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Genome-wide Profiling of the Histone Modification Status in Hutchinson-Gilford Progeria Syndrome

Secchia, Stefano (2016) MOBN01 20161
Degree Projects in Molecular Biology
Abstract
Children affected by the multisystem genetic disorder Hutchinson-Gilford Progeria Syndrome look prematurely aged, suffer from elderly-related conditions and die during adolescence due to cardiovascular complications. The cause of the disease is single point gain-of-function mutations in the LMNA gene, which encodes the lamin A and lamin C proteins, major components of the nuclear lamina. These mutations cause errors during post-translational processing, that generate a permanently farnesylated lamin A/C called progerin. Despite our knowledge of lamin A/C function, understanding of the molecular mechanisms of the disease is lacking. Earlier studies reported alterations of histone modifications in progeria-patient cells, suggesting a... (More)
Children affected by the multisystem genetic disorder Hutchinson-Gilford Progeria Syndrome look prematurely aged, suffer from elderly-related conditions and die during adolescence due to cardiovascular complications. The cause of the disease is single point gain-of-function mutations in the LMNA gene, which encodes the lamin A and lamin C proteins, major components of the nuclear lamina. These mutations cause errors during post-translational processing, that generate a permanently farnesylated lamin A/C called progerin. Despite our knowledge of lamin A/C function, understanding of the molecular mechanisms of the disease is lacking. Earlier studies reported alterations of histone modifications in progeria-patient cells, suggesting a possible connection between the mutated lamin A/C and chromatin regulation. Here, I investigated the occurrence of chromatin defects in skin fibroblasts of progeria patients more systematically, by profiling the genome-wide distributions of key histone modifications associated with activity of gene transcription using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Specifically, I determined the distributions of acetylation of lysine 27 on histone H3 (H3K27ac), and mono- and tri- methylation of lysine 4 on histone H3 (H3K4me1, H3K4me3), which are marks associated with active genes and regulatory elements, and of tri-methylation of lysine 27 on histone H3 (H3K27me3), a modification that marks heterochromatin and silenced genes. While my analysis showed a small subset of genomic regions with differences of histone modification states between normal and progeria cells, there were no global changes of histone marks in progeria cells. I then hypothesized that if progeria-patient cells are defective in the regulation of their chromatin marks, these defects should become more apparent during environmental shifts that induce drastic changes in the transcriptome. I tested this hypothesis by profiling the above histone modifications during starvation-induced quiescence and the subsequent recovery from starvation. In both healthy and progeria cell lines, tri-methylation of lysine 4 on histone 3 (H3K4me3), a mark associated with the transcription start sites of active genes and transcriptional activation, was decreased genome-wide during quiescence. I did not detect changes of H3K4me1 and H3K27ac at promoters or distal regulatory elements and the decrease in H3K4me3 was not paralleled by an increase in H3K27me3. I propose that the H3K4me3 reduction is the outcome of a global promoter-targeted active demethylation occurring upon quiescence entry in human skin fibroblasts. After 24 hours of recovery, the H3K4me3 signal was re-established to levels similar to the proliferating state in the healthy cell line, indicating an active regulation of this mark during quiescence entry and exit. Furthermore, the reduction of H3K4me3 was more drastic in the progeria-patient cell line, suggesting defects in the regulation of quiescence in progeria. In-vivo fibroblasts and adult stem cells need to efficiently switch between periods of quiescence and proliferation, therefore alterations in this process can have profound implications for the disease. (Less)
Popular Abstract
Chromatin Defects in Progeria Syndrome

If you could extract the DNA of a human cell and stretch it out, you would hold in your hands a string of about one meter in length. Now consider this mind-numbing fact: the cellular compartment that stores the DNA, the nucleus, is one million times smaller in diameter than the DNA string! Cells achieve this seemingly impossible task by wrapping the DNA around proteins called histones, which are then smart packed into a more tight structure, the chromatin. You might think that this process is completely random, just like hastily fitting a long rope in an extremely small closet. Instead, cells perform the packaging very rigorously, because they need to be able to access instructions written in the... (More)
Chromatin Defects in Progeria Syndrome

If you could extract the DNA of a human cell and stretch it out, you would hold in your hands a string of about one meter in length. Now consider this mind-numbing fact: the cellular compartment that stores the DNA, the nucleus, is one million times smaller in diameter than the DNA string! Cells achieve this seemingly impossible task by wrapping the DNA around proteins called histones, which are then smart packed into a more tight structure, the chromatin. You might think that this process is completely random, just like hastily fitting a long rope in an extremely small closet. Instead, cells perform the packaging very rigorously, because they need to be able to access instructions written in the DNA in order to survive. The tails of the histone proteins harbor a large variety of chemical modifications, which researchers suspect to be involved in the regulation of the packaging. Alterations of these histone marks are present in a growing number of human diseases, including cancer. In my project, I investigated the occurrence of chromatin defects in the genetic disorder Hutchison-Gilford Progeria Syndrome.

