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RNA editing and alternative splicing of human serotonin 2C receptor in schizophrenia.

Serotonin 2C receptor (5-HT2CR) heterogeneity in the brain occurs mostly from two different sources: (i) 5-HT2CR mRNA undergoes adenosine-to-inosine editing events at five positions, which leads to amino acid substitutions that produce receptor variants with different pharmacological properties; (ii) 5-HT2CR mRNA is alternatively spliced, resulting in a truncated mRNA isoform (5-HT2CR-tr) which encodes a non-functional serotonin receptor. 5-HT2CR mRNA editing efficiencies and the expression of the full-length and the truncated 5-HT2CR mRNA splice isoforms were analyzed in the prefrontal cortex of elderly subjects with schizophrenia vs. matched controls (ns = 15). No significant differences were found, indicating that there are no alterations in editing or alternative splicing of 5-HT2CRs that are associated with schizophrenia in persons treated with antipsychotic medications. Quantitation of 5-HT2CR and 5-HT2CR-tr mRNA variants revealed that the expression of 5-HT2CR-tr was approximately 50% of that observed for the full-length isoform.

Adenosine↗

circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.

Although extensive evidence has underscored the critical role of alternative splicing (AS) in generating mature circular RNA (circRNA) isoforms and augmenting their functional diversity, a significant gap remains in the availability of specialized databases housing circRNA AS events. To bridge this gap, we develop circASbase, a pioneering and comprehensive database that catalogs 452,129 AS events in 884,047 full-length circRNAs from 581 samples across 13 species, and provides rich annotations to facilitate understanding the splicing regulation of circRNA. Our findings reveal substantial differences between circRNAs and linear transcripts regarding the distribution and occurrence of AS events, highlighting the unique regulatory landscape of circRNAs. These special splicing events result in functional differences of circRNAs by affecting internal ribosome entry sites, N6-methyladenosine sites, open reading frames, protein features, microRNA targets, and more. In summary, circASbase not only meets the urgent need of the research community for data repositories, but also represents a significant advancement in our understanding of circRNA biology. With its user-friendly interfaces and web-based visualization tools, circASbase is poised to become an indispensable resource for researchers exploring the regulatory mechanisms and functional roles of AS events in circRNAs. This database will continuously drive new insights and discoveries in the field, setting the stage for further advancements in circRNA research. circASbase is freely available at http://reprod.njmu.edu.cn/cgi-bin/circASbase/.

Alternative Splicing↗

An unappreciated role for RNA surveillance.

BACKGROUND: Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA surveillance mechanism that detects and degrades mRNAs with premature termination codons (PTC+ mRNAs). In mammals, a termination codon is recognized as premature if it lies more than about 50 nucleotides upstream of the final intron position. More than a third of reliably inferred alternative splicing events in humans have been shown to result in PTC+ mRNA isoforms. As the mechanistic details of NMD have only recently been elucidated, we hypothesized that many PTC+ isoforms may have been cloned, characterized and deposited in the public databases, even though they would be targeted for degradation in vivo. RESULTS: We analyzed the human alternative protein isoforms described in the SWISS-PROT database and found that 144 (5.8% of 2,483) isoform sequences amenable to analysis, from 107 (7.9% of 1,363) SWISS-PROT entries, derive from PTC+ mRNA. CONCLUSIONS: For several of the PTC+ isoforms we identified, existing experimental evidence can be reinterpreted and is consistent with the action of NMD to degrade the transcripts. Several genes with mRNA isoforms that we identified as PTC+--calpain-10, the CDC-like kinases (CLKs) and LARD--show how previous experimental results may be understood in light of NMD.

Alternative Splicing↗

A+U-rich-element RNA-binding factor 1/heterogeneous nuclear ribonucleoprotein D gene expression is regulated by oestrogen in the rat uterus.

