disrupted endogenous gene sequences using S.aureus Cas9 and confirmed a stress-dependent localization response of a song system specialized gene, SAP30L. The utility of CFS414 cells enhances the comprehensive molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.
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Affiliation(s)
- Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Paul Collier
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Hagen U Tilgner
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Aamodt CM, White SA. Inhibition of miR-128 Enhances Vocal Sequence Organization in Juvenile Songbirds. Front Behav Neurosci 2022; 16:833383. [PMID: 35283744 PMCID: PMC8914539 DOI: 10.3389/fnbeh.2022.833383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
The molecular mechanisms underlying learned vocal communication are not well characterized. This is a major barrier for developing treatments for conditions affecting social communication, such as autism spectrum disorder (ASD). Our group previously generated an activity-dependent gene expression network in the striatopallidal song control nucleus, Area X, in adult zebra finches to identify master regulators of learned vocal behavior. This dataset revealed that the two host genes for microRNA-128, ARPP21 and R3HDM1, are among the top genes whose expression correlates to how much birds sing. Here we examined whether miR-128 itself is behaviorally regulated in Area X and found that its levels decline with singing. We hypothesized that reducing miR-128 during the critical period for vocal plasticity would enhance vocal learning. To test this, we bilaterally injected an antisense miR-128 construct (AS miR-128) or a control scrambled sequence into Area X at post-hatch day 30 (30 d) using sibling-matched experimental and control pupils. The juveniles were then returned to their home cage and raised with their tutors. Strikingly, inhibition of miR-128 in young birds enhanced the organization of learned vocal sequences. Tutor and pupil stereotypy scores were positively correlated, though the correlation was stronger between tutors and control pupils compared to tutors and AS miR-128 pupils. This difference was driven by AS miR-128 pupils achieving higher stereotypy scores despite their tutors’ lower syntax scores. AS miR-128 birds with tutors on the higher end of the stereotypy spectrum were more likely to produce songs with faster tempos relative to sibling controls. Our results suggest that low levels of miR-128 facilitate vocal sequence stereotypy. By analogy, reducing miR-128 could enhance the capacity to learn to speak in patients with non-verbal ASD. To our knowledge, this study is the first to directly link miR-128 to learned vocal communication and provides support for miR-128 as a potential therapeutic target for ASD.
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Affiliation(s)
- Caitlin M. Aamodt
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, United States
- *Correspondence: Caitlin M. Aamodt,
| | - Stephanie A. White
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
- Stephanie A. White,
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6
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Dong X, Cheng Y, Qiao L, Wang X, Zeng C, Feng Y. Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1. Genes (Basel) 2021; 12:1325. [PMID: 34573307 PMCID: PMC8470131 DOI: 10.3390/genes12091325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.
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Affiliation(s)
| | | | | | | | | | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (Y.C.); (L.Q.); (X.W.); (C.Z.)
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7
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Nair PS, Raijas P, Ahvenainen M, Philips AK, Ukkola-Vuoti L, Järvelä I. Music-listening regulates human microRNA expression. Epigenetics 2020; 16:554-566. [PMID: 32867562 DOI: 10.1080/15592294.2020.1809853] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Music-listening and performance have been shown to affect human gene expression. In order to further elucidate the biological basis of the effects of music on the human body, we studied the effects of music-listening on gene regulation by sequencing microRNAs of the listeners (Music Group) and their controls (Control Group) without music exposure. We identified upregulation of six microRNAs (hsa-miR-132-3p, hsa-miR-361-5p, hsa-miR-421, hsa-miR-23a-3p, hsa-miR-23b-3p, hsa-miR-25-3p) and downregulation of two microRNAs (hsa-miR-378a-3p, hsa-miR-16-2-3p) in Music Group with high musical aptitude. Some upregulated microRNAs were reported to be responsive to neuronal activity (miR-132, miR-23a, miR-23b) and modulators of neuronal plasticity, CNS myelination, and cognitive functions like long-term potentiation and memory. miR-132 plays a critical role in regulating TAU protein levels and is important for preventing tau protein aggregation that causes Alzheimer's disease. miR-132 and DICER, upregulated after music-listening, protect dopaminergic neurons and are important for retaining striatal dopamine levels. Some of the transcriptional regulators (FOS, CREB1, JUN, EGR1, and BDNF) of the upregulated microRNAs were immediate early genes and top candidates associated with musical traits. BDNF and SNCA, co-expressed and upregulated in music-listening and music-performance, are both are activated by GATA2, which is associated with musical aptitude. Several miRNAs were associated with song-learning, singing, and seasonal plasticity networks in songbirds. We did not detect any significant changes in microRNA expressions associated with music education or low musical aptitude. Our data thereby show the importance of inherent musical aptitude for music appreciation and for eliciting the human microRNA response to music-listening.
