Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Yong Zhang; Jie Wang; Shoujun Huang; Xiaopeng Zhu; Jun Liu; Ning Yang; Dandan Song; Rimao Wu; Wei Deng; Geir Skogerbø; Xiu Jie Wang; Runsheng Chen; Dahai Zhu

doi:10.1093/nar/gkp704

Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Yong Zhang, Jie Wang, Shoujun Huang, Xiaopeng Zhu, Jun Liu, Ning Yang, Dandan Song, Rimao Wu, Wei Deng, Geir Skogerbø, Xiu Jie Wang, Runsheng Chen, Dahai Zhu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

Abstract

Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50-500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.

Original language	English
Pages (from-to)	6562-6574
Number of pages	13
Journal	Nucleic Acids Research
Volume	37
Issue number	19
DOIs	https://doi.org/10.1093/nar/gkp704
Publication status	Published - 2009
Externally published	Yes

Access to Document

10.1093/nar/gkp704

Cite this

@article{0c3f4a65f30f4ee7925048e2caf7f5f3,

title = "Systematic identification and characterization of chicken (Gallus gallus) ncRNAs",

abstract = "Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50-500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.",

author = "Yong Zhang and Jie Wang and Shoujun Huang and Xiaopeng Zhu and Jun Liu and Ning Yang and Dandan Song and Rimao Wu and Wei Deng and Geir Skogerb{\o} and Wang, \{Xiu Jie\} and Runsheng Chen and Dahai Zhu",

year = "2009",

doi = "10.1093/nar/gkp704",

language = "English",

volume = "37",

pages = "6562--6574",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "19",

}

TY - JOUR

T1 - Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

AU - Zhang, Yong

AU - Wang, Jie

AU - Huang, Shoujun

AU - Zhu, Xiaopeng

AU - Liu, Jun

AU - Yang, Ning

AU - Song, Dandan

AU - Wu, Rimao

AU - Deng, Wei

AU - Skogerbø, Geir

AU - Wang, Xiu Jie

AU - Chen, Runsheng

AU - Zhu, Dahai

PY - 2009

Y1 - 2009

N2 - Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50-500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.

AB - Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50-500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.

UR - http://www.scopus.com/inward/record.url?scp=71049154451&partnerID=8YFLogxK

U2 - 10.1093/nar/gkp704

DO - 10.1093/nar/gkp704

M3 - Article

C2 - 19720738

AN - SCOPUS:71049154451

SN - 0305-1048

VL - 37

SP - 6562

EP - 6574

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 19

ER -

Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Abstract

Access to Document

Other files and links

Fingerprint

Cite this