Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosom...

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Autores principales:	Tulika Prakash, Vineet K Sharma, Naoki Adati, Ritsuko Ozawa, Naveen Kumar, Yuichiro Nishida, Takayoshi Fujikake, Tadayuki Takeda, Todd D Taylor
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c00a41db78e443b183a467cf488fce12
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spelling	oai:doaj.org-article:c00a41db78e443b183a467cf488fce122021-11-18T07:03:27ZExpression of conjoined genes: another mechanism for gene regulation in eukaryotes.1932-620310.1371/journal.pone.0013284https://doaj.org/article/c00a41db78e443b183a467cf488fce122010-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20967262/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.Tulika PrakashVineet K SharmaNaoki AdatiRitsuko OzawaNaveen KumarYuichiro NishidaTakayoshi FujikakeTadayuki TakedaTodd D TaylorPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 10, p e13284 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tulika Prakash Vineet K Sharma Naoki Adati Ritsuko Ozawa Naveen Kumar Yuichiro Nishida Takayoshi Fujikake Tadayuki Takeda Todd D Taylor Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
description	From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.
format	article
author	Tulika Prakash Vineet K Sharma Naoki Adati Ritsuko Ozawa Naveen Kumar Yuichiro Nishida Takayoshi Fujikake Tadayuki Takeda Todd D Taylor
author_facet	Tulika Prakash Vineet K Sharma Naoki Adati Ritsuko Ozawa Naveen Kumar Yuichiro Nishida Takayoshi Fujikake Tadayuki Takeda Todd D Taylor
author_sort	Tulika Prakash
title	Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
title_short	Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
title_full	Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
title_fullStr	Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
title_full_unstemmed	Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
title_sort	expression of conjoined genes: another mechanism for gene regulation in eukaryotes.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/c00a41db78e443b183a467cf488fce12
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Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.

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