Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells

Smarajit Das; Pijush Das; Sanga Mitra; Medhanjali Dasgupta; Jayprokas Chakrabarti; Eric Larsson

doi:doi:10.11648/j.bs.20150103.11

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Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells

Smarajit Das, Pijush Das, Sanga Mitra, Medhanjali Dasgupta, Jayprokas Chakrabarti, Eric Larsson

Published in Biomedical Sciences (Volume 1, Issue 3)

Received: 9 September 2015 Accepted: 8 October 2015 Published: 14 October 2015

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Abstract

Chromatin immune precipitation followed by high-throughput sequencing (Chip-Seq), investigate the genome-wide distribution of all histone modifications. Lysine residues within histones di or tri-methylated in Saccharomyces cerevisiae have been studied earlier. Tri-methylation of Lys 4 of histone H3K4me3 correlates with transcriptional activity, but little is known about this methylation state in human. It was also previously proved that deposition of H3K4me2 modification at TSS is associated with gene repression in the yeast cell. Overlapping non-coding RNA (ncRNA) transcript assumes a crucial role in this repression. Here, we examine the H3K4me2 and H3K4me3 methylation dynamics at the TSS region of human genes across the ENCODE (https://www. encode project. org/) Consortium 8 cell lines GM12878, H1-hESC, HeLa-S3, HepG2, HSMM, HUVEC, K562 and NHEK, we identified clear divergence of histone modification profiles in H1-hESC with respect to others. While, H3K4me2 modifications were found to be associated with the vast majority of genes in the H1-hESC with a significantly decreased amount in other differentiated cell lines, H3K4me3 modification showed completely reverse trends. By the process of differentiation, a distinct set of genes lose H3K4me2 in H1-hESCand gain H3K4me3 in differentiated cell, thereby, enhancing the expression level of the corresponding genes. On the level of gene ontology molecular function classification, these genes are mostly associated with protein binding, nucleotide binding, DNA binding and ATP binding. Other than that, signaling and receptor activity, metal ion binding and phosphorylation-dephosphorylating action can be correlated with these genes. We expect a crosstalk between the change of methylation status and gene functionality, as all these functions can be allied to transcriptional regulation and gene activation, which once again is linked to H3K4me3 mark.

Published in	Biomedical Sciences (Volume 1, Issue 3)
DOI	10.11648/j.bs.20150103.11
Page(s)	18-33
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Epigenetic, H3K4me2, H3K4me3, RNA-Seq, Chip-Seq, UCSC, Methylation Dynamics

References

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Smarajit Das, Pijush Das, Sanga Mitra, Medhanjali Dasgupta, Jayprokas Chakrabarti, et al. (2015). Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomedical Sciences, 1(3), 18-33. https://doi.org/10.11648/j.bs.20150103.11

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ACS Style

Smarajit Das; Pijush Das; Sanga Mitra; Medhanjali Dasgupta; Jayprokas Chakrabarti, et al. Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomed. Sci. 2015, 1(3), 18-33. doi: 10.11648/j.bs.20150103.11

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AMA Style

Smarajit Das, Pijush Das, Sanga Mitra, Medhanjali Dasgupta, Jayprokas Chakrabarti, et al. Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomed Sci. 2015;1(3):18-33. doi: 10.11648/j.bs.20150103.11

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@article{10.11648/j.bs.20150103.11,
  author = {Smarajit Das and Pijush Das and Sanga Mitra and Medhanjali Dasgupta and Jayprokas Chakrabarti and Eric Larsson},
  title = {Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells},
  journal = {Biomedical Sciences},
  volume = {1},
  number = {3},
  pages = {18-33},
  doi = {10.11648/j.bs.20150103.11},
  url = {https://doi.org/10.11648/j.bs.20150103.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bs.20150103.11},
  abstract = {Chromatin immune precipitation followed by high-throughput sequencing (Chip-Seq), investigate the genome-wide distribution of all histone modifications. Lysine residues within histones di or tri-methylated in Saccharomyces cerevisiae have been studied earlier. Tri-methylation of Lys 4 of histone H3K4me3 correlates with transcriptional activity, but little is known about this methylation state in human. It was also previously proved that deposition of H3K4me2 modification at TSS is associated with gene repression in the yeast cell. Overlapping non-coding RNA (ncRNA) transcript assumes a crucial role in this repression. Here, we examine the H3K4me2 and H3K4me3 methylation dynamics at the TSS region of human genes across the ENCODE (https://www. encode project. org/) Consortium 8 cell lines GM12878, H1-hESC, HeLa-S3, HepG2, HSMM, HUVEC, K562 and NHEK, we identified clear divergence of histone modification profiles in H1-hESC with respect to others. While, H3K4me2 modifications were found to be associated with the vast majority of genes in the H1-hESC with a significantly decreased amount in other differentiated cell lines, H3K4me3 modification showed completely reverse trends. By the process of differentiation, a distinct set of genes lose H3K4me2 in H1-hESCand gain H3K4me3 in differentiated cell, thereby, enhancing the expression level of the corresponding genes. On the level of gene ontology molecular function classification, these genes are mostly associated with protein binding, nucleotide binding, DNA binding and ATP binding. Other than that, signaling and receptor activity, metal ion binding and phosphorylation-dephosphorylating action can be correlated with these genes. We expect a crosstalk between the change of methylation status and gene functionality, as all these functions can be allied to transcriptional regulation and gene activation, which once again is linked to H3K4me3 mark.},
 year = {2015}
}

