The de novo sequence origin of two long non-coding genes from an inter-genic region

Yulin Dai; Shengdi Li; Xiao Dong; Han Sun; Chao Li; Zhi Liu; Beili Ying; Guohui Ding; Yixue Li

doi:10.1186/1471-2164-14-S8-S6

The de novo sequence origin of two long non-coding genes from an inter-genic region

Yulin Dai, Shengdi Li, Xiao Dong, Han Sun, Chao Li, Zhi Liu, Beili Ying, Guohui Ding, Yixue Li

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

3 Scopus citations

Abstract

Background: The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can only be expressed in mouse testis with a mouse-specific transcription start site. The consensus sequence of Pldi is also part of an antisense transcript AK158810 expressed in a wide range of mouse tissues.Result: We focused on sequence origin of Pldi and Ak158810. We demonstrated that their sequence was originated from an inter-genic region and is only presented in mammalians. Transposable events and chromosome rearrangements were involved in the evolution of ancestral sequence. Moreover, we discovered high conservation in part of this region was correlated with chromosome rearrangements, CpG demethylation and transcriptional factor binding motif. These results demonstrated that multiple factors contributed to the sequence origin of Pldi.Conclusions: We comprehensively analyzed the sequence origin of Pldi-Ak158810 loci. We provided various factors, including rearrangement, transposable elements, contributed to the formation of the sequence.

Original language	English (US)
Article number	S6
Journal	BMC Genomics
Volume	14
Issue number	SUPP 8
DOIs	https://doi.org/10.1186/1471-2164-14-S8-S6
State	Published - Dec 9 2013
Externally published	Yes

Bibliographical note

Funding Information:
Funding for the publication fee comes from National Natural Science Foundation of China (grant number: 31070752). This article has been published as part of BMC Genomics Volume 14 Supplement 8, 2013: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenomics/supplements/14/S8.

Funding Information:
We thank Prof. Lei Liu, Dr. Guangyong Zheng, Dr. Zhen Wang, Jie Wang, and Tiancheng Liu, for their helpful comments and suggestions. This work was supported by the National Key Basic Research Program of China, known as 973 Program (grant number: 2011CB910204, grant number: 2010CB529206, grant number: 2010CB912702), the Research Program of The Chinese Academy of Sciences (grant number: KSCX2-EW-R-04, grant number: KSCX2-YW-R-190, grant number: 2011KIP204) and National Natural Science Foundation of China (grant number: 31070752).

Keywords

Conserved Element
Overlapping transcripts
Sequence Origin of Pldi and Ak158810 loci
Substitution rate

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10.1186/1471-2164-14-S8-S6

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@article{7d05f1fecd5d40168a45591dbb2b4943,

title = "The de novo sequence origin of two long non-coding genes from an inter-genic region",

abstract = "Background: The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can only be expressed in mouse testis with a mouse-specific transcription start site. The consensus sequence of Pldi is also part of an antisense transcript AK158810 expressed in a wide range of mouse tissues.Result: We focused on sequence origin of Pldi and Ak158810. We demonstrated that their sequence was originated from an inter-genic region and is only presented in mammalians. Transposable events and chromosome rearrangements were involved in the evolution of ancestral sequence. Moreover, we discovered high conservation in part of this region was correlated with chromosome rearrangements, CpG demethylation and transcriptional factor binding motif. These results demonstrated that multiple factors contributed to the sequence origin of Pldi.Conclusions: We comprehensively analyzed the sequence origin of Pldi-Ak158810 loci. We provided various factors, including rearrangement, transposable elements, contributed to the formation of the sequence.",

keywords = "Conserved Element, Overlapping transcripts, Sequence Origin of Pldi and Ak158810 loci, Substitution rate",

author = "Yulin Dai and Shengdi Li and Xiao Dong and Han Sun and Chao Li and Zhi Liu and Beili Ying and Guohui Ding and Yixue Li",

