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PubMed2004

Genome-wide high-throughput screens in functional genomics.

The availability of complete genome sequences from many organisms has yielded the ability to perform high-throughput, genome-wide screens of gene function. Within the past year, rapid advances have been made towards this goal in many major model systems, including yeast, worms, flies, and mammals. Yeast genome-wide screens have taken advantage of libraries of deletion strains, but RNA-interference has been used in other organisms to knockdown gene function. Examples of recent large-scale functional genetic screens include drug-target identification in yeast, regulators of fat accumulation in worms, growth and viability in flies, and proteasome-mediated degradation in mammalian cells. Within the next five years, such screens are likely to lead to annotation of function of most genes across multiple organisms. Integration of such data with other genomic approaches will extend our understanding of cellular networks.

Animals↗
PubMed2005

Current advances in unraveling the function of the Werner syndrome protein.

Werner syndrome (WS) is an autosomal recessive premature aging disease manifested by the mimicry of age-related phenotypes such as atherosclerosis, arteriosclerosis, cataracts, osteoporosis, soft tissue calcification, premature thinning, graying, and loss of hair, as well as a high incidence of some types of cancers. The gene product defective in WS, WRN, is a member of the RecQ family of DNA helicases that are widely distributed in nature and believed to play central roles in genomic stability of organisms ranging from prokaryotes to mammals. Interestingly, WRN is a bifunctional protein that is exceptional among RecQ helicases in that it also harbors an exonuclease activity. Furthermore, it preferentially operates on aberrant DNA structures believed to exist in vivo as intermediates in specific DNA transactions such as replication (forked DNA), recombination (Holliday junction, triplex and tetraplex DNA), and repair (partial duplex with single stranded bubble). In addition, WRN has been shown to physically and functionally interact with a variety of DNA-processing proteins, including those that are involved in resolving alternative DNA structures, repair DNA damage, and provide checkpoints for genomic stability. Despite significant research activity and considerable progress in understanding the biochemical and molecular genetic function of WRN, the in vivo molecular pathway(s) of WRN remain elusive. The following review focuses on the recent advances in the biochemistry of WRN and considers the putative in vivo functions of WRN in light of its many protein partners.

DNA Helicases↗
PubMed2025

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome.

Predicting and deciphering the regulatory logic of enhancers is a challenging problem, due to the intricate sequence features and lack of consistent genetic or epigenetic signatures that can accurately discriminate enhancers from other genomic regions. Recent machine-learning based methods have spotlighted the importance of extracting nucleotide composition of enhancers but failed to learn the sequence context and perform suboptimally. Motivated by advances in genomic language models, we developed DNABERT-Enhancer, a novel enhancer prediction method, by applying DNABERT pre-trained language model on the human genome. We trained two different models, using large collection of enhancers curated from the ENCODE registry of candidate cis-Regulatory Elements. The best fine-tuned model achieved 88.05% accuracy with Matthews correlation coefficient of 76% on independent set aside data. Further, we present the analysis of the predicted enhancers for all chromosomes of the human genome by comparing with the enhancer regions reported in publicly available databases. Finally, we applied DNABERT-Enhancer along with other DNABERT based regulatory genomic region prediction models to predict candidate SNPs with allele-specific enhancer and transcription factor binding activity. The genome-wide enhancer annotations and candidate loss-of-function genetic variants predicted by DNABERT-Enhancer provide valuable resources for genome interpretation in functional and clinical genomics studies.

Journal Article↗
PubMed1994

Control of Arabidopsis flower and seed development by the homeotic gene APETALA2.

APETALA2 (AP2) plays a central role in the establishment of the floral meristem, the specification of floral organ identity, and the regulation of floral homeotic gene expression in Arabidopsis. We show here that in addition to its functions during flower development, AP2 activity is also required during seed development. We isolated the AP2 gene and found that it encodes a putative nuclear protein that is distinguished by an essential 68-amino acid repeated motif, the AP2 domain. Consistent with its genetic functions, we determined that AP2 is expressed at the RNA level in all four types of floral organs--sepals, petals, stamens, and carpels--and in developing ovules. Thus, AP2 gene transcription does not appear to be spatially restricted by the floral homeotic gene AGAMOUS as predicted by previous studies. We also found that AP2 is expressed at the RNA level in the inflorescence meristem and in nonfloral organs, including leaf and stem. Taken together, our results suggest that AP2 represents a new class of plant regulatory proteins that may play a general role in the control of Arabidopsis development.

Amino Acid Sequence↗
PubMed2006

Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A.