Oestrogen-mediated gene expression is regulated at both the transcriptional and post-transcriptional levels. The molecular mechanism of transcriptional regulation has been well characterized. On the other hand, there is little understanding of the mechanism of post-transcriptional regulation. To clarify the mechanism of oestrogen-mediated post-transcriptional regulation, we focused on A+U-rich-element RNA-binding factor 1/heterogeneous nuclear ribonucleoprotein D (AUF1/hnRNP D), which is known as a regulator of cytosolic mRNA degradation and nuclear pre-mRNA maturation. However, little is known about the expression levels and the regulation of AUF1/hnRNP D mRNA in tissues. We further investigated the expression levels of AUF1/hnRNP D isoform mRNAs to determine whether AUF1/hnRNP D gene expression is regulated by oestrogen in the ovariectomized adult female rat uterus. Uterine AUF1/hnRNP D mRNA was induced by a single subcutaneous injection (1 microg/kg) of 17beta-oestradiol (E2), reaching a peak level within 6 h. Furthermore, we observed that the E2-induced AUF1/hnRNP D isoform mRNAs are p45 and p40 transcripts, and that E2-mediated induction is suppressed by the oestrogen receptor antagonist ICI 182,780. Finally, using the transcriptional inhibitor actinomycin D, we confirmed that the E2-mediated increase in AUF1/hnRNP D mRNA is caused by E2-dependent AUF1/hnRNP D mRNA stabilization.

Animals↗

Properties of Ryr3 ryanodine receptor isoform in mammalian brain.

Although the RNA for the third isoform (Ryr3) of ryanodine receptor (RyR), a Ca2+ release channel, is detected in specific regions of mammalian brain, little is known about the protein. We investigated Ryr3 in rabbit brain, using an antibody raised against the synthetic peptide corresponding to amino acid sequence 4375-4387 of rabbit Ryr3, the homologue of bullfrog beta-RyR. The antibody which reacted with bullfrog beta-RyR, but not with the other isoforms, Ryr1 or Ryr2, specifically precipitated a single polypeptide from rabbit brain microsomes having a size similar to beta-RyR. Sucrose gradient ultracentrifugation revealed that Ryr3 forms a homotetramer, as true of the other isoforms. Being consistent with the distribution of its RNA, Ryr3 was abundantly expressed in hippocampus, corpus striatum, and diencephalon. Ryr3 demonstrated Ca2+-dependent [3H]ryanodine binding, and caffeine increased its Ca2+ sensitivity. The Ca2+ sensitivity of Ryr3 was also enhanced in a medium containing 1 m NaCl, as observed with beta-RyR. [3H]Ryanodine binding gave an estimate of Ryr3 which would be only 2% or less of total RyR in rabbit brain. These results confirm the expression of functional Ryr3 in mammalian brain which is similar to nonmammalian beta-RyR.

Amino Acid Sequence↗

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

Alternative Splicing↗

The complement component C5 of the common carp (Cyprinus carpio): cDNA cloning of two distinct isotypes that differ in a functional site.

The complement component C5 plays important roles in inflammatory responses and complement-mediated cytolysis. In bony fish, although C5 has been identified at the DNA or the protein level in trout, carp and gilthead seabream, only partial C5 sequences are available. The present study was designed to obtain the complete primary structure of C5 from the common carp ( Cyprinus carpio) and to examine its possible structural diversity. Reverse-transcribed polymerase chain reaction amplification from carp hepatopancreatic RNA resulted in isolation of six distinct C5-like cDNA segments, which were grouped into two divergent types (type I and type II). Using two sequences representative of the two types as probes, two distinct full-length cDNA clones (C5-1 and C5-2) were isolated, in addition to a truncated isoform of C5-1 (C5-1'). The deduced amino acid sequences of C5-1 and C5-2 share 83% identity and predict a typical two-chain structure of the mature protein that lacks the thioester bond, as in C5 from other animals. Southern hybridization of genomic DNA suggested the presence of multiple genes encoding C5-type I and a single gene encoding C5-type II. Interestingly, carp C5-type I contains novel subtypes like C5-1 that have a histidine instead of the well-conserved arginine at the cleavage site for the C5 convertase, both in the complete and truncated forms. Northern blotting analysis suggested that C5-type I and C5-type II are mainly expressed in hepatopancreas, and the expression levels are significantly increased by stimulating carp with lipopolysaccharide or beta-1,3-glucan. Possible functional divergence among the C5 isotypes in carp is discussed.

