Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling

The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the...

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Autores principales:	Ryo Ishibashi, Y-h. Taguchi
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	multidimensional scaling high-throughput chromosome conformation capture enhancer promoter Genetics QH426-470
Acceso en línea:	https://doaj.org/article/22e8432a0643466e810e65ad342ad7b2
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id	oai:doaj.org-article:22e8432a0643466e810e65ad342ad7b2
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spelling	oai:doaj.org-article:22e8432a0643466e810e65ad342ad7b22021-11-25T17:40:37ZIdentification of Enhancers and Promoters in the Genome by Multidimensional Scaling10.3390/genes121116712073-4425https://doaj.org/article/22e8432a0643466e810e65ad342ad7b22021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1671https://doaj.org/toc/2073-4425The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops were directly derived from Hi-C heat maps. Multidimensional Scaling (MDS) is used in this assessment to more precisely locate enhancers and promoters. MDS is a multivariate analysis method that reproduces the original coordinates from the distance matrix between elements. We used Hi-C data of cultured osteosarcoma cells and applied MDS as the distance matrix of the genome. In addition, we selected columns 2 and 3 of the orthogonal matrix U as the desired structure. Overall, the DNA loops from the reconstructed genome structure contained bioprocesses involved in transcription, such as the pre-transcriptional initiation complex and RNA polymerase II initiation complex, and transcription factors involved in cancer, such as Foxm1 and CREB3. Therefore, our results are consistent with the biological findings. Our method is suitable for identifying enhancers and promoters in the genome.Ryo IshibashiY-h. TaguchiMDPI AGarticlemultidimensional scalinghigh-throughput chromosome conformation captureenhancerpromoterGeneticsQH426-470ENGenes, Vol 12, Iss 1671, p 1671 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	multidimensional scaling high-throughput chromosome conformation capture enhancer promoter Genetics QH426-470
spellingShingle	multidimensional scaling high-throughput chromosome conformation capture enhancer promoter Genetics QH426-470 Ryo Ishibashi Y-h. Taguchi Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
description	The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops were directly derived from Hi-C heat maps. Multidimensional Scaling (MDS) is used in this assessment to more precisely locate enhancers and promoters. MDS is a multivariate analysis method that reproduces the original coordinates from the distance matrix between elements. We used Hi-C data of cultured osteosarcoma cells and applied MDS as the distance matrix of the genome. In addition, we selected columns 2 and 3 of the orthogonal matrix U as the desired structure. Overall, the DNA loops from the reconstructed genome structure contained bioprocesses involved in transcription, such as the pre-transcriptional initiation complex and RNA polymerase II initiation complex, and transcription factors involved in cancer, such as Foxm1 and CREB3. Therefore, our results are consistent with the biological findings. Our method is suitable for identifying enhancers and promoters in the genome.
format	article
author	Ryo Ishibashi Y-h. Taguchi
author_facet	Ryo Ishibashi Y-h. Taguchi
author_sort	Ryo Ishibashi
title	Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
title_short	Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
title_full	Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
title_fullStr	Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
title_full_unstemmed	Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling
title_sort	identification of enhancers and promoters in the genome by multidimensional scaling
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/22e8432a0643466e810e65ad342ad7b2
work_keys_str_mv	AT ryoishibashi identificationofenhancersandpromotersinthegenomebymultidimensionalscaling AT yhtaguchi identificationofenhancersandpromotersinthegenomebymultidimensionalscaling
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Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling

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