Mechanisms of epigenetic memory and addiction

Epigenetic regulation of cellular identity and function is at least partly achieved through changes in covalent modifications on DNA and histones. Much progress has been made in recent years to understand how these covalent modifications affect cell identity and function. Despite the advances, whether and how epigenetic factors contribute to memory formation is still poorly understood. In this review, we discuss recent progress in elucidating epigenetic mechanisms of learning and memory, primarily at the DNA level, and look ahead to discuss their potential implications in reward memory and development of drug addiction.     

Epigenetic biomarkers in colorectal cancer: premises and prospects

Context: Colorectal cancer is one of the most common cancers worldwide. Epigenetic alterations play an important role in the pathogenesis of the colorectal cancer.

Objective: This review has focused on the most recent investigations, which has suggested potential epigenetic biomarkers in colorectal cancer.

Methods: Evidences were achieved by searching online medical databases including Google scholar, Pubmed, Scopus and Science Direct.

Results: Extensive studies have indicated that aberrant epigenetic modifications could serve as potential biomarkers for diagnosis, prognosis and prediction of colorectal cancer.

Conclusion: Advances in aberrant epigenetic modifications can open new avenues for exploration of reliable and robust biomarkers to improve the management of CRC patients.     

表观遗传学——耳聋研究的新视野

耳聋是一种常见的人类感觉系统缺陷,新生儿发病率可达1/1000～3/1000。耳蜗感觉神经上皮毛细胞的结构或功能异常可导致耳聋,遗传因素在其中起重要作用。虽然一些与遗传性耳聋相关的基因及染色体位点已经被定位或克隆,仍有很多耳聋的病因尚不清楚。人们发现,除了常见的热点基因突变(GJB2、SLC26A4、线粒体DNA C1494T和A1555G等)外,一些表观遗传学的改变也在耳聋的发生中起重要作用。例如,miR-96突变会导致人和小鼠的渐进性失聪,异常的CpG岛甲基化与一些耳聋综合征的发生有关等。文章着重对表观遗传学在耳聋领域的研究现状和进展进行了综述。     

German-Catalan workshop on epigenetics and cancer

In the First German-Catalan Workshop on Epigenetics and Cancer held in Heidelberg, Germany (June 17–19, 2013), cutting-edge laboratories (PEBC, IMPPC, DKFZ, and the Collaborative Research Centre Medical Epigenetics of Freiburg) discussed the latest breakthroughs in the field. The importance of DNA demethylation, non-coding and imprinted genes, metabolic stress, and cell transdifferentiation processes in cancer and non-cancer diseases were addressed in several lectures in a very participative and dynamic atmosphere.

The meeting brought together leading figures in the field of cancer epigenetics to present their research work from the last five years. Experts in different areas of oncology described important advances in colorectal, lung, neuroblastoma, leukemia, and lymphoma cancers. The workshop also provided an interesting forum for pediatrics, and focused on the need to improve the treatment of childhood tumors in order to avoid, as far as possible, brain damage and disruption of activity in areas of high plasticity. From the beginning, the relevance of “omics” and the advances in genome-wide analysis platforms, which allow cancer to be studied in a more comprehensive and inclusive way, was very clear. Modern “omics” offer the possibility of identifying metastases of uncertain origin and establishing epigenetic signatures linked to a specific cluster of patients with a particular prognosis. In this context, invited speakers described novel tumor-associated histone variants and DNA-specific methylation, highlighting their close connection with other processes such as cell-lineage commitment and stemness.     

Generation of an arrayed CRISPR-Cas9 library targeting epigenetic regulators: from high-content screens to in vivo assays

The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Screens employing genome-scale pooled small guide RNA (sgRNA) libraries are demanding, particularly when complex assays are used. Furthermore, pooled libraries are not suitable for microscopy-based high-content screens or for systematic interrogation of protein function. To overcome these limitations and exploit CRISPR-based technologies to comprehensively investigate epigenetic mechanisms, we have generated a focused sgRNA library targeting 450 epigenetic regulators with multiple sgRNAs in human cells. The lentiviral library is available both in an arrayed and pooled format and allows temporally-controlled induction of gene knock-out. Characterization of the library showed high editing activity of most sgRNAs and efficient knock-out at the protein level in polyclonal populations. The sgRNA library can be used for both selection and high-content screens, as well as for targeted investigation of selected proteins without requiring isolation of knock-out clones. Using a variety of functional assays we show that the library is suitable for both in vitro and in vivo applications, representing a unique resource to study epigenetic mechanisms in physiological and pathological conditions.     

Virion-mediated transfer of SV40 epigenetic information

In eukaryotes, epigenetic information can be encoded in parental cells through modification of histones and subsequently passed on to daughter cells in a process known as transgenerational epigenetic regulation. Simian Virus 40 (SV40) is a well-characterized virus whose small circular DNA genome is organized into chromatin and, as a consequence, undergoes many of the same biological processes observed in cellular chromatin. In order to determine whether SV40 is capable of transgenerational epigenetic regulation, we have analyzed SV40 chromatin from minichromosomes and virions for the presence of modified histones using various ChIP techniques and correlated these modifications with specific biological effects on the SV40 life cycle. Our results demonstrate that, like its cellular counterpart, SV40 chromatin is capable of passing biologically relevant transgenerational epigenetic information between infections.     

