cDNA libraries from a few neural cells

Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines

Objective

RNA interference is employed extensively in Drosophila research to study gene function within a specific cell-type or tissue. Thousands of transgenic Drosophila lines have been generated to express double stranded RNA for gene knockdown; however, no standardized method exists for quantifying their knockdown efficiency. Since antibodies are not available for many proteins, quantitative real-time PCR is often used. Here, we explore how primer design and RNA isolation method can influence detection of gene knockdown using qPCR.

Results

We tested differences in detected gene knockdown efficiency when using purified polyadenylated mRNA or total RNA as templates for cDNA synthesis. We also tested two different primer locations for each gene: one to amplify a region 5′ of the RNAi cut site, and one to amplify a region 3′ of the cut site. Consistently, the strongest gene knockdown was detected when qPCR was performed using 5′ primer sets in combination with mRNA-derived cDNA. Our results indicate that detection of undegraded mRNA cleavage fragments can result in underestimation of true knockdown efficiency for a RNAi construct. Purification of polyadenylated mRNA, combined with primers designed to amplify the non-polyadenylated 5′ mRNA cleavage fragment can avoid this problem.

Electronic supplementary material

The online version of this article (10.1186/s13104-017-2959-0) contains supplementary material, which is available to authorized users.

Hirudo medicinalis: a platform for investigating genes in neural repair

We have used the nervous system of the medicinal leech as a preparation to study the molecular basis of neural repair. The leech central nervous system, unlike mammalian CNS, can regenerate to restore function, and contains identified nerve cells of known function and connectivity. We have constructed subtractive cDNA probes from whole and regenerating ganglia of the ventral nerve cord and have used these to screen a serotonergic Retzius neuron library. This identifies genes that are regulated as a result of axotomy, and are expressed by the Retzius cell. This approach identifies many genes, both novel and known. Many of the known genes identified have homologues in vertebrates, including man. For example, genes encoding thioredoxin (TRX), Rough Endoplasmic Reticulum Protein 1 (RER-1) and ATP synthase are upregulated at 24 h postinjury in leech nerve cord. To investigate the functional role of regulated genes in neuron regrowth we are using microinjection of antisense oligonucleotides in combination with horseradish peroxidase to knock down expression of a chosen gene and to assess regeneration in single neurons in 3-D ganglion culture. As an example of this approach we describe experiments to microinject antisense oligonucleotide to a leech isoform of the structural protein, Protein 4.1. Our approach thus identifies genes regulated at different times after injury that may underpin the intrinsic ability of leech neurons to survive damage, to initiate regrowth programs and to remake functional connections. It enables us to determine the time course of gene expression in the regenerating nerve cord, and to study the effects of gene knockdown in identified neurons regenerating in defined conditions in culture.

Identifying genes for neuron survival and axon outgrowth in Hirudo medicinalis

We have studied the molecular basis of nervous system repair in invertebrate (Hirudo medicinalis) nerve cells. Unlike in mammals, neurons in invertebrates survive injury and regrow processes to restore the connections that they held before the damage occurred. To identify genes whose expression is regulated after injury, we have used subtractive probes, constructed from regenerating and non-regenerating ganglia from the leech Hirudo medicinalis, to screen cDNA libraries made from whole leech CNS or from identified microdissected neurons. We have identified genes of known or predicted function as well as novel genes. Known genes up-regulated within hours of injury and that are widely expressed in invertebrate and mammalian cells include thioredoxin and tubulin. Other known genes, e.g. Cysteine Rich Intestinal Protein (CRIP), have previously been identified in mammalian cells though not in regenerating adult neurons. Two regulated genes identified, myohemerythrin and the novel protein ReN3 are exclusively expressed in invertebrates. Thus our approach has enabled us to identify genes, present in a neuron of known function, that are up- and down-regulated within hours of axotomy, and that may underpin the intrinsic ability of invertebrate neurons to survive damage and initiate regrowth programmes.