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TY - JOUR
T1 - Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells
AU - Smarajit Das
AU - Pijush Das
AU - Sanga Mitra
AU - Medhanjali Dasgupta
AU - Jayprokas Chakrabarti
AU - Eric Larsson
Y1 - 2015/10/14
PY - 2015
N1 - https://doi.org/10.11648/j.bs.20150103.11
DO - 10.11648/j.bs.20150103.11
T2 - Biomedical Sciences
JF - Biomedical Sciences
JO - Biomedical Sciences
SP - 18
EP - 33
PB - Science Publishing Group
SN - 2575-3932
UR - https://doi.org/10.11648/j.bs.20150103.11
AB - Chromatin immune precipitation followed by high-throughput sequencing (Chip-Seq), investigate the genome-wide distribution of all histone modifications. Lysine residues within histones di or tri-methylated in Saccharomyces cerevisiae have been studied earlier. Tri-methylation of Lys 4 of histone H3K4me3 correlates with transcriptional activity, but little is known about this methylation state in human. It was also previously proved that deposition of H3K4me2 modification at TSS is associated with gene repression in the yeast cell. Overlapping non-coding RNA (ncRNA) transcript assumes a crucial role in this repression. Here, we examine the H3K4me2 and H3K4me3 methylation dynamics at the TSS region of human genes across the ENCODE (https://www. encode project. org/) Consortium 8 cell lines GM12878, H1-hESC, HeLa-S3, HepG2, HSMM, HUVEC, K562 and NHEK, we identified clear divergence of histone modification profiles in H1-hESC with respect to others. While, H3K4me2 modifications were found to be associated with the vast majority of genes in the H1-hESC with a significantly decreased amount in other differentiated cell lines, H3K4me3 modification showed completely reverse trends. By the process of differentiation, a distinct set of genes lose H3K4me2 in H1-hESCand gain H3K4me3 in differentiated cell, thereby, enhancing the expression level of the corresponding genes. On the level of gene ontology molecular function classification, these genes are mostly associated with protein binding, nucleotide binding, DNA binding and ATP binding. Other than that, signaling and receptor activity, metal ion binding and phosphorylation-dephosphorylating action can be correlated with these genes. We expect a crosstalk between the change of methylation status and gene functionality, as all these functions can be allied to transcriptional regulation and gene activation, which once again is linked to H3K4me3 mark.
VL - 1
IS - 3
ER -

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Author Information

Smarajit Das

Department of Genetics, University of Georgia, Athens GA, USA
Pijush Das

Cancer Biology & Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
Sanga Mitra

Computational Biology Group, Indian Association for the Cultivation of Science, Kolkata, India
Medhanjali Dasgupta

Department of Chemical Engineering (Bioprocess Engineering), Jadavpur University, Kolkata, India
Jayprokas Chakrabarti

Computational Biology Group, Indian Association for the Cultivation of Science, Kolkata, India
Eric Larsson

Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

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APA Style

Smarajit Das, Pijush Das, Sanga Mitra, Medhanjali Dasgupta, Jayprokas Chakrabarti, et al. (2015). Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomedical Sciences, 1(3), 18-33. https://doi.org/10.11648/j.bs.20150103.11

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Smarajit Das; Pijush Das; Sanga Mitra; Medhanjali Dasgupta; Jayprokas Chakrabarti, et al. Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomed. Sci. 2015, 1(3), 18-33. doi: 10.11648/j.bs.20150103.11

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AMA Style

Smarajit Das, Pijush Das, Sanga Mitra, Medhanjali Dasgupta, Jayprokas Chakrabarti, et al. Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells. Biomed Sci. 2015;1(3):18-33. doi: 10.11648/j.bs.20150103.11

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@article{10.11648/j.bs.20150103.11,
  author = {Smarajit Das and Pijush Das and Sanga Mitra and Medhanjali Dasgupta and Jayprokas Chakrabarti and Eric Larsson},
  title = {Epigenetic Transfiguration of H3K4me2 to H3K4me3 During Differentiation of Embryonic Stem Cell into Non-embryonic Cells},
  journal = {Biomedical Sciences},
  volume = {1},
  number = {3},
  pages = {18-33},
  doi = {10.11648/j.bs.20150103.11},
  url = {https://doi.org/10.11648/j.bs.20150103.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bs.20150103.11},
  abstract = {Chromatin immune precipitation followed by high-throughput sequencing (Chip-Seq), investigate the genome-wide distribution of all histone modifications. Lysine residues within histones di or tri-methylated in Saccharomyces cerevisiae have been studied earlier. Tri-methylation of Lys 4 of histone H3K4me3 correlates with transcriptional activity, but little is known about this methylation state in human. It was also previously proved that deposition of H3K4me2 modification at TSS is associated with gene repression in the yeast cell. Overlapping non-coding RNA (ncRNA) transcript assumes a crucial role in this repression. Here, we examine the H3K4me2 and H3K4me3 methylation dynamics at the TSS region of human genes across the ENCODE (https://www. encode project. org/) Consortium 8 cell lines GM12878, H1-hESC, HeLa-S3, HepG2, HSMM, HUVEC, K562 and NHEK, we identified clear divergence of histone modification profiles in H1-hESC with respect to others. While, H3K4me2 modifications were found to be associated with the vast majority of genes in the H1-hESC with a significantly decreased amount in other differentiated cell lines, H3K4me3 modification showed completely reverse trends. By the process of differentiation, a distinct set of genes lose H3K4me2 in H1-hESCand gain H3K4me3 in differentiated cell, thereby, enhancing the expression level of the corresponding genes. On the level of gene ontology molecular function classification, these genes are mostly associated with protein binding, nucleotide binding, DNA binding and ATP binding. Other than that, signaling and receptor activity, metal ion binding and phosphorylation-dephosphorylating action can be correlated with these genes. We expect a crosstalk between the change of methylation status and gene functionality, as all these functions can be allied to transcriptional regulation and gene activation, which once again is linked to H3K4me3 mark.},
 year = {2015}
}

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