note = "Funding Information: Funding for the publication fee comes from National Natural Science Foundation of China (grant number: 31070752). This article has been published as part of BMC Genomics Volume 14 Supplement 8, 2013: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenomics/supplements/14/S8. Funding Information: We thank Prof. Lei Liu, Dr. Guangyong Zheng, Dr. Zhen Wang, Jie Wang, and Tiancheng Liu, for their helpful comments and suggestions. This work was supported by the National Key Basic Research Program of China, known as 973 Program (grant number: 2011CB910204, grant number: 2010CB529206, grant number: 2010CB912702), the Research Program of The Chinese Academy of Sciences (grant number: KSCX2-EW-R-04, grant number: KSCX2-YW-R-190, grant number: 2011KIP204) and National Natural Science Foundation of China (grant number: 31070752).",

year = "2013",

month = dec,

day = "9",

doi = "10.1186/1471-2164-14-S8-S6",

language = "English (US)",

volume = "14",

journal = "BMC Genomics",

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T1 - The de novo sequence origin of two long non-coding genes from an inter-genic region

AU - Dai, Yulin

AU - Li, Shengdi

AU - Dong, Xiao

AU - Sun, Han

AU - Li, Chao

AU - Liu, Zhi

AU - Ying, Beili

AU - Ding, Guohui

AU - Li, Yixue

N1 - Funding Information: Funding for the publication fee comes from National Natural Science Foundation of China (grant number: 31070752). This article has been published as part of BMC Genomics Volume 14 Supplement 8, 2013: Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenomics/supplements/14/S8. Funding Information: We thank Prof. Lei Liu, Dr. Guangyong Zheng, Dr. Zhen Wang, Jie Wang, and Tiancheng Liu, for their helpful comments and suggestions. This work was supported by the National Key Basic Research Program of China, known as 973 Program (grant number: 2011CB910204, grant number: 2010CB529206, grant number: 2010CB912702), the Research Program of The Chinese Academy of Sciences (grant number: KSCX2-EW-R-04, grant number: KSCX2-YW-R-190, grant number: 2011KIP204) and National Natural Science Foundation of China (grant number: 31070752).

PY - 2013/12/9

Y1 - 2013/12/9

N2 - Background: The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can only be expressed in mouse testis with a mouse-specific transcription start site. The consensus sequence of Pldi is also part of an antisense transcript AK158810 expressed in a wide range of mouse tissues.Result: We focused on sequence origin of Pldi and Ak158810. We demonstrated that their sequence was originated from an inter-genic region and is only presented in mammalians. Transposable events and chromosome rearrangements were involved in the evolution of ancestral sequence. Moreover, we discovered high conservation in part of this region was correlated with chromosome rearrangements, CpG demethylation and transcriptional factor binding motif. These results demonstrated that multiple factors contributed to the sequence origin of Pldi.Conclusions: We comprehensively analyzed the sequence origin of Pldi-Ak158810 loci. We provided various factors, including rearrangement, transposable elements, contributed to the formation of the sequence.

AB - Background: The gene Polymorphic derived intron-containing, known as Pldi, is a long non-coding RNA (lncRNA) first discovered in mouse. Although parts of its sequence were reported to be conserved in rat and human, it can only be expressed in mouse testis with a mouse-specific transcription start site. The consensus sequence of Pldi is also part of an antisense transcript AK158810 expressed in a wide range of mouse tissues.Result: We focused on sequence origin of Pldi and Ak158810. We demonstrated that their sequence was originated from an inter-genic region and is only presented in mammalians. Transposable events and chromosome rearrangements were involved in the evolution of ancestral sequence. Moreover, we discovered high conservation in part of this region was correlated with chromosome rearrangements, CpG demethylation and transcriptional factor binding motif. These results demonstrated that multiple factors contributed to the sequence origin of Pldi.Conclusions: We comprehensively analyzed the sequence origin of Pldi-Ak158810 loci. We provided various factors, including rearrangement, transposable elements, contributed to the formation of the sequence.

KW - Conserved Element

KW - Overlapping transcripts

KW - Sequence Origin of Pldi and Ak158810 loci

KW - Substitution rate

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AN - SCOPUS:84889675080

SN - 1471-2164

VL - 14

JO - BMC Genomics

JF - BMC Genomics

IS - SUPP 8

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ER -

The de novo sequence origin of two long non-coding genes from an inter-genic region

Abstract

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Keywords

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