A 45 kb DNA sequencing analysis from Streptomyces hygroscopicus 5008 involved in validamycin A (VAL-A) biosynthesis revealed 16 structural genes, 2 regulatory genes, 5 genes related transport, transposition/integration or tellurium resistance; another 4 genes had no obvious identity. The VAL-A biosynthetic pathway was proposed, with assignment of the required genetic functions confined to the sequenced region. A cluster of eight reassembled genes was found to support VAL-A synthesis in a heterologous host, S. lividans 1326. In vivo inactivation of the putative glycosyltransferase gene (valG) abolished the final attachment of glucose for VAL production and resulted in accumulation of the VAL-A precursor, validoxylamine, while the normal production of VAL-A could be restored by complementation with valG. The role of valG in the glycosylation of validoxylamine to VAL-A was demonstrated in vitro by enzymatic assay.

Base Sequence↗
PubMed1974

Mixed lymphocyte culture responses of mice. Genetic analysis of the responses to H-2Dd specificities.

Cellular responses in vitro to H-2D region histocompatibility antigens were demonstrated to be under the genetic control of two or three (P = 0.013) independently segregating loci. The H-2 region itself accounts for one of these loci, however, its activity appears to be dependent upon an association with other non-H-2-associated genetic information. The ability to stimulate a response and to respond to that stimulus are two separate genetic functions in certain MLR combinations. The stimuli in our studies were products of the H-2D region and cell donors must differ at that region in order for a response to occur. The control of the level of responses was determined by other genetic material. Differences at these "response loci" were not necessary for the induction of a proliferative response in the mixed lymphocyte cultures.

Alleles↗
PubMed2006

Cytokine polymorphisms influence treatment outcomes in SLE patients treated with antimalarial drugs.

Antimalarial agents have been widely used as disease-modifying antirheumatic drugs in the treatment of systemic lupus erythematosus (SLE) and other rheumatological diseases, although their mechanism of action has not yet been fully defined. It is known, however, that effective response to treatment is variable among patients. Thus, the identification of genetic predictors of treatment response would provide valuable information for therapeutic intervention. The aim of the present study was to analyze the effect of antimalarial treatment on tumor necrosis factor (TNF)alpha serum levels and evaluate the possible influence of TNFalpha and IL-10 functional genetic polymorphisms on the response to antimalarial drugs. To this end, TNFalpha serum levels were quantified in 171 SLE patients and 215 healthy controls by ELISA techniques and polymorphisms at positions -1,082 and -308 of the IL-10 and TNFalpha gene promoters were determined by PCR amplification followed by hybridization with fluorescent-labeled allele-specific probes in 192 SLE patients and 343 matched controls. Data were related to clinical features and treatment at the time of sampling and during the course of the disease. Results showed a significantly higher amount of serum TNFalpha in the entire SLE population compared with controls. However, TNFalpha serum levels correlated negatively with the use of antimalarial treatment during at least three months before sampling. Patients under single or combined treatment with these drugs had TNFalpha serum levels similar to healthy controls, whereas untreated patients and those under corticosteroid or immunosuppressive therapies had increased amounts of this cytokine. This suggests, however, that antimalarial-mediated inhibition of TNFalpha was only significant in patients who were genetically high TNFalpha or low IL-10 producers. In addition, evaluation of SLE patients administered antimalarial drugs for three or more years who did not require any other specific SLE treatment indicates that patients with the combined genotype low IL-10/high TNFalpha are the best responders to antimalarial therapy, developing mild disease with a good course under this treatment. In conclusion, we proposed that an antimalarial-mediated downregulation of TNFalpha levels in SLE patients is influenced by polymorphisms at IL-10 and TNFalpha promoters. Our results may thus find important clinical application through the identification of patients who are the most likely to benefit from antimalarial therapy.

Adult↗
PubMed1994

[Human major histocompatibility complex: the HLA system].

The HLA (human leukocyte antigens) system, or human major histocompatibility complex, is the most polymorphic functional genetic entity known at present. It consists of HLA class I genes and molecules (A, B and C) which control CD8+ cell-mediated antiviral responses, and class II genes and molecules (DR, DQ and DP) which control CD4+ cell responses (anti-bacterial and anti-toxin). HLA molecules function by presenting antigenic peptides to CD8+ cells (class I) and CD4+ cells (class II). Antigen presentation depends on the intracellular location of the antigen. Antigens present in the exocytosis pathway are presented by class I molecules, while class II molecules present antigens associated with the endocytosis pathway. More than 200 alleles have been detected by means of serological testing (microlymphocytotoxicity) and biochemical methods (IEF) in the HLA class I system, and now by means of molecular biology techniques for class II molecules (PCR-SSO and PCR-RFLP). This molecular typing has revealed the amino acids in HLA molecules that confer genetic susceptibility or resistance to numerous HLA-associated diseases. This is the case for example of ankylosing spondylitis (region 45-46 of HLA-B27 molecules), juvenile diabetes (aa 57 of D beta Q) and rheumatoid arthritis (aa 65-71 of DR beta). Thus, the HLA system is a genetic tool for diagnostic and therapeutic decision-making.

