First name
Sri Ganesh
Last name
Jammula
Year of Study
Research Center
Thesis Title
ChIP_QC, computational platform for multivariate epigenetic studies and its application in uncovering role of polycomb dependent methylations states
Thesis Abstract
During my PhD tenure, I have been involved in developing a user-friendly crossplatform
system capable of analyzing epigenomic data and further use it in
understanding the role of the Polycomb Repressive Complex 2 (PRC2) in genome
regulation.
From current trending in epigenetics research, we can sense increasing ease of high
throughput sequencing and greater interest towards genome wide epigenomic
studies. As a result of which we experience an exponential flooding of epigenetic
related data such as Chromatin immunoprecipitation followed by sequencing (ChIPseq),
and RNA sequencing (RNA-seq) in public domain. This creates an opportunity
for crowd sourcing and exploring data outside the boundaries of specific query
centered studies. Such data has to undergo standard primary analysis, which with the
aid of multiple programs has been stabilized courtesy to the scientific community.
Further downstream, out of many, genome wide comparative, correlative and
quantitative studies have proven to be critical and helpful in deciphering key
biological features. For such studies we lack platforms, which can be capable of
handling, analyzing and linking multiple interdisciplinary (ChIP-seq/RNA-seq)
datasets with efficient analytical methods. With this aim we developed ChIP_QC, a
user-friendly standalone computational program with an ability to support numerous
datasets with high/moderate sequencing depth for performing genome wide analysis.
First, using ENCODE project (Consortium, 2012) data, we illustrated few applications
of the program by posing different biological scenarios and showed the comfort with
which some known observations can be verified and also how it can be helpful in
deducing some other novel observations.
17
Second, we were interested in understanding the functionality of the products
generated through catalytic activity of PRC2. It is known that Lysine 27 of histone H3
(H3K27) undergoes posttranslational modification (PTM) and methylation is one
such dominant PTM. Methylation on H3K27 can be either mono/di/tri-methylation
form. Out of all three forms, it is very well demonstrated that trimethylation of H3K27
(H3K27me3) is PRC2 dependent and at the same time its role in gene repression is
well characterized, but functional roles of other forms of methylation on H3K27 are
still poorly characterized. For understanding this, we used mouse embryonic stem
cells (mESC) as model system of our study and we were able to provide an extensive
characterization of other forms of methylation, highlighting their differential
deposition along the genome, their fundamental role in transcriptional regulation,
and their indispensability during differentiation program. Using ChIP_QC and with
other computational methods along with experimental evidences, our data
demonstrated that the monomethylation of Lys27 (H3K27me1) is required for
correct transcription of genes and positively correlates with trimethylated Lys36
(H3K36me3); on the other hand dimethylated Lys27 (H3K27me2), that we identified
to be the principal activity of PRC2, prevents firing of non cell type specific enhancers.
system capable of analyzing epigenomic data and further use it in
understanding the role of the Polycomb Repressive Complex 2 (PRC2) in genome
regulation.
From current trending in epigenetics research, we can sense increasing ease of high
throughput sequencing and greater interest towards genome wide epigenomic
studies. As a result of which we experience an exponential flooding of epigenetic
related data such as Chromatin immunoprecipitation followed by sequencing (ChIPseq),
and RNA sequencing (RNA-seq) in public domain. This creates an opportunity
for crowd sourcing and exploring data outside the boundaries of specific query
centered studies. Such data has to undergo standard primary analysis, which with the
aid of multiple programs has been stabilized courtesy to the scientific community.
Further downstream, out of many, genome wide comparative, correlative and
quantitative studies have proven to be critical and helpful in deciphering key
biological features. For such studies we lack platforms, which can be capable of
handling, analyzing and linking multiple interdisciplinary (ChIP-seq/RNA-seq)
datasets with efficient analytical methods. With this aim we developed ChIP_QC, a
user-friendly standalone computational program with an ability to support numerous
datasets with high/moderate sequencing depth for performing genome wide analysis.
First, using ENCODE project (Consortium, 2012) data, we illustrated few applications
of the program by posing different biological scenarios and showed the comfort with
which some known observations can be verified and also how it can be helpful in
deducing some other novel observations.
17
Second, we were interested in understanding the functionality of the products
generated through catalytic activity of PRC2. It is known that Lysine 27 of histone H3
(H3K27) undergoes posttranslational modification (PTM) and methylation is one
such dominant PTM. Methylation on H3K27 can be either mono/di/tri-methylation
form. Out of all three forms, it is very well demonstrated that trimethylation of H3K27
(H3K27me3) is PRC2 dependent and at the same time its role in gene repression is
well characterized, but functional roles of other forms of methylation on H3K27 are
still poorly characterized. For understanding this, we used mouse embryonic stem
cells (mESC) as model system of our study and we were able to provide an extensive
characterization of other forms of methylation, highlighting their differential
deposition along the genome, their fundamental role in transcriptional regulation,
and their indispensability during differentiation program. Using ChIP_QC and with
other computational methods along with experimental evidences, our data
demonstrated that the monomethylation of Lys27 (H3K27me1) is required for
correct transcription of genes and positively correlates with trimethylated Lys36
(H3K36me3); on the other hand dimethylated Lys27 (H3K27me2), that we identified
to be the principal activity of PRC2, prevents firing of non cell type specific enhancers.
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