Akhtar, Most. Maluluda
(2013)
Epigenetic modifications in CpG islands and signatures
of selective pressure in human genome.
[Tesi di dottorato]
Item Type: |
Tesi di dottorato
|
Resource language: |
English |
Title: |
Epigenetic modifications in CpG islands and signatures
of selective pressure in human genome |
Creators: |
Creators | Email |
---|
Akhtar, Most. Maluluda | mauluda82@gmail.com |
|
Date: |
30 March 2013 |
Number of Pages: |
103 |
Institution: |
Università degli Studi di Napoli Federico II |
Department: |
Biologia e patologia cellullare e molecolare "L. Califano" |
Scuola di dottorato: |
Biotecnologie |
Dottorato: |
Biologia computazionale e bioinformatica |
Ciclo di dottorato: |
25 |
Coordinatore del Corso di dottorato: |
nome | email |
---|
Cocozza, Sergio | cocozza@unina.it |
|
Tutor: |
nome | email |
---|
Cocozza, Sergio | cocozza@unina.it | Miele, Gennaro | miele@na.infn.it |
|
Date: |
30 March 2013 |
Number of Pages: |
103 |
Keywords: |
Epigenetic, Selective pressure, CpG islands,DNA methylation, H3K4me3, H3K27ac, H3K36me3 |
Settori scientifico-disciplinari del MIUR: |
Area 06 - Scienze mediche > MED/03 - Genetica medica |
Aree tematiche (7° programma Quadro): |
SALUTE e TUTELA DEL CONSUMATORE > Biotecnologie, strumenti e tecnologie generiche per la salute umana |
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Date Deposited: |
03 Apr 2013 10:18 |
Last Modified: |
17 Jun 2014 06:04 |
URI: |
http://www.fedoa.unina.it/id/eprint/9283 |

Collection description
Epigenetics deals the heritable changes in gene regulation which is not related with the changes of
DNA sequence itself. Among several molecular mechanisms that mediate epigenetic phenomena,
DNA methylation and histone modifications are well known markers. CpG islands (CGIs) are the key
epigenomic elements in mammalian genome. CGIs are defined as the segments of the genome that
show increased level of CpG dinucleotides and GC content. These CGIs are enriched at genes, about
60% of all genes in the human genome containing a CGI upstream. DNA methylation at CGIs is one of
the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and
control of transcriptional potential. DNA methylation is involved also in several processes that are
central to evolutionary biology, including phenotypic plasticity and evolvability. Furthermore, histone
modifications in CGIs are associated with the changes in chromatin states and with transcription
activity. Changes in gene expression play a crucial role in adaptation and evolution. Considering the
role of DNA methylation and histone modifications in gene expression changes, our aim was to
explore the relationship between these two epigenetic marks and selective pressure in human
genome.
In the first step, we explored a relationship between CpG islands methylation and signatures of
selective pressure in Homo sapiens, using a computational biology approach. For this we analyzed
methylation data of 25 human cell lines from the Encyclopedia of DNA Elements (ENCODE)
Consortium. To define regions under selective pressure, we used three distinct signatures that mark
selective events from different evolutionary periods. We compared the DNA methylation of CpG
islands in genomic regions under selective pressure with the methylation of CpG islands in the
remaining part of the genome. We found that CpG islands in the regions under selective pressure are
undermethylated than the CpG islands of the other group.
In the second step, we have studied, using a computational biology approach, the relationship
between histone modifications in CGIs and selective pressure in Homo sapiens. We considered three
histone modifications: histone H3 lysine 4 trimethylation (H3K4me3), acetylation of histone H3 at
lysine 27 (H3K27ac) and trimethylation of histone H3 at lysine 36 (H3K36me3), and we used the
publicly available genomic-scale histone modification data of 23 human cell lines. To define regions
under selective pressure, we used the similar approach as used in the first step. We found that, CGIs
under selective pressure showed significant enrichments for histone modifications.
In conclusion, our overall findings suggest that CpG islands that experienced selective pressure are
characterized by distinct epigenetic signatures.
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