Virion-mediated transfer of SV40 epigenetic information

In eukaryotes, epigenetic information can be encoded in parental cells through modification of histones and subsequently passed on to daughter cells in a process known as transgenerational epigenetic regulation. Simian Virus 40 (SV40) is a well-characterized virus whose small circular DNA genome is organized into chromatin and, as a consequence, undergoes many of the same biological processes observed in cellular chromatin. In order to determine whether SV40 is capable of transgenerational epigenetic regulation, we have analyzed SV40 chromatin from minichromosomes and virions for the presence of modified histones using various ChIP techniques and correlated these modifications with specific biological effects on the SV40 life cycle. Our results demonstrate that, like its cellular counterpart, SV40 chromatin is capable of passing biologically relevant transgenerational epigenetic information between infections.     

表观遗传学——耳聋研究的新视野

耳聋是一种常见的人类感觉系统缺陷, 新生儿发病率可达1/1000～3/1000。耳蜗感觉神经上皮毛细胞的结构或功能异常可导致耳聋,遗传因素在其中起重要作用。虽然一些与遗传性耳聋相关的基因及染色体位点已经被定位或克隆, 仍有很多耳聋的病因尚不清楚。人们发现, 除了常见的热点基因突变(GJB2、SLC26A4、线粒体DNA C1494T和A1555G等)外, 一些表观遗传学的改变也在耳聋的发生中起重要作用。例如, miR-96 突变会导致人和小鼠的渐进性失聪, 异常的CpG岛甲基化与一些耳聋综合征的发生有关等。文章着重对表观遗传学在耳聋领域的研究现状和进展进行了综述。     

表观遗传学: 生物细胞非编码RNA调控的研究进展

表观遗传学是研究基因表达发生了可遗传的改变, 而DNA序列不发生改变的一门生物学分支, 对细胞的生长分化及肿瘤的发生发展至关重要。表观遗传学的主要机制包括DNA甲基化、组蛋白修饰及新近发现的非编码RNA。非编码RNA 是指不能翻译为蛋白的功能性RNA分子, 其中常见的具调控作用的非编码RNA包括小干涉RNA、miRNA、piRNA 以及长链非编码RNA。近年来大量研究表明非编码RNA在表观遗传学的调控中扮演了越来越重要的角色。文章综述了近年来生物细胞非编码RNA调控的表观遗传学研究进展, 以有助于理解哺乳动物细胞中非编码RNA及其调控机制和功能。     

Np95 interacts with de novo DNA methyltransferases,Dnmt3a and Dnmt3b,and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells

Recent studies have indicated that nuclear protein of 95 kDa (Np95) is essential for maintaining genomic methylation by recruiting DNA methyltransferase (Dnmt) 1 to hemi‐methylated sites. Here, we show that Np95 interacts more strongly with regulatory domains of the de novo methyltransferases Dnmt3a and Dnmt3b. To investigate possible functions, we developed an epigenetic silencing assay using fluorescent reporters in embryonic stem cells (ESCs). Interestingly, silencing of the cytomegalovirus promoter in ESCs preceded DNA methylation and was strictly dependent on the presence of either Np95, histone H3 methyltransferase G9a or Dnmt3a and Dnmt3b. Our results indicate a regulatory role for Np95, Dnmt3a and Dnmt3b in mediating epigenetic silencing through histone modification followed by DNA methylation.     

A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells

The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.     

Epigenetic therapy approaches in non-small cell lung cancer: Update and perspectives

Non-small cell lung cancer (NSCLC) still constitutes the most common cancer-related cause of death worldwide. All efforts to introduce suitable treatment options using chemotherapeutics or targeted therapies have, up to this point, failed to exhibit a substantial effect on the 5-year-survival rate. The involvement of epigenetic alterations in the evolution of different cancers has led to the development of epigenetics-based therapies, mainly targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes. So far, their greatest success stories have been registered in hematologic neoplasias. As the effects of epigenetic single agent treatment of solid tumors have been limited, the investigative focus now lies on combination therapies of epigenetically active agents with conventional chemotherapy, immunotherapy, or kinase inhibitors. This review includes a short overview of the most important preclinical approaches as well as an extensive discussion of clinical trials using epigenetic combination therapies in NSCLC, including ongoing trials. Thus, we are providing an overview of what lies ahead in the field of epigenetic combinatory therapies of NSCLC in the coming years.     

Chromatin proteomics and epigenetic regulatory circuits

Many phenotypic changes of eukaryotic cells due to changes in gene expression depend on alterations in chromatin structure. Processes involved in the alteration of chromatin are diverse and include post-translational modifications of histone proteins, incorporation of specific histone variants, methylation of DNA and ATP-dependent chromatin remodeling. Interconnected with these processes are the localization of chromatin domains within the nuclear architecture and the appearance of various classes of noncoding regulatory RNAs. Recent experiments underscore the role of these processes in influencing diverse biological functions. However, the evidence to date implies the importance of an interplay of all these chromatin-changing functions, generating an epigenetic regulatory circuit that is still not well understood.