Animals↗
PubMed2002

Differentiation of pluripotent embryonic stem cells into cardiomyocytes.

Embryonic stem (ES) cells have been established as permanent lines of undifferentiated pluripotent cells from early mouse embryos. ES cells provide a unique system for the genetic manipulation and the creation of knockout strains of mice through gene targeting. By cultivation in vitro as 3D aggregates called embryoid bodies, ES cells can differentiate into derivatives of all 3 primary germ layers, including cardiomyocytes. Protocols for the in vitro differentiation of ES cells into cardiomyocytes representing all specialized cell types of the heart, such as atrial-like, ventricular-like, sinus nodal-like, and Purkinje-like cells, have been established. During differentiation, cardiac-specific genes as well as proteins, receptors, and ion channels are expressed in a developmental continuum, which closely recapitulates the developmental pattern of early cardiogenesis. Exploitation of ES cell-derived cardiomyocytes has facilitated the analysis of early cardiac development and has permitted in vitro "gain-of-function" or "loss-of-function" genetic studies. Recently, human ES cell lines have been established that can be used to investigate cardiac development and the function of human heart cells and to determine the basic strategies of regenerative cell therapy. This review summarizes the current state of ES cell-derived cardiogenesis and provides an overview of how genomic strategies coupled with this in vitro differentiation system can be applied to cardiac research.

Animals↗
PubMed1983

One-step gene disruption in yeast.

The one-step gene disruption techniques described here are versatile in that a disruption can be made simply by the appropriate cloning experiment. The resultant chromosomal insertion is nonreverting and contains a genetically linked marker. Detailed knowledge of the restriction map of a fragment is not necessary. It is even possible to "probe" a fragment that is unmapped for genetic functions by constructing a series of insertions and testing each one for its phenotype.

Base Composition↗
PubMed2002

The thankless task of playing genetics with mammalian mitochondrial DNA: a 30-year review.

The advances obtained through the genetic tools available in yeast for studying the oxidative phosphorylation (OXPHOS) biogenesis and in particular the role of the mtDNA encoded genes, strongly contrast with the very limited benefits that similar approaches have generated for the study of mammalian mtDNA. Here we review the use of the genetic manipulation in mammalian mtDNA, its difficulty and the main types of mutants accumulated in the past 30 years and the information derived from them. We also point out the need for a substantial improvement in this field in order to obtain new tools for functional genetic studies and for the generation of animal models of mtDNA-linked diseases.

Journal Article↗
PubMed2004

Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans.

The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans bacteriophage Aa Phi 23 was sequenced. Linear DNA contained in the phage particles is circularly permuted and terminally redundant. Therefore, the physical map of the phage genome is circular. Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%. Sixty-six potential open reading frames (ORFs) were identified, including an ORF resulting from a translational frameshift. A putative function could be assigned to 23 of them. Twenty-three other ORFs share homologies only with hypothetical proteins present in several bacteria or bacteriophages, and 20 ORFs seem to be specific for phage Aa Phi 23. The organization of the phage genome and several genetic functions share extensive similarities to that of the lambdoid phages. However, Aa Phi 23 encodes a DNA adenine methylase, and the DNA packaging strategy is more closely related to the P22 system. The attachment sites of Aa Phi 23 (attP) and several A. actinomycetemcomitans hosts (attB) are 49 bp long.

Aggregatibacter actinomycetemcomitans↗
PubMed2000

Therapeutic target discovery using Caenorhabditis elegans.

Use of the human genome sequence in disease therapy will require efficient identification of disease-causing and disease-associated genes with functions that are amenable to pharmacological manipulation. The validation and development of such genes as therapeutic targets requires information about both the genes' functions and the biochemical pathways in which they participate. One powerful means of obtaining such information is the study of homologous genes in model organisms amenable to laboratory manipulation. Among model organisms the nematode Caenorhabditis elegans offers several advantages, including well-established techniques for genetic and experimental manipulation and the first completed genome sequence for a multicellular organism. Molecular genetic experiments using C. elegans can contribute at several levels to drug discovery programs, from elucidation of genetic functions and pathways to the validation of candidate targets. Additionally, the ease of culture allows adaptation of the nematode for use in high-throughput chemical screens for the identification of lead compounds in drug development.

Animals↗
PubMed2004

The methionine synthase polymorphism D919G alters susceptibility to primary central nervous system lymphoma.