Children affected by progeria, suffer from elderly-related conditions and they look prematurely aged. Unfortunately, they die because of heart complications during adolescence. We know that the disease is caused by a mutation in the lamin A protein, a component of the nucleus of cells. However, we lack a clear picture of how the mutated lamin A induces the onset of the disease. In my project, I determined how specific histone modifications are distributed along the DNA in cells of progeria patients. By comparing these histone marks profiles with the ones of healthy cells, I identified a small set of DNA sites where the levels of the histone modifications are altered.

I found these defects when cells were constantly dividing to produce new daughter cells. I used the same approach, to search for chromatin changes when cells are in a sort resting state, called quiescence. Most cells in our body are in quiescence and if necessary, they can exit their rest and become active again. For example, your skin cells can start dividing to close a wound. I found that, in both healthy and disease cells, one specific histone mark is strongly reduced during quiescence. This change has not been previously characterized, and it provides a clue for understanding the role that histone modifications play in cellular processes.

Moreover, the reduction of the histone mark was more dramatic in progeria cells, to the point that it was almost completely lost. This event can potentially have profound implications for the disease, by contributing to difficulties in exiting the resting state and entering cell activation. For example, a reduced ability to repair damaged blood vessels may lead to the cardiovascular complications that are the major cause of death of progeria patients.

Future studies should aim at clarifying the relevance of my findings for the development of progeria syndrome. Insights into the chromatin alterations of this disease could provide a possible therapeutical target to ameliorate the condition of progeria patients.

Supervisor: Dr. Kohta Ikegami
MasterĀ“s Degree Project, 45 ECTS credits, 2016
Department of Biology, Lund University, Sweden
Department of Human Genetics, University of Chicago, USA (Less)
Please use this url to cite or link to this publication:
author
Secchia, Stefano
supervisor
organization
course
MOBN01 20161
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8891432
date added to LUP
2016-09-12 11:27:53
date last changed
2016-09-12 11:27:53
@misc{8891432,
  abstract     = {Children affected by the multisystem genetic disorder Hutchinson-Gilford Progeria Syndrome look prematurely aged, suffer from elderly-related conditions and die during adolescence due to cardiovascular complications. The cause of the disease is single point gain-of-function mutations in the LMNA gene, which encodes the lamin A and lamin C proteins, major components of the nuclear lamina. These mutations cause errors during post-translational processing, that generate a permanently farnesylated lamin A/C called progerin. Despite our knowledge of lamin A/C function, understanding of the molecular mechanisms of the disease is lacking. Earlier studies reported alterations of histone modifications in progeria-patient cells, suggesting a possible connection between the mutated lamin A/C and chromatin regulation. Here, I investigated the occurrence of chromatin defects in skin fibroblasts of progeria patients more systematically, by profiling the genome-wide distributions of key histone modifications associated with activity of gene transcription using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Specifically, I determined the distributions of acetylation of lysine 27 on histone H3 (H3K27ac), and mono- and tri- methylation of lysine 4 on histone H3 (H3K4me1, H3K4me3), which are marks associated with active genes and regulatory elements, and of tri-methylation of lysine 27 on histone H3 (H3K27me3), a modification that marks heterochromatin and silenced genes. While my analysis showed a small subset of genomic regions with differences of histone modification states between normal and progeria cells, there were no global changes of histone marks in progeria cells. I then hypothesized that if progeria-patient cells are defective in the regulation of their chromatin marks, these defects should become more apparent during environmental shifts that induce drastic changes in the transcriptome. I tested this hypothesis by profiling the above histone modifications during starvation-induced quiescence and the subsequent recovery from starvation. In both healthy and progeria cell lines, tri-methylation of lysine 4 on histone 3 (H3K4me3), a mark associated with the transcription start sites of active genes and transcriptional activation, was decreased genome-wide during quiescence. I did not detect changes of H3K4me1 and H3K27ac at promoters or distal regulatory elements and the decrease in H3K4me3 was not paralleled by an increase in H3K27me3. I propose that the H3K4me3 reduction is the outcome of a global promoter-targeted active demethylation occurring upon quiescence entry in human skin fibroblasts. After 24 hours of recovery, the H3K4me3 signal was re-established to levels similar to the proliferating state in the healthy cell line, indicating an active regulation of this mark during quiescence entry and exit. Furthermore, the reduction of H3K4me3 was more drastic in the progeria-patient cell line, suggesting defects in the regulation of quiescence in progeria. In-vivo fibroblasts and adult stem cells need to efficiently switch between periods of quiescence and proliferation, therefore alterations in this process can have profound implications for the disease.},
  author       = {Secchia, Stefano},
  language     = {eng},
  note         = {Student Paper},
  title        = {Genome-wide Profiling of the Histone Modification Status in Hutchinson-Gilford Progeria Syndrome},
  year         = {2016},
}