Amino Acid Sequence↗

Modeling and alanine scanning mutagenesis studies of recombinant pokeweed antiviral protein.

The Phytolacca americana-derived naturally occurring ribosome inhibitory protein pokeweed antiviral protein (PAP) is an N-glycosidase that catalytically removes a specific adenine residue from the stem loop of ribosomal RNA. We have employed molecular modeling studies using a novel model of PAP-RNA complexes and site-directed mutagenesis combined with bioassays to evaluate the importance of the residues at the catalytic site and a putative RNA binding active center cleft between the catalytic site and C-terminal domain for the enzymatic deadenylation of ribosomal RNA by PAP. As anticipated, alanine substitutions by site-directed mutagenesis of the PAP active site residues Tyr(72), Tyr(123), Glu(176), and Arg(179) that directly participate in the catalytic deadenylation of RNA resulted in greater than 3 logs of loss in depurinating and ribosome inhibitory activity. Similarly, alanine substitution of the conserved active site residue Trp(208), which results in the loss of stabilizing hydrophobic interactions with the ribose as well as a hydrogen bond to the phosphate backbone of the RNA substrate, caused greater than 3 logs of loss in enzymatic activity. By comparison, alanine substitutions of residues (28)KD(29), (80)FE(81), (111)SR(112), (166)FL(167) that are distant from the active site did not significantly reduce the enzymatic activity of PAP. Our modeling studies predicted that the residues of the active center cleft could via electrostatic interactions contribute to both the correct orientation and stable binding of the substrate RNA molecule in the active site pocket. Notably, alanine substitutions of the highly conserved, charged, and polar residues of the active site cleft including (48)KY(49), (67)RR(68), (69)NN(70), and (90)FND(92) substantially reduced the depurinating and ribosome inhibitory activity of PAP. These results provide unprecedented evidence that besides the active site residues of PAP, the conserved, charged, and polar side chains located at its active center cleft also play a critical role in the PAP-mediated depurination of ribosomal RNA.

Alanine↗

The use of RNA interference to analyze protein phosphatase function in mammalian cells.

The use of RNA interference to knock down protein phosphatases has proven to be a valuable approach to understanding the functions of these enzymes in mammalian cells. Many protein phosphatases exist as multisubunit and multigene families, which has made it difficult to assess their physiological functions using traditional approaches. The ability to selectively knock down specific subunits and individual isoforms with RNA interference has begun to make it possible to determine the contributions of individual phosphatase proteins to cellular signaling. This chapter describes methods for knocking down protein phosphatases with small interfering RNAs in easily transfectable cells and by the introduction of short-hairpin RNAs into less tractable cells using lentivirus vectors.

Base Sequence↗

Using the histone H2a transcript as an endogenous standard to study relative transcript abundance during bovine early development.

The requirement for sample standardization is basic to any relative RNA abundance assessment. In 2002, we published on the RNA abundance profiling of several housekeeping targets during early bovine embryonic development. It was then concluded that histone H2a was the most stable transcript across the studied developmental period. Since that time, several teams have applied this information, yet neglected to use the published set of primers. Here, we show that these other primer sets do not target the same histone H2a variant. Within the present report, the RNA abundance profiles of their respective targets, for example, histone H2a.1, H2a.z, and H2a.o were measured in developmental series spanning the immature oocyte to the blastocyst stage embryo. In order to more clearly define the conditions that impact the RNA abundance level measurement of these candidates, the state of polyadenylation and the origin of the transcript either from de novo transcription or from maternal stocks were taken into consideration. The histone H2a.z transcript is principally regulated by de novo transcription following embryonic genome activation, whereas the levels of H2a.1 and H2a.o variants are largely of maternal origin, conferring a more stable profile throughout the studied developmental window. The histone H2a.z was found solely in a polyadenylated state whereas the H2a.1 and H2a.o were found to be more abundant in a nonadenylated form. The presence of serum in the in vitro embryo production system also had some impact on the histone H2a.1 RNA level at the blastocyst stage.

Animals↗

Isoenergetic dietary protein restriction decreases myosin heavy chain IIx fraction and myosin heavy chain production in humans.

