Study of cell differentiation by phylogenetic analysis using histone modification data

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. Results: In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We precisely defined the notion of cell-type trees and provided a procedure of building such trees. We propose new data representation techniques and distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful cell-type trees that indicate how diverse types of cells are related. We demonstrate our approach on various kinds of histone modifications for various cell types, also using the datasets to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. We use the results to get some interesting biological findings like important patterns of histone modification changes during cell differentiation process. Conclusions: We introduced and studied the novel problem of inferring cell type trees from histone modification data. The promising results we obtain point the way to a new approach to the study of cell differentiation. We also discuss how cell-type trees can be used to study the evolution of cell types.

A Tale of Two Tumors: Unraveling the Complexities of Epigenetic Dysregulation in Cancer

Maria Christine Donaldson

Epigenetics plays an important role in cancer development and progression. Cancer cells hijack the epigenome by modifying the histone protein units responsible for packaging DNA, or by modifying the DNA itself, resulting in changes to chromatin topology and transcriptional programming within the cell. In this thesis, I report our investigation to uncover the mechanisms of epigenetic regulation and how epigenetic control of transcriptional programming goes awry in cancer. We investigate these processes in two separate contexts. In our first study, we investigate the mechanisms by which EZH2 oncogenic mutations alter structure and function of topologically associating domains in non-Hodgkin lymphoma. The process of chromatin folding leads to a systematic arrangement of hierarchical structural and regulatory elements found within the nucleus. A topologically associating domain (TAD) is a regulatory unit of self interacting DNA, where the transcription of the genes within a TAD is usually dictated by the presence of active (H3K36me3) or inactive (H3K27me3) histone marks. In cancer, the somatic point mutation in EZH2Y646X leads to a genome wide increase in H3K27me3, associated with transcriptional repression. While this alteration leads to changes in the global epigenetic status of the cell, its impact on chromatin organization and TAD-related function remain unclear. By combining transcriptomics and epigenetics with analyses of chromatin structure, we demonstrate a functional interplay between TADs and the epigenetic and transcriptional program of the genes found within them. This balance is altered by EZH2Y646X, leading to the synergistic silencing of entire domains directly targeting cell differentiation and tumor suppressive programs. A closer look reveals that the silencing of tumor suppressive TADs are coupled with structural modifications and changes in promoter interactions within EZH2Y646X target TAD6.139. Impressively, the TADâs transcriptional and epigenetic programs are restored by pharmacological inhibition of EZH2Y646X. Our results indicate that EZH2Y646X alters the topology and function of chromatin domains to promote synergistic oncogenic programs. In our second study, we dissect the epigenetic, transcriptomic, and metabolic signaling dependencies using a novel model of central nervous system primitive neural ectodermal tumors (CNS-PNETs). Central nervous system (CNS) tumors are the leading cause of cancer-associated death in children. Primitive neural-ectodermal tumors (CNS-PNETs) are a particularly aggressive subtype of embryonal CNS-tumor, with a five-year overall survival rate in less than 50% of patients. Despite sharing a similar cell of origin of other CNS tumors, CNS-PNETs have a different anatomical location, unique genetic and epigenetic features, and significantly worse clinical outcome. In addition, a lack of in vivo models for studying CNS tumors challenges the opportunity to dissect the genetic variables that underlie the origin of these tumors. We developed a novel CNS-PNET mouse model, called CNS-NPCs, using neural progenitor cells derived from human-iPS cells. Through histological, DNA methylation, and RNA sequencing analyses, we find that the CNS-NPC model recapitulates the the morphologic, epigenetic, and transcriptomic features of primary CNS-PNETs. In addition, through in vivo metabolic analyses of CNS-NPCs and the patient derived cell line, PFSK-1, we identified dysregulation in the neurotransmitter...

EPFL2019

Transposable elements and their KRAB/KAP1 controllers broadly regulate transcription in adult human cells

Flavia Marzetta

KAP1 is a universal corepressor for the large family of KRAB-ZFP proteins that coordinates epigenetic silencing of endogenous retroelements (EREs) during early embryonic development. This process is essential not just to prevent replication of EREs, but also to control their regulatory influence on host genes. Although in differentiated cells the control of EREs is believed to be mainly DNA methylation-dependent, emerging evidence suggests that KAP1-dependent, histone-based repression might remain a key regulator of ERE expression and its influence on cellular gene networks. Using a combination of transcriptional and histone modification profiling, we have investigated the impact of KAP1 epigenetic regulation on the transcriptional dynamics of human CD4+ T cells. We found that KAP1 binding on subsets of EREs is maintained in differentiated CD4+ T cells, where its locus-specific recruitment is dynamically modulated along with the T cell activation status. KAP1 depletion by RNA interference leads to a global decrease in repressive histone modifications that is accompanied by broad transcriptional alterations. Indeed, not only a large fraction of EREs become derepressed, but their deregulation correlates with illegittimate activation of nearby genes. Correspondingly, loss of KAP1 unleashes the intrinsic regulatory activities that some EREs are endowed with, suggesting a functional link between control of mobile genetic elements and protection of lineage-specific transcriptional networks. These findings establish the KRAB/KAP1 system as an important safeguard of CD4+ T cells transcriptional identity and suggest a critical role in maintaining epigenetic silencing of ERE-based regulatory sequences in adult tissues. Furthermore, our study shed light onto a previously unappreciated contribution of retrotransposon-derived sequences to the complexity of the human T cell transcriptome. A better knowledge of the physiological transcriptional activity of these mobile genetic elements, as well as their control mechanisms throughout development, would greatly help the debate on their pathologic implications.

EPFL2015

Computational studies in epigenomics using histone modification data

Nishanth Ulhas Nair

Epigenetic factors like histone modifications are known to play an important role in gene regulation and cell differentiation. Recently, thanks to advances in technologies like ChIP-Seq which is a high-throughput, high resolution, and low cost technology for studying histone modifications and transcription factors, we have large amounts of data available. Therefore computational techniques become important for studying and interpreting this data. In this thesis, we have focused on primarily building computational methods to analyze and study ChIP-Seq histone modification data. The work can be divided into two broad topics : (a) to process ChIP-Seq data computationally and to identify regions of biological interest ; (b) to use processed data for higher-level analysis to study problems in cell differentiation and evolution of cell types, based on phylogenetic approaches. In the first topic, this thesis makes a contribution by addressing two problems : (i) We propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-Seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that our method removes most of the bias in the data and also provides a normalization that enables direct comparison of values between the two cell types. We show that our method outperforms the state of the art techniques in literature. (ii) We propose probabilistic partitioning methods to discover significant patterns in ChIP-Seq data. Our methods work on the principle of expectation-maximization, is simple and flexible, and takes into account signal magnitude, shape, strand orientation, and shifts. It runs in linear time and gives improved results on the state of the art techniques especially when used on sparse data. In the second topic, we try to provide a link between the fields of epigenomics and evolution. We introduce the concept of cell-type trees based on the principles of phylogenetic inference on ChIP-Seq histone modification data. These cell-type trees are precisely defined and algorithmic techniques are designed to infer these trees from the data. In the process, we develop new data representation techniques and also a peak-finder to help us build good cell-type trees. We obtain biologically meaningful results and show that cell-type trees have the potential to study cell differentiation and the evolution of cell types across species.

EPFL2014