Single-cell analysis reveals cell-specific patterns of expression of a family of putative voltage-gated sodium channel genes in the leech

To understand the molecular basis of nervous system function in the leech, Hirudo medicinalis, we have isolated four novel cDNAs encoding putative voltage-gated sodium (Na) channel alpha subunits, and have analyzed the expression of these genes in individual neurons of known function. To begin, degenerate oligonucleotide primers were used in combination with pre-existing cDNA libraries and reverse transcriptase-coupled polymerase chain reactions (RT-PCR). The putative leech Na channel cDNAs (LeNas) exhibit a higher degree of sequence homology to Na channel genes in other species than to voltage-gated calcium or potassium channel genes, including those expressed in leech. All LeNa cDNAs contain sequences corresponding to regions of functional importance in Na channel alpha subunits, including the "S4 region" involved in activation, the "pore loops" responsible for ion selectivity, and the "inactivation loop" between the third and fourth domains, though the latter lacks the highly conserved "IFM" motif critical for mammalian Na channel inactivation. Sequences corresponding to important determinants of tetrodotoxin sensitivity are found in some, but not all, LeNa cDNAs, consistent with prior electrophysiological evidence of Na channel heterogeneity in the leech with respect to this toxin. Subsequently, two different sets of isoform-specific primers and methods of RT-PCR, including a sensitive, fluorescence-based "real time" RT-PCR, were used to analyze LeNa isoform expression in functionally distinct neurons. The results from both approaches were consistent, and not only demonstrated that individual neurons often express more than one LeNa isoform, but also revealed cell-specific patterns of Na channel isoform expression in the leech nervous system.

Single cell expression analysis--pharmacogenomic potential

A fundamental challenge in biology is to correlate physiology with gene expression in specific cell types. This can only be achieved by understanding gene expression at the level of the single cell because, in many systems, each cell has the capacity to express a unique set of genes. Therefore, each cell can be considered to be functionally distinct. A clearer understanding of gene expression differences at such a discrete level provides an opportunity to develop drugs with more targeted pharmacologies or with decreased side effects.

Gene expression profile and identification of differentially expressed transcripts during human intrathymic T-cell development by cDNA sequencing analysis

The development of immature thymocytes to mature T-lymphocytes is a central process for establishing a functional immune system. The gene regulatory events involved in this process are of outstanding interest in understanding the generation of the T-cell repertoire as well as the differentiation of lineage-specific cells, such as CD4(+) helper T-cells or CD8(+) cytotoxic T-lymphocytes. While some essential genes involved in lineage decision and thymocyte differentiation have been already identified, the exact regulatory mechanisms and differential gene expressions are still unknown. The present study was performed to analyze the gene expression profile during T-cell development, in particular, during the differentiation of immature thymocytes into CD4(+) mature T-cells by analyses of expressed sequence tags (ESTs), and to elucidate novel human genes involved in this process. Based on distinct developmental stages, three PCR-based cDNA libraries from immature CD3(-),4(-),8(-) triple-negative, CD4(+),8(+) double-positive, and mature CD4(+),8(-) single-positive thymocytes were constructed. A total of 1477 randomly selected clones were analyzed by automated single-pass sequencing, and the assembly of ESTs resulted in 1027 different species of contig sequences. Among them, 392 contig sequences were matched to known genes, and several novel transcripts were discovered. The matched clones were classified into seven categories according to their functional aspects, and the gene expression profiles of the three thymocyte subsets were compared. The information obtained in current study will serve as a valuable resource for elucidating the molecular mechanism of intrathymic T-cell development.

Steps in the formation of neurites and synapses studied in cultured leech neurons

Leech neurons in culture have provided novel insights into the steps in the formation of neurite outgrowth patterns, target recognition and synapse formation. Identified adult neurons from the central nervous system of the leech can be removed individually and plated in culture under well-controlled conditions, where they retain their characteristic physiological properties, grow neurites and form specific chemical or electrical synapses. Different identified neurons develop distinctive outgrowth patterns that depend on their identities and on the molecular composition of the substrate. On native substrates, the patterns displayed by these neurons reproduce characteristics from the adult or the developing neurons. In addition, the substrate may induce selective directed growth between pairs of neurons that normally make contact in the ganglion. Upon contact, pairs of cultured leech neurons form chemical or electrical synapses, or both types depending on the neuronal identities. Anterograde and retrograde signals during membrane contact and synapse formation modify the distribution of synaptic terminals, calcium currents, and responses to 5-hydroxytryptamine.

