Targeting 'histone mark': Advanced approaches in epigenetic regulation of telomere dynamics in cancer

Telomere integrity is required for the maintenance of genome stability and prevention of oncogenic transformation of cells. Recent evidence suggests the presence of epigenetic modifications as an important regulator of mammalian telomeres. Telomeric and subtelomeric regions are rich in epigenetic marks that regulate telomere length majorly through DNA methylation and post-translational histone modifications. Specific histone modifying enzymes play an integral role in establishing telomeric histone codes necessary for the maintenance of structural integrity. Alterations of crucial histone moieties and histone modifiers cause deregulations in the telomeric chromatin leading to carcinogenic manifestations. This review delves into the significance of histone modifications and their influence on telomere dynamics concerning cancer. Additionally, it highlights the existing research gaps that hold the potential to drive the development of therapeutic interventions targeting the telomere epigenome.

Present and future challenges for the investigation of transgenerational epigenetic inheritance

Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.

Selective transcriptional regulation by Myc: Experimental design and computational analysis of high-throughput sequencing data

The gene expression programs regulated by the Myc transcription factor were evaluated by integrated genome-wide profiling of Myc binding sites, chromatin marks and RNA expression in several biological models. Our results indicate that Myc directly drives selective transcriptional regulation, which in certain physiological conditions may indirectly lead to RNA amplification. Here, we illustrate in detail the experimental design concerning the high-throughput sequencing data associated with our study (Sabò et al., Nature. (2014) 511:488–492) and the R scripts used for their computational analysis.

Re-print of "Histone extraction protocol from the two model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana"

Post-translational modifications of histones affect many biological processes by influencing higher order chromatin structure that affects gene and genome regulation. It is therefore important to develop methods for extracting histones while maintaining their native post-translational modifications. While histone extraction protocols have been developed in multicellular and single celled organisms such as yeast and Arabidopsis, they are inefficient in diatoms that have a silica cell wall that is likely to hinder histone extraction. We report in this work a rapid and reliable method for extraction of large amounts of high quality histones from the two model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. The protocol is an important enabling step permitting downstream applications such as western blotting and mass spectrometry.

Histone extraction protocol from the two model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana

Post-translational modifications of histones affect many biological processes by influencing higher order chromatin structure that affects gene and genome regulation. It is therefore important to develop methods for extracting histones while maintaining their native post-translational modifications. While histone extraction protocols have been developed in multicellular and single celled organisms such as yeast and Arabidopsis, they are inefficient in diatoms that have a silica cell wall that is likely to hinder histone extraction. We report in this work a rapid and reliable method for extraction of large amounts of high quality histones from the two model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. The protocol is an important enabling step permitting downstream applications such as western blotting and mass spectrometry.