ISSN (Print): 1389-2029
ISSN (Online): 1875-5488
Volume 21, 8 Issues, 2020
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ISSN (Print): 1389-2029
ISSN (Online): 1875-5488
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Christian Néri Institute of Biology Paris-Seine CNRS UMR 8256 and UPMC Paris, 75005 France
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Special Issue Submission
""Current Genomics is establishing itself as a leader in the field of functional genomics."
Univ. of California, USA
The Critical Role of Epigenetic Regulation in Developmental Programming of Higher Organisms
Guest Editor(s): Luis María Vaschetto
I must tell you that we had a wonderful experience with Bentham Science Publication specifically with the journal "Current Genomics". We had good rapport with the team that handled our mansucript right from the review stage to the final publication.
P. Suprasanna (Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 4000085, India.)
Has contributed: Looking at Halophytic Adaptation to High Salinity Through Genomics Landscape
7 Articles Ahead of Print are available electronically
Except for mRNA that encodes proteins, there is another kind of RNA, known as non-coding RNA (ncRNAs), that does not
encode proteins. ncRNAs control various levels of gene expression in physiology and development, such as RNA splicing,
RNA translation, cell proliferation and apoptosis. Accumulated evidence have demonstrated that ncRNAs are correlated with
the progression of a series of diseases.
Besides ncRNAs, RNA modification is another layer of epigenetic regulation of gene expression. Since the first modified
RNA ribonucleic acid was found in 1957, more than 150 kinds of known RNA modifications have been reported. RNA modifications
play critical roles in a series of biological processes, such as RNA degradation, localization and degradation, and even
circadian rhythm. Recent studies revealed that RNA modifications are also associated with metabolic diseases, cancer, neurological
disorders and cardiovascular diseases.
Due to their important roles, more researchers have devoted to the researches on ncRNAs and RNA modification. However,
the biological functions and mechanisms of ncRNAs and RNA modification are still unclear. Since experimental methods are
cost-ineffective to rapidly and effectively reveal their biological functions, it is highly desirable to develop computational
methods which are good complements to experimental techniques for this aim. In recent years, a series of computational methods
have been developed to infer the regulatory functions of RNA modification and ncRNA. Therefore, the thematic issue was
proposed with the aim to collect a diverse and complementary set of articles that demonstrate new developments and applications
of machine learning methods in computational RNA epigenetics.
This thematic issue has attracted 6 papers from highly regarded researchers around the world. After the rigorous peer review,
3 of them were accepted for publication.
Guan et al.  contributed a review article, where they summarized the recent advances in pre-miRNA recognition from the
following aspects, namely the benchmark dataset, feature extraction, prediction algorithms, and the evaluation of existing models.
The challenges and future perspectives are also discussed. It is believed that this review will provide novel insights into
researches on computational identification of miRNA precursors.
In a mini review paper contributed by Li et al. , the authors reviewed available machine learning based methods for identifying
RNA 5-methylcytosine (m5C) sites. Three essential elements, namely dataset, sequence encoding scheme, and machinelearning
algorithms, required to constitute a predictor for identifying m5C sites were firstly discussed. More importantly, the
bottleneck of those predictors was also pointed out, which should be considered when developing predictors for identifying
m5C and even the other kinds of RNA modifications.
Govindaraj et al.  proposed a novel computational predictor termed as ERT-m6Apred based on extremely randomized
tree to identify N6-methyladenosine (m6A), in which a two-step feature selection technique was used to obtain the optimal feature
Finally, the guest editor would like to thank all the authors who contributed their original works to the thematic issue and to
the reviewers for their valuable comments on those works. The guest editor would also like to express sincere gratitude to the
Editor in Chief, Dr. Christian Néri, of Current Genomics and the Assistant Manager Publications, Ms. Iqra Shafi for their excellent
supports and providing the opportunity to organize the thematic issue.