Cloning, characterisation and expression of the alpha-tubulin genes of the leech, Hirudo medicinalis

We have isolated two alpha-tubulin cDNAs from the leech, Hirudo medicinalis. Both encode putative proteins of 451 amino-acids which differ from each other at only two positions. Southern blotting suggests that there are only two alpha-tubulin genes in the leech. The genes contain two introns and, because of the extremely high homology of the nucleotide sequence from the second intron to the end of the genes, we have inferred that a gene conversion event about 9.5 million years ago has homogenised the Hirudo alpha-tubulin sequences. Using in situ hybridisation to tissue sections, we have shown that the two genes are probably expressed in all neurons of the leech ganglia and that their spatial distribution remains unchanged during neuronal regeneration. The deduced amino-acid sequences of the leech alpha-tubulins show that they have greatest similarity to those from a platyhelminth, echiuran and mollusc with rather less to arthropod alpha-tubulins. The protein sequences of the leech alpha-tubulins have been compared with representatives of those from across all phyla to determine if any specific feature labels certain isotypes of tubulin for neuronal expression.

Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones

To study the gene expression profile in the mouse blastocyst and to identify embryonic stage-specific genes, we randomly selected cDNAs derived from mouse blastocysts and sequenced a total of 3995 clones from one or both ends. Excluding the uninformative clones, 3395 clones were grouped as 937 different kinds of genes. Among these, 465 and 406 species showed similarity to known genes and expressed sequence tags (ESTs), respectively, whereas 66 species showed no significant similarity to any genes in known databases. Analysis of these cDNAs revealed that this library contained a variety of functional genes as well as genes that have not been detected in the human EST database; it should provide us with a useful resource for molecular analysis of developmental mechanisms. Although the human EST project is considered to represent roughly half of all genes, our findings indicate that many early stage developmental genes remain to be identified.

A subtractive cDNA library from an identified regenerating neuron is enriched in sequences up-regulated during nerve regeneration

We have constructed a subtractive cDNA library from regenerating Retzius cells of the leech, Hirudo medicinalis. It is highly enriched in sequences up-regulated during nerve regeneration. Sequence analysis of selected recombinants has identified both novel sequences and sequences homologous to molecules characterised in other species. Homologies include alpha-tubulin, a calmodulin-like protein, CAAT/enhancer-binding protein (C/EBP), protein 4.1 and synapsin. These types of proteins are exactly those predicted to be associated with axonal growth and their identification confirms the quality of the library. Most interesting, however, is the isolation of 5 previously uncharacterised cDNAs which appear to be up-regulated during regeneration. Their analysis is likely to provide new information on the molecular mechanisms of neuronal regeneration.

Promotion of regeneration and axon growth following injury in an invertebrate nervous system by the use of three-dimensional collagen gels

We describe the application of three-dimensional collagen matrices to the study of nerve cord repair in the leech. Our experiments show that ganglia and connectives of the leech ventral nerve cord can be maintained for up to four weeks embedded in 3D gels constructed from mammalian type I collagen. Severed nerve cords embedded in the collagen gel reliably repaired within a few days of culture. The gel was penetrable by cells emigrating from the cut ends of nerves and connectives, and we consistently saw regenerative outgrowth of severed peripheral and central axons into the gel matrix. Thus, 3D gels provide an in vitro system in which we can reliably obtain repair of severed nerve cords in the dish, and visualize cell behaviour underlying regenerative growth at the damage site: and which offers the possibility of manipulating the regenerating cells and their extracellular environment in various ways at stages during repair. Using this system it should be possible to test the effect on the repair process of altering expression of selected genes in identified nerve cells.

cDNA libraries from identified neurons

One approach to studying the changes in gene expression which underlie differentiation is to construct cDNA libraries from different tissues or at different stages of development. However, generating representative cDNA libraries from heterogeneous tissues such as the nervous system is often a real problem. Here, we describe a reproducible method for the construction of large and complex cDNA libraries from a few leech Retzius or P neurons (equivalent to about 50 pg of mRNA) using polymerase chain reaction-based technology. The libraries contain about 10(6) independent recombinants and are remarkably free from contaminating rRNA or polymerase chain reaction artefacts. Sequence analysis of randomly picked clones shows that the libraries contain a high proportion (more than 90%) of cDNAs larger than 500 b.p. As expected, many of the clones are novel, but two (alpha-tubulin and cyclophilin-A) have been extensively characterized in other species. To our knowledge, this is the first report of a cDNA library from identified neurons.