The synthesis of muscle protein is restrained during dietary protein restriction. This is widely understood to vary quantitatively with the degree of nutritional deprivation, but there has been little discussion of qualitative changes in muscle protein deriving from dietary protein restriction. We studied 14 healthy subjects in a 2-sample study. Subjects were randomly assigned to a diet providing an ample, American-style protein intake (1.67 g. kg fat-free mass(-1). d(-1)) or a diet approximating the mean minimum adult protein requirement (0.71 g. kg fat-free mass(-1). d(-1)). We found that consumption of an isoenergetic diet at the mean adult minimum protein requirement for 4 wk produced an 81% lower fractional synthesis rate of myosin heavy chain (MHC) proteins in vastus lateralis muscle than did consumption of an ample protein diet (P = 0.05). Protein deprivation altered the skeletal muscle myosin composition such that the proportion of the total myosin content represented by fast-twitch MHC IIx was 51% lower than with ample intake (P = 0.013). The steady state content of MHC IIx messenger RNA (mRNA) did not differ in subjects consuming the minimum requirement of protein, suggesting that the reduced proportion of MHC IIx arises from posttranscriptional events. A 68% lower rate of 3-methylhistidine excretion with protein restriction (P < 0.01) suggests that myofibrillar protein degradation was lower. We conclude that dietary amino acid scarcity produces a change in myosin isoform distribution via posttranscriptional mechanisms. The relative contribution of inhibited myosin synthesis and inhibited degradation to the altered myosin isoform composition remains unknown. This has implications for the mechanisms by which amino acids govern muscle protein composition in vivo, and further exploration is required.

Adult↗

Identification of mRNAs associated with alphaCP2-containing RNP complexes.

Posttranscriptional controls in higher eukaryotes are central to cell differentiation and developmental programs. These controls reflect sequence-specific interactions of mRNAs with one or more RNA binding proteins. The alpha-globin poly(C) binding proteins (alphaCPs) comprise a highly abundant subset of K homology (KH) domain RNA binding proteins and have a characteristic preference for binding single-stranded C-rich motifs. alphaCPs have been implicated in translation control and stabilization of multiple cellular and viral mRNAs. To explore the full contribution of alphaCPs to cell function, we have identified a set of mRNAs that associate in vivo with the major alphaCP2 isoforms. One hundred sixty mRNA species were consistently identified in three independent analyses of alphaCP2-RNP complexes immunopurified from a human hematopoietic cell line (K562). These mRNAs could be grouped into subsets encoding cytoskeletal components, transcription factors, proto-oncogenes, and cell signaling factors. Two mRNAs were linked to ceroid lipofuscinosis, indicating a potential role for alphaCP2 in this infantile neurodegenerative disease. Surprisingly, alphaCP2 mRNA itself was represented in alphaCP2-RNP complexes, suggesting autoregulatory control of alphaCP2 expression. In vitro analyses of representative target mRNAs confirmed direct binding of alphaCP2 within their 3' untranslated regions. These data expand the list of mRNAs that associate with alphaCP2 in vivo and establish a foundation for modeling its role in coordinating pathways of posttranscriptional gene regulation.

3' Untranslated Regions↗

Identification of a novel AU-rich-element-binding protein which is related to AUF1.

The AU-rich element (ARE) is an important instability determinant for a large number of early-response-gene mRNAs. AREs also mediate the stabilization of certain pro-inflammatory mRNAs, such as tumour necrosis factor (TNF)-alpha and cyclo-oxygenase-2 (COX-2), in response to inflammatory stimuli. To understand how AREs control mRNA stability, it is necessary to identify trans-acting factors. We have purified a new ARE-binding protein and identified it as CArG box-binding factor-A (CBF-A). The amino acid sequence of CBF-A is highly similar to that of the ARE-binding protein AUF1. Recombinant CBF-A bound the COX-2 and TNF-alpha AREs, but not a non-specific control RNA. In contrast, in an electrophoretic-mobility-shift assay (EMSA) of crude RAW 264.7 macrophage-like cell extracts, an antiserum that recognizes both AUF1 and CBF-A failed to supershift complexes formed on the TNF-alpha ARE, but did supershift a complex specific for the COX-2 ARE. CBF-A exists as two isoforms, p37 and p42, that differ by a 47-amino-acid insertion close to the C-terminus. By expressing epitope-tagged isoforms of CBF-A it was shown that the p42 isoform binds the COX-2 ARE in EMSA of crude cell extracts. In a HeLa-cell tetracycline-regulated reporter system, overexpression of the p42 CBF-A isoform resulted in stabilization of a COX-2 ARE reporter mRNA. Epitope-tagged p42 CBF-A expressed in HeLa cells co-immunoprecipitated with endogenous COX-2 mRNA, but not glyceraldehyde-3-phosphate dehydrogenase mRNA, as shown by reverse-transcription PCR. The similarity between CBF-A and AUF1 suggests that CBF-A could be re-named AUF2.