With systems genomics burgeoning, there is always a need to prioritise candidates post bioinformatics
analyses. This is where machine learning approaches have steadfastly been in use. While the
articles in part I have seen a seminal research on the applications of the genes, this second part constituting
three articles emphasizing the need for machine learning heuristics.
Roy et al. in their article entitled, “Deciphering the novel target genes involved in the epigenetics
of hepatocellular carcinoma using graph theory approach”  applied graph theory approaches for
drawing a network of genes in identifying novel targets for hepatocellular carcinoma epigenetic therapy.
The candidates they found were statistically coherent for the therapeutic use.
Natarajan et al., in their article entitled, “Helicobacter pylori reactivates Human Immunodeficiency
Virus-1 in latently infected monocytes with increased expression of IL-1β and CXCL8”  have aptly used HIV infected
monocytes for measuring the expression of genes reactivated by H. Pylori.
Parveen et al. emphasized a review on “Applications of machine learning in miRNA discovery and target prediction” 
which brings a subtle understanding of these approaches for miRNA target prediction and early phase discovery.
In conclusion, systems genomics has shaped up from nascent stage to a phase where we set actions to prevent diseases,
thanks to machine learning approaches.
“The goal of getting your genome done is not to tell you what you will die from, but it's how to learn how to take action to
prevent disease”. George M. Church.
In the last years, research efforts have been focused on the understanding of the evolutionary mechanisms linked to the control
of the transcriptional activity and developmental processes. The study of developmental mechanisms has advanced significance
over the last decade, and developmental programs that have undergone evolutionary specialization among species have
recently been characterized. Epigenetics, which includes analysis of DNA methylation, histone code (i.e., histone methylation/
demethylation, acetylation/deacetylation, phosphorylation, ubiquitination, etc.), noncoding RNA (ncRNA) pathways and
3D genome organization, has made important progress towards understanding of the complexity of developmental processes.
Epigenetic factors involved in the regulation of development are increasingly being identified in organisms ranging from yeast
to humans, and it has been shown that epigenetic phenomena such as genomic imprinting, paramutation and transgenerational
epigenetic inheritance are often closely linked to these processes. The main objective of this thematic issue is to present current
research into the epigenetic mechanisms involved in developmental programming, their evolution and their roles in disease
In the first article of this issue, Vaschetto and Ortiz  provide an opinion on the role of the duplication of sequence in
the mechanisms of gene regulation and its importance in genome evolution and developmental programming. By the analysis
of information based on master developmental genes (i.e., HOX genes), repetitive ribosomal DNA (rDNA) arrays, sequences
encoding noncoding RNAs (ncRNAs,) and distinct classes of Transposable Elements (i.e., MITEs, SINEs, R2, etc.),
the authors explain how sequence duplication may function as an evolutionary strategy to regulate the transcriptional expression
at genome-level. In the next article, Csaba  provides a review on the mechanisms associated with the hormonal
imprinting, an epigenetic phenomenon that involves the first encounter between a hormone and the target receptor, which
occurs in the perinatal period. Remarkably, Dr. Csaba postulated the theory of hormonal imprinting , and his laboratory
has made important research efforts to understand the faulty hormonal imprinting in the Developmental Origin of Health and
In the third article, Şanlı and Kabaran  examine the consequences of the maternal obesity and maternal overnutrition on
fetal programming. In this article, the authors analyze how maternal obesity is associated with epigenetic modifications that
influence fetal growth and underlie metabolic diseases during adulthood. Next, Lecoutre et al. review the mechanisms for
which maternal obesity may induce adipose tissue remodeling of offspring and explore the role of the epigenetic inheritance in
developmental programming of obesity .
In the next article, Alsayegh et al.  examine the potential of pluripotent stem cells (PSCs) as de novo source of Hematopoietic
Stem Cells (HSCs), and the mechanism of regulation of HOX and GATA factors in hematopoiesis. In this review,
the authors also evaluate the relationships existing between the HOX and GATA master regulators and microRNA (miRNA)
pathways. Lastly, Kadayifci et al.  discuss the importance of the epigenetic mechanisms for the nutritional programming
of Type 2 Diabetes Mellitus and their roles in the developmental origin of this worldwide chronic disease.