Construction of a mouse blastocyst cDNA library by PCR amplification from total RNA

Studies of the development and differentiation of early mammalian embryos have been severely limited by the paucity of material. Such studies have been largely restricted to the examination of abundant genes/proteins or to developmental expression studies of known genes for which DNA sequence data are available, allowing the use of reverse transcription and polymerase chain reaction amplification (RT-PCR). To eliminate the need for hundreds or thousands of oocytes or embryos in the construction of representative cDNA libraries, we describe a technique for generating and cloning cDNA using small caesium chloride gradient centrifugation to isolate total RNA from oocytes or embryos, followed by RT-PCR of mRNA from this total RNA. Total RNA was isolated from 70 mouse blastocysts. A portion of the cDNA generated (equivalent to seven blastocysts) was cloned, yielding a mouse blastocyst cDNA library of 1 million clones. We show that the library is representative in that it contains beta-actin, intracisternal A-type particles, tissue plasminogen activator, and B1 and B2 repetitive elements in frequencies comparable with published data from conventionally constructed libraries and estimates of mRNA abundance from expression studies. Furthermore, DNA sequencing of 22 clones chosen at random and compared with DNA sequence databases shows that approximately half are novel sequences. These data demonstrate that representative cDNA libraries can be constructed in situations where cell numbers are limiting and will facilitate the isolation of novel and interesting clones.

Use of the teleost saccule to identify genes involved in inner ear function

The vertebrate inner ear sensory epithelia contain different types of hair cells and supporting cells. The teleost saccule is anatomically similar to the mammalian saccule and is primarily involved in the detection of translational acceleration and orientation with respect to gravity. To facilitate molecular studies of the teleost saccule cDNA libraries were constructed from microdissected Lepomis macrochirus (bluegill sunfish) saccular maculae. To our knowledge, this is the first report of cDNA libraries constructed from the saccule. In one instance, a non-polymerase chain reaction-based method of amplifying a mRNA population from limited amounts of starting tissue was employed that allowed construction of cDNA libraries from nanogram amounts of tissue mRNA. Conventional cDNA libraries were constructed from the sunfish saccular maculae as well. These cDNA libraries enriched in hair cell and supporting cell transcripts should facilitate molecular biological studies of inner ear sensory epithelia. As an example of their utility, efforts to identify tyrosine kinases expressed in the saccular endorgan using low-stringency hybridization screening of these cDNA libraries and the partial sequence of a cDNA found to encode an erbB-2-related tyrosine kinase are also reported.

Peripheral nervous system-specific genes identified by subtractive cDNA cloning

An improved method for constructing and screening subtractive cDNA libraries has been used to identify 46 mRNA transcripts that are expressed selectively in neonatal rat dorsal root ganglia (DRG) as judged by Northern blots and in situ hybridization. Sequence analysis demonstrates that both known (e.g. peripherin, calcitonin gene-related peptide, myelin P0) and novel identifiable transcripts (e.g. C-protein-like, synuclein-like, villin-like) are present in the library. Half of the transcripts (23) are undetectable in liver, kidney, heart, spleen, cerebellum, and cerebral cortex. Of the DRG-specific transcripts, 12 contain putative open reading frames that show no identity with known proteins. The construction of such a subtractive library thus provides us with both known and novel markers, and identifies new predicted DRG-specific proteins. In addition, the DRG-specific clones provide probes to define the regulatory elements that specify peripheral nervous-system-specific gene expression.

Synapse formation and function: insights from identified leech neurons in culture

Identified leech neurons in culture are providing novel insights to the signals underlying synapse formation and function. Identified neurons from the central nervous system of the leech can be removed individually and plated in culture, where they retain their characteristic physiological properties, grow neurites, and form specific synapses that are directly accessible by a variety of approaches. Synapses between cultured neurons can be chemical or electrical (either rectifying or not) or may not form, depending on the neuronal identities. Furthermore, the characteristics of these synapses depend on the regions of the cells that come into contact. The formation and physiology of synapses between the Retzius cell and its partners have been well characterized. Retzius cells form purely chemical, inhibitory synapses with pressure-sensitive (P) cells where serotonin (5-HT) is the transmitter. Retzius cells synthesize 5-HT, which is stored in vesicles that recycle after 5-HT is secreted on stimulation. The release of 5-HT is quantal, calcium-dependent, and shows activity-dependent facilitation and depression. Anterograde and retrograde signals during synapse formation modify calcium currents, responses to 5-HT, and neurite outgrowth. The nature of these synaptogenic signals is being elucidated. For example, contact specifically with Retzius cells induces a localized selection of transmitter responses in postsynaptic P cells. This effect is signaled by tyrosine phosphorylation prior to synapse formation.