3' Untranslated Regions↗

Cellular and subcellular mRNA localization of glutamate transporter isoforms GLT1a and GLT1b in rat brain by in situ hybridization.

GLT1, the predominant glutamate transporter of the forebrain, exists in two splice variant isoforms, i.e., GLT1a and GLT1b. Although GLT1 was originally detected only in astrocytes, we have recently demonstrated that GLT1a protein is expressed by neurons in the hippocampus as well. In the present study, the mRNA distribution patterns for the two isoforms were examined throughout the rat brain by using nonisotopic in situ hybridization and variant-specific RNA probes. Both isoforms were expressed in neuronal subgroups outside the hippocampus, such as in the cerebral cortex layer VI, or the neurons in the olfactory tubercle. As was the case in the hippocampus, GLT1a was the predominant transcript in neurons in these regions as well. Both GLT1 isoforms were widely expressed in astrocytes throughout the brain. GLT1a mRNA expression in astrocytes showed noticeable variation in labeling intensity in subregions of the hippocampus and other areas, whereas GLT1b expression in astrocytes was relatively homogeneous. On the subcellular level, GLT1a mRNA was expressed primarily in astrocyte processes, whereas GLT1b mRNA was more restricted to the astrocyte cell body. The two isoforms showed similar distributions in the subfornical organ and in tanycytes of the third ventricle. However, GLT1 expression in the pineal gland and the retina was due primarily to GLT1b, whereas GLT1a was more strongly expressed in Bergman glia in the cerebellum. These findings suggest that the expression of the two GLT1 isoforms is regulated by different mechanisms. Moreover, the function of the two isoforms may be subject to different regulatory processes.

Animals↗

Second generation antitumour human RNase: significance of its structural and functional features for the mechanism of antitumour action.

A second generation mutant of dimeric human pancreas RNase (HHP2-RNase), was obtained by a single residue mutation (Glu(111)-->Gly) of the previously described dimeric human pancreas RNase variant (HHP-RNase). HHP2-RNase was found to be a highly specific antitumour agent, with an enhanced cytotoxic activity compared with HHP-RNase. The structural and functional requisites of the antitumour action of HHP2-RNase were investigated and compared with those of other dimeric antitumour RNases. The stability of the dimeric structure, i.e. the resistance of human dimeric RNase variants to reductive cleavage of the two intersubunit disulphide bonds that bridge the subunits, was determined to be an essential feature of antitumour dimeric RNases. The stability of the dimeric structure is in turn responsible for the resistance to inhibition by the cytosolic RNase inhibitor (cRI). Both the stability of the dimeric structure and the resistance to cRI inhibition appeared to be highly enhanced by an RNase substrate. This suggests a possible role for RNA in the amplification of the antitumour potential of dimeric RNases.

Antineoplastic Agents↗

Inverse agonist actions of typical and atypical antipsychotic drugs at the human 5-hydroxytryptamine(2C) receptor.