As anticipated in the editorial of the Part I of this special issue, Early Life Stress (ELS) profoundly impairs child’s brain
development and behavior giving rise to either temporary or permanent effects on cognitive, behavioral and psychological
functions. Furthermore, possible long-term cumulative effects of various types of early adversity may show up in adulthood .
ELS-related pathological consequences greatly vary among individuals and depend upon genetic and environmental factors.
This second part of the issue includes four additional reviews and provides novel exciting aspects linking genomics and epigenomics
to neuropsychiatric disorders associated to Early-Life Stress. A natural extension of this second part of the thematic
issue is the double-edged sword of epigenetic processes: their potential reversibility and long-term stability via non-Mendelian
inheritance mechanisms. A growing amount of evidence has showed that our DNA remembers past traumatic experiences
through the storage of epigenetic marks that can be transmitted into subsequent generations. Epigenetic alterations may cause a
variety of latent biological dysfunctions in the stress system of the offspring and result as pre-traumatic vulnerable factors [2,
3]. These novel and exciting mechanisms of trans-generational inheritance suggest the possibility to deliver integrative solutions
in the clinical diagnosis and therapeutic approach against various long-term consequences to ELS, and in later family life.
Based on these observations, the paper by Lux highlights the role of a parallel synaptic and hormonal activation of epigenetic
programming in human and rodent models. Liu et al. elucidate both genomic and non-genomic mechanisms related to stress
modulation of the hypothalamic-pituitary-adrenal (HPA) axis leading to methylation of the glucocorticoid receptor gene
(NR3C1) and activation of lifelong impairments. Bearer et al. provide an in-depth introduction to genome-wide changes in the
child's methylome pattern induced by early adversity in life, potentially linked to the development and function of brain circuits,
immune and endocrine system. Stenz et al. describe the still largely unexplored concept of the intergenerational transmission
of DNA methylation signatures associated to the increased risk for developmental psychopathology. The aforementioned
reviews are mostly focused on genomic and epigenomic variations in neuropsychiatric disorders associated to ELS phenomena.
Moving these advanced findings into the routine medical practice will offer a revolutionary care and rehabilitation approach for
patients, either adults or children generally poorly managed, who suffer from psychopathologies following ELS exposure. The
overall aim of this Special Issue is to prove how the developmental age may represent a window of opportunity to implement
novel early interventions in the diagnosis and treatment of individuals subjected to ELS. Likewise, the resulting collection of
the present reviews examines wider strategic significance. A greater understanding of neuroplasticity and the brain interactions
with the social environment will promote a fertile ground of investigations to the pathogenesis of neurodegenerative disorders
and other psychiatric illnesses (e.g. schizophrenia), characterized by disruptive processes of cerebral growth and synaptic plasticity
Early Life Stress (ELS) profoundly impairs child’s brain development and behaviour giving rise to either temporary or permanent
effects on cognitive, behavioural and psychological functions. Furthermore, possible long-term cumulative effects of
various types of early adversity may show up in adulthood . ELS-related pathological consequences greatly vary among individuals
and depend on genetic and environmental factors. With regard to the onset of neurodevelopmental and psychiatric
disorders associated to ELS exposure, great emphasis must be laid on the influence of various pre-, peri- and post-traumatic
components in the environmental social context in which childhood abuse occurs. Namely, other influence factors related to the
nature of the early trauma, such as its duration, chronicity, and severity, strongly predispose towards either pathological outcomes
or resilient reactions. Together, genetic and environmental factors influence the individual stress responses although the
most remarkable effects of such an interplay are those concerning a critical period of vulnerability spanning from fetal to postnatal
development and adolescence. During this developmental window, the genome within neurons appears to be more plastic
and sensitive to both positive and negative environmental stimuli. These gene-environment interactions contribute to optimal
brain development, establishing a proper neural and behavioural developmental trajectory . As previously anticipated, it is
now clear that there is a causal link between ELS and the onset of neuropsychiatric and behavioural consequences, both with
short- and long-term effects .