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Affiliation(s)
| | | | - Minna Ahvenainen
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Anju K Philips
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Liisa Ukkola-Vuoti
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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8
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Nair PS, Kuusi T, Ahvenainen M, Philips AK, Järvelä I. Music-performance regulates microRNAs in professional musicians. PeerJ 2019; 7:e6660. [PMID: 30956902 PMCID: PMC6442922 DOI: 10.7717/peerj.6660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal growth inhibitor, PTEN, and by activating CREB expression and phosphorylation. The up-regulation of microRNAs previously found to be regulators of auditory and nervous system functions (miR-30d, miR-92a and miR-222) is indicative of the sensory perception processes associated with music-performance. Akt signalling pathway which has roles in cell survival, cell differentiation, activation of CREB signalling and dopamine transmission was one of the functions regulated by the up-regulated microRNAs; in accordance with functions identified from songbird learning. The up-regulated microRNAs were also found to be regulators of apoptosis, suggesting repression of apoptotic mechanisms in connection with music-performance. Furthermore, comparative analyses of the target genes of differentially expressed microRNAs with that of the song-responsive microRNAs in songbirds suggest convergent regulatory mechanisms underlying auditory perception.
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Affiliation(s)
| | - Tuire Kuusi
- DocMus Doctoral School, Sibelius Academy, University of the Arts, Helsinki, Finland
| | - Minna Ahvenainen
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Anju K Philips
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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9
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Jiang L, Wang Q, Yu J, Gowda V, Johnson G, Yang J, Kan X, Yang X. miRNAome expression profiles in the gonads of adult Melopsittacus undulatus. PeerJ 2018; 6:e4615. [PMID: 29666766 PMCID: PMC5896495 DOI: 10.7717/peerj.4615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/22/2018] [Indexed: 01/11/2023] Open
Abstract
The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.
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Affiliation(s)
- Lan Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qingqing Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Jue Yu
- College of Foreign Studies, Anhui Normal University, Wuhu, China
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Jianke Yang
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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10
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Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res 2017; 27:1961-1973. [PMID: 29079676 PMCID: PMC5741053 DOI: 10.1101/gr.225391.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022]
Abstract
Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set to analyze male and female miRNA expression profiles in mouse, opossum, and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, with the largest proportion found in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z Chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W Chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z Chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalize male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.
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11
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Garcia‐Riart B, Lorda‐Diez CI, Marin‐Llera JC, Garcia‐Porrero JA, Hurle JM, Montero JA. Interdigital tissue remodelling in the embryonic limb involves dynamic regulation of the miRNA profiles. J Anat 2017; 231:275-286. [PMID: 28543398 PMCID: PMC5522895 DOI: 10.1111/joa.12629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2017] [Indexed: 11/26/2022] Open
Abstract
Next-generation sequencing in combination with quantitative polymerase chain reaction analysis revealed a dynamic miRNA signature in the interdigital mesoderm of the chick embryonic hinlimb in the course of interdigit remodelling. During this period, 612 previously known chicken miRNAs (gga-miRNAs) and 401 non-identified sequences were expressed in the interdigital mesoderm. Thirty-six microRNAs, represented by more than 750 reads per million, displayed differential expression between stages HH29 (6 id) and HH32 (7.5 id), which correspond to the onset and the peak of interdigital cell death. Twenty miRNAs were upregulated by at least 1.5-fold, and sixteen were downregulated by at least 0.5-fold. Upregulated miRNAs included miRNAs with recognized proapoptotic functions in other systems (miR-181 family, miR-451 and miR-148a), miRNAs associated with inflammation and cell senescence (miR-21 and miR-146) and miRNAs able to induce changes in the extracellular matrix (miR-30c). In contrast, miRNAs with known antiapoptotic effects in other systems, such as miR-222 and miR-205, became downregulated. In addition, miR-92, an important positive regulator of cell proliferation, was also downregulated. Together, these findings indicate a role for miRNAs in the control of tissue regression and cell death in a characteristic morphogenetic embryonic process based on massive apoptosis.