Atypical antipsychotic drugs, which are distinguished from typical antipsychotic drugs by a lower incidence of extra-pyramidal side effects and less propensity to elevate serum prolactin levels (e.g., clozapine, olanzapine, risperidone, quetiapine, ziprasidone), have become the most widely used treatments for schizophrenia, although their precise mechanism of action remains controversial. It has been suggested that this group of atypical antipsychotic drugs is characterized by preferentially high affinities for 5-hydroxytryptamine (5-HT)2A serotonin receptors and relatively low affinities for D2-dopamine receptors. It has recently been proposed that these atypical antipsychotic drugs may also be distinguished from typical antipsychotic drugs (e.g., haloperidol, fluphenazine, chlorpromazine, and so on) by inverse agonist actions at the 5-HT2C-INI RNA edited isoform of the human 5-HT2C receptor transiently expressed in COS-7 cells. We have examined the relationship among 5-HT2C inverse agonist potency, efficacy, and atypical antipsychotic drug status in HEK-293 cells of a large number of typical and atypical antipsychotic drugs using human embryonic kidney (HEK)-293 cells stably transfected with the h5-HT2C-INI receptor. Inverse agonist actions at h5-HT2C-INI receptors were measured for both typical and atypical antipsychotic drugs. Thus, some typical antipsychotic drugs (chlorpromazine, mesoridazine, fluphenazine, and loxapine) were efficient inverse agonists, whereas several clinically effective atypical antipsychotic drugs (remoxapride, quetiapine, sulpiride, melperone, amperozide) were not. Additionally, several drugs without significant antipsychotic actions (M100907, ketanserin, mianserin, ritanserin, and amitriptyline) were potent inverse agonists at the 5-HT2C-INI isoform expressed in HEK-293 cells. Taken together, these results demonstrate that both typical and atypical antipsychotic drugs may exhibit inverse agonist effects at the 5-HT2C-INI isoform of the human 5-HT2C receptor and that no relationship exists between inverse agonist actions and atypicality.

3T3 Cells↗

Stretch-induced upregulation of VEGF gene expression in murine pulmonary culture: a role for angiogenesis in lung development.

BACKGROUND/PURPOSE: The authors' have shown pulmonary alveolarization (capillary and alveolar growth) both after fetal tracheal occlusion and postnatal pulmonary distension. The trophic and developmental mechanisms responsible for this growth remain largely unknown; however, experimental systems have defined an enhanced expression of angiogenic proteins in response to tissue stretch. The authors hypothesize that the stimulation of pulmonary alveolarization after stretch is secondary to upregulation of the potent endothelial cell mitogen vascular endothelial growth factor (VEGF) and that the endothelial cell represents the central stimulus of parenchymal growth. METHODS: A mixed primary pulmonary cell culture obtained by enzymatic digestion of fetal, neonatal, and adult mouse lung was plated on Bioflex elastomer bottom plates, grown to confluence, rendered quiescent, and subjected to continuous cycles of stretch-relaxation with nonstretched cells as controls. Cells were harvested at time-points 0, 30 minutes, 2 hours, 4 hours, 8 hours, and 24 hours. RNA was extracted and VEGF gene expression analyzed by semiquantitative reverse transcription polymerase chain reaction (RT-PCR). Similar cell groups were harvested, processed, and analyzed utilizing Western Blot techniques. VEGF PCR of mRNA isolated from fetal sheep subjected to surgical creation of diaphragmatic hernia both with (DH-TL) and without (DH) tracheal ligation also was analyzed. RESULTS: VEGF mRNA isoforms 120, 164, and 188 showed increased expression in all stretched groups, which was noted by 30 minutes with maximal expression seen at 2 to 4 hours and a return to baseline expression by 24 hours. VEGF protein was similarly elevated in all stretched cell groups. In preliminary studies, DH/TL sheep showed upregulation of VEGF compared with DH sheep alone. CONCLUSIONS: These data show in an in vitro system that "pulmonary stretch" upregulates VEGF mRNA and protein expression supporting the role of angiogenesis in the stretch-induced pulmonary alveolarization. The authors speculate that such angiogenic activity is a rate-limiting factor in stimulating alveolar epithelial development, and as a treatment modality, therapeutic angiogenesis may provide a noninvasive method with which to treat pulmonary hypoplasia.

Aging↗

Future perspectives.

Transcription is coupled to splicing and other post-transcriptional processes. The importance of transcription factors in developmental biology and disease is underlined by genetic analysis in flies and humans. The genome project is identifying large numbers of novel transcription factors and RNA-binding proteins. Proteins may have multiple functions, acting at the transcriptional and post-transcriptional levels. The vast amount of novel biological information requires new, high-throughput approaches and bioinformatics.

Animals↗