With the advent of Omic technologies, we are getting a considerable amount of information on the gene-environment interplay
mechanisms, and learning biological underpinnings of those long-lasting changes that influence the pathological effects of
ELS during the development of brain and behavioural traits . In recent years, we have witnessed the rapid evolution of
knowledge about several potential mediators responsible for the high phenotypic heterogeneity observed among individuals
exposed to ELS. Ultimately, epigenetic changes in response to stress signalling are also known to influence the development
and susceptibility to early trauma-related pathologies. Epigenetic variations depict potentially reversible and transitory biochemical
changes that cause altered gene expression without modifying the DNA sequence and dynamically switch transcription
rates in response to a multitude of environmental stimuli and developmental states. These epigenetic changes mirror the
great flexibility of diverse biological processes of the organism including the modulation of proper and adaptive neurobiological
responses to various stressor agents throughout the life. However, experiencing prematurely a stress challenge causes widespread
alterations in brain plasticity and neuroendocrine system that correlate with marked and persistent changes in functional
activity of a large number of stress responsive genes . It follows that the epigenetic deregulation may be implicated in many
long-term pathological consequences of physical and mental health.
The above key concepts are well represented by the seven reviews selected for the present Special Issue, which aims to provide
an extensive overview of the interplay between ELS and the genome. This Special Issue is divided into two parts: the first
comprises two papers and features a very constructive analysis of ELS-driven processes that program the cerebral decline to
neurodevelopment and neuropsychiatric disorders. To this end, Drake et al. examine the intriguing and relatively little-known
mechanisms linking preterm birth with neurodevelopmental effects. From the viewpoint of clinical neuroscience, there is substantial
interest in studying the delayed effects of ELS in neurodegeneration. Therefore, the scope of the paper by Lemche is to
provide a highly informative overview of genomic association studies supporting the relevance of ELS as a powerful mediator
of Late-Onset Alzheimer’s Disease (LOAD).
Taken as a whole, the pioneering works of this first part of the Issue invite the readers to discover some interesting genomics
and epigenomics insights into the programming of the neuronal cell fate during the developmental age. These new findings
build the foundation for precision medicine to improve the treatment of neuropathological sequelae induced by ELS injury,
develop preclinical screening and, possibly, offer more reliable and integrative therapeutic models.
The past twenty-five years significantly expanded our knowledge of Copy Number Variants (CNVs), genomic imbalances
belonging to structural genetic variations, and their role in both human health and disease, particularly in the neurological field.
In 1991, Lupski was the first to associate a CNV (a DNA duplication) to a human autosomal dominant neurodegenerative disease,
the Charcot-Marie-Tooth Disease Type 1A . In the last years, different technologies succeeded one another, increasing
the power of resolution and the regions of application. However, technological and conceptual barriers have hampered the investigation
of neurodegenerative diseases from a polygenic point of view, not only for complex neurodegenerative diseases but
also for monogenic ones. For example, even if Neurofibromatosis type 1 represents a monogenic autosomal dominant disorder
with complete penetrance, it is characterized by a variable expressivity that is hard to address in a genotype-phenotype correlation
In this mini-thematic issue, we aim to describe the progress in the study of these important types of structural variations in
medicine, exploring the use of CNVs analysis in neurological disorders, as recently reviewed for Alzheimer’s Disease, Parkinson’s
Disease and Amyotrophic Lateral Sclerosis studies [4-6]. Taken together, the three manuscripts published in the present
mini-thematic issue provide the reader an overview of the recent findings regarding inherited neuropathies (Salpietro et al.) and
adult-onset neuropsychiatric disorders, i.e. Schizophrenia and Alzheimer’s disease (Lew et al.), and emphasize the need of custom
technologies, such as a customized exon-centric aCGH, to detect overlapping gene signatures among neurological conditions
(La Cognata et al.).
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