Primary central nervous system lymphomas (PCNSL) frequently reveal genomic instability. We analysed different functional genetic variants affecting the folate and homocysteine metabolism important for DNA integrity in 31 PCNSL patients and 142 controls. We found significantly less carriers of the methionine synthase c.2756A>G (D919G) missense polymorphism among the patients (0.16 vs 0.42; odds ratio 0.26, CI(95%): 0.09-0.74; P=0.005), suggesting a protective function of the G allele. These data stimulate further epidemiological and functional studies focusing on the role of homocysteine and folate metabolism in lymphoma tumorigenesis.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
PubMed2025

KIF18A promotes chromosome congression in cooperation with CENP-E downstream of CENP-C.

Chromosome congression is a key process that acts to align chromosomes at the spindle equator via kinetochore-microtubule interactions, with defects in chromosome alignment leading to chromosomal instability. However, defining the mechanisms that underlie chromosome congression is limited due to the multiple factors that act in parallel to regulate chromosome movement. Here, we conducted a genome-wide Cas9-based functional genetics screen using a hypomorphic CENP-C mutant that affects its kinetochore interactions. Our analysis identified KIF18A, whose knockout resulted in synthetic lethality with the CENP-C mutant. Further analysis revealed that the synthetic defect was due to a reduction in CENP-E function in the CENP-C mutant. Our work suggests that KIF18A promotes chromosome alignment in cooperation with CENP-E downstream of CENP-C during early prometaphase. Thus, our analysis enables us to dissect parallel molecular mechanisms for chromosome congression and identify sensitivities and biomarkers that might guide anti-KIF18A chemotherapeutics.

Kinesins↗
PubMedDate not supplied

Life history evolution and comparative developmental biology of echinoderms.

Evolutionary biologists studying life history variation have used echinoderms in experimental, laboratory, and field studies of life history evolution. This focus on echinoderms grew originally from the tradition of comparative embryology, in which echinoderms were central. The tools for obtaining and manipulating echinoderm gametes and larvae were taken directly from comparative embryological research. In addition, the comparative embryologists employed a diverse array of echinoderms, not a few model species, and this diversity has led to a broad understanding of the development, function, and evolution of echinoderm larvae. As a result, this branch of life history evolution has deep roots in comparative developmental biology of echinoderms. Here two main aspects of this relationship are reviewed. The first is a broad range of studies of fertilization biology, dispersal, population genetics, functional morphology, and asexual reproduction in which developmental biologists might take a keen interest because of the historical origins of this research in echinoderm comparative embryology. The second is a similarly broad variety of topics in life history research in which evolutionary biologists require techniques or data from developmental biology in order to make progress on understanding patterns of life history variation among echinoderm species and higher taxa. Both sets of topics provide opportunities for interaction and collaboration.

Animals↗
PubMed1999

Normal pregnancy outcome after inadvertent exposure to long-acting gonadotrophin-releasing hormone agonist in early pregnancy.

Five infertile women exposed to long-acting gonadotrophin-releasing hormone agonist (GnRHa) during early pregnancy were studied to assess the risks of embryotoxicity on the outcome of their pregnancies. All the patients were diagnosed as stage 3-4 endometriosis following laparoscopy. Long-acting GnRHa (3.75 mg) was given in the first 3 days of their preceding menstrual period. Four of the five patients had two GnRHa injections and the last patient had three GnRHa injections. All patients were advised to use a barrier contraception (condoms) throughout the treatment period. Since all complained of no bleeding following the initial injections, human chorionic gonadotrophin (beta-HCG) concentrations were tested in order to rule out any pregnancy. Ultrasonographic examinations were commenced routinely and all patients had amniocentesis at 16-18 weeks gestational age. Genetic analysis revealed a normal karyotype in all fetuses. All five pregnancies progressed to term without complication, and normal healthy infants were delivered. Although there are still no clear answers concerning teratogenic and hormonal effects of GnRHa exposure in pregnancy, our data may suggest that luteal function, genetic structure and pregnancy outcome are not adversely affected by GnRHa. Since possible subtle effects on fetal endocrine organs cannot be disregarded, close monitoring is still needed in GnRHa-exposed pregnancies.

Adult↗
PubMed2026

Culture, Psychiatry and Epigenetics.

Regarding the methodology of ethnopsychiatric research, for example, on the Vietnamese Mo Mường's burial rituals or the health-promoting and healing effects of the Chinese Tujia dances, three different approaches can be distinguished: phenomenological-descriptive methods, hermeneutic-interpretive techniques and studies on underlying mechanisms such as hypnotherapeutic or neuroendocrine dynamics. Since epigenetics has shown that cultural and artistic experiences can influence gene expression and genetic functioning, even across generations, the article argues for greater consideration of epigenetics in medical anthropology and ethnopsychiatry. Epigenetic dynamics can significantly influence health promoting and healing effects of rituals in ethnic traditions and determine an individual's responsiveness to such practices. In this context, the interplay between genetics and epigenetics, various concepts of the collective unconscious, transcultural psychiatry, culturally sensitive arts therapies, and issues of migration and transcultural identities are discussed.

Humans↗