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Affiliation(s)
- Beatriz Garcia‐Riart
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
| | - Carlos I. Lorda‐Diez
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
| | - Jessica C. Marin‐Llera
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
- Present address:
Instituto de Investigaciones BiomédicasUniversidad Nacional Autónoma de MéxicoDistrito FederalMéxico
| | - Juan A. Garcia‐Porrero
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
| | - Juan M. Hurle
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
| | - Juan A. Montero
- Departamento de Anatomía y Biología Celular and IDIVALUniversidad de CantabriaSantanderSpain
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Hofmeister EK, Lund M, Shearn-Bochsler V, Balakrishnan CN. Susceptibility and Antibody Response of the Laboratory Model Zebra Finch (Taeniopygia guttata) to West Nile Virus. PLoS One 2017; 12:e0167876. [PMID: 28045891 PMCID: PMC5207765 DOI: 10.1371/journal.pone.0167876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/22/2016] [Indexed: 11/18/2022] Open
Abstract
Since the introduction of West Nile virus (WNV) into North America in 1999 a number of passerine bird species have been found to play a role in the amplification of the virus. Arbovirus surveillance, observational studies and experimental studies have implicated passerine birds (songbirds, e.g., crows, American robins, house sparrows, and house finches) as significant reservoirs of WNV in North America, yet we lack a tractable passerine animal model for controlled studies of the virus. The zebra finch (Taeniopygia guttata) serves as a model system across a diversity of fields, and here we develop the zebra finch a songbird model for WNV. Like many natural hosts of WNV, we found that zebra finches developed sufficient viremia to serve as a competent host, yet in general resisted mortality from infection. In the Australian zebra finch (AZF) T. g. castanotis, we detected WNV in the majority of sampled tissues by 4 days post injection (dpi). However, WNV was not detected in tissues of sacrificed birds at 14 dpi, shortly after the development of detectable anti-WNV antibodies in the majority of birds indicating successful viral clearance. We compared susceptibility between the two zebra finch subspecies AZF and Timor zebra finch (TZF) T. g. guttata. Compared to AZF, WNV RNA was detected in a larger proportion of challenged TZF and molecular detection of virus in the serum of TZF was significantly higher than in AZF. Given the observed moderate host competence and disease susceptibility, we suggest that zebra finches are appropriate as models for the study of WNV and although underutilized in this respect, may be ideal models for the study of the many diseases carried and transmitted by songbirds.
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Affiliation(s)
- Erik K. Hofmeister
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Melissa Lund
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Valerie Shearn-Bochsler
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
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Miao N, Wang X, Hou Y, Feng Y, Gong Y. Identification of male-biased microRNA-107 as a direct regulator for nuclear receptor subfamily 5 group A member 1 based on sexually dimorphic microRNA expression profiling from chicken embryonic gonads. Mol Cell Endocrinol 2016; 429:29-40. [PMID: 27036932 DOI: 10.1016/j.mce.2016.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/08/2016] [Accepted: 03/27/2016] [Indexed: 12/15/2022]
Abstract
Several studies indicate that sexual dimorphic microRNAs (miRNAs) in chicken gonads are likely to have important roles in sexual development, but a more global understanding of the roles of miRNAs in sexual differentiation is still needed. To this end, we performed miRNA expression profiling in chicken gonads at embryonic day 5.5 (E5.5). Among the sex-biased miRNAs validated by qRT-PCR, twelve male-biased and six female-biased miRNAs were consistent with the sequencing results. Bioinformatics analysis revealed that some sex-biased miRNAs were potentially involved in gonadal development. Further functional analysis found that over-expression of miR-107 directly inhibited nuclear receptor subfamily 5 group A member 1 (NR5a1), and its downstream cytochrome P450 family 19 subfamily A, polypeptide 1 (CYP19A1). However, anti-Mullerian hormone (AMH) was not directly or indirectly regulated by miR-107. Overall results indicate that miR-107 may specifically mediate avian ovary-development by post-transcriptional regulation of NR5a1 and CYP19A1 in estrogen signaling pathways.
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Affiliation(s)
- Nan Miao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xin Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yue Hou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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