The construction of a recombinant cDNA library representative of the poly(A)+ mRNA population from normal human lymphocytes

Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing

The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach. However, due to inherent limitations of this approach in de novo transcriptome assembly and isoform quantification, long-read RNA-Seq approaches, which also happen to be single molecule sequencing approaches, are increasingly becoming the standard for de novo transcriptome assembly and isoform quantification. In this chapter, we review the technical aspects of the current methods of RNA-Seq, both short and long-read approaches, and data analysis methods available. We discuss recent advances in single-cell RNA-Seq and direct RNA-Seq approaches, which perhaps will dominate the future of RNA-Seq.

The T-cell receptor gamma chain-CD3 complex: implication in the cytotoxic activity of a CD3+ CD4- CD8- human natural killer clone

A subset of human T cells has recently been described. These cells express the CD3 complex but they do not carry the classical T-cell receptor (TCR)-alpha/-beta heterodimer on their surface (WT31- CD3+). Instead, they express a TCR-gamma chain associated with another type of polypeptide termed TCR-delta. We report here that a T-cell clone with natural killer (NK)-like activity, WM-14, had a disulfide bridged TCR-gamma homodimer associated with CD3 on its surface. The TCR-gamma chains of WM-14 cells were present in three different glycosylation forms of 43, 40, and 38 kDa, but they appeared to contain the same polypeptide backbone. Since cytotoxicity by WM-14 could be inhibited by anti-CD3 antibodies, we concluded that the TCR-gamma-CD3 complex was involved in the NK-like unrestricted killer activity. Although normal CD3-gamma, CD3-delta, and CD3-epsilon chains were present in this clone, the association with the TCR-gamma homodimer may be the cause of a complete processing of the N-linked oligosaccharides attached to the CD3-delta chain.

Characterization of cDNA clones for human myeloperoxidase: predicted amino acid sequence and evidence for multiple mRNA species

Myeloperoxidase is a component of the microbicidal network of polymorphonuclear leukocytes. The enzyme is a tetramer consisting of two heavy and two light subunits. A large proportion of humans demonstrate genetic deficiencies in the production of myeloperoxidase. As a first step in analyzing these deficiencies in more detail, we have isolated cDNA clones for myeloperoxidase from an expression library of the HL-60 human promyelocytic leukemia cell line. Two overlapping plasmids (pMP02 and pMP062) were identified as myeloperoxidase cDNA clones based on the detection with myeloperoxidase antiserum of 70 kDa protein expressed in pMP02-containing bacteria and a 75 kDa polypeptide produced by hybridization selection and translation using pMP062 and HL-60 RNA. Formal identification of the clones was made by matching the predicted amino acid sequences with the amino terminal sequences of the heavy and light subunits. Both subunits are encoded by one mRNA in the following order: pre-pro-sequences--light subunit--heavy subunit. The molecular weight of the predicted primary translation product is 83.7 kDa. Northern blots reveal two size classes of hybridizing RNAs (approximately 3.0-3.3 and 3.5-4.0 kilobases) whose expression is restricted to cells of the granulocytic lineage and parallels the changes in enzymatic activity observed during differentiation.

Isolation of cDNA clones encoding the 20K non-glycosylated polypeptide chain of the human T-cell receptor/T3 complex

The antigen receptor on human T lymphocytes consists of two variable immunoglobulin-like glycoproteins, alpha and beta, which occur in association with three invariable T3 membrane proteins. In humans two of these proteins, T3-gamma and T3-delta, are glycoproteins of relative molecular mass (Mr) 25,000 (25K) and 20,000 (20K), respectively, while the third, T3-epsilon, is a 20K non-glycosylated protein. On the surface of murine T cells, a non-glycosylated protein dimer composed of 17K subunits (T3-zeta) is found associated with the T-cell receptor alpha and beta chains and the three T3-like polypeptide chains. It is generally accepted that major histocompatibility complex-restricted antigen recognition is a function of the alpha-beta heterodimer. This has led to the postulation that the proteins of the T3 complex are involved in the signal transduction that immediately follows antigen recognition via the antigen receptor. Events believed to be involved in early T-cell activation, such as rapid increases in phosphatidylinositol turnover and free intracellular calcium, can be triggered by antibodies directed against either the T3 complex or the clonotypic receptor. We have previously reported our findings on the cloning of the complementary DNA and genomic structure encoding both the human and murine 20K glycoprotein, T3-delta (refs 11-13). We now present our results on the cloning of the cDNA encoding the human 20K non-glycosylated chain, T3-epsilon.

High-efficiency cloning of DNA sequences complementary to mouse neuroblastoma polyadenylated RNA

A cDNA library was efficiently synthesized from mouse neuroblastoma poly(A)+RNA. Several modifications of the oligo(dC)(dG) tailing procedure were used. After first strand synthesis, a dATP tail was added to the 3'-end of the cDNA. The second strand was primed for synthesis with oligo(dT). Blunt ends were produced on the cDNA by treatment with S1 nuclease. Size-enriched fractions of high molecular weight DNAs were obtained by passing the cDNA over a Sepharose CL-4B column. The optimal tailing time for each cDNA fraction was individually tested. Tailing reactions used terminal deoxynucleotidyl transferase and annealing reactions used a (G)-tailed Pst I cut pBR322. E. coli K12 RR1 cells were transformed and 2.5-5 X 10(6) transformants per microgram cDNA insert were obtained for each size fraction. The transformants had an average insert size of 1200 base pairs and were 98% ampicillin sensitive. Our modifications in the method for cDNA library synthesis had 3 advantages. (1) Homopolymer-primed cDNA treated with S1 nuclease allowed the blunt ends to be tailed synchronously. This allowed a higher transformation efficiency without loss of 5'-sequences. (2) Time tailing determined the most efficient tail length and optimized the transformation efficiency in each size fraction. (3) A Sephadex G-50 mini-column was used to desalt and dry nitrogen was used to concentrate the ds cDNA instead of the usual ethanol precipitation. This resulted in almost 100% recovery of synthesized products at each step of this procedure.

A pBR322-derived vector for cloning blunt-ended cDNA: its use to detect molecular clones of low-abundance mRNAs

In place of the unique Pst I site in pBR322, we have engineered by GC tailing a unique Sma I site bracketed by Pst I sites. The resulting vector, pDE61, and an improved derivative with greater symmetry around the Sma I site, pDE613, have been used to clone blunt-ended duplex cDNA molecules in Escherichia coli in an efficient manner (5 X 10(5) clones from 1 microgram of double-stranded cDNA). When DNA is cloned into the Sma I site, the ability of both vectors to confer ampicillin resistance is lost. Evidence suggests that functional beta-lactamase is made only after the GC-rich sequence containing the Sma I site is deleted: an insert in the Sma I site prevents this. Libraries in either vector, with single or multiple inserts, can be used to generate amplified amounts of cloned heterogeneous cDNA for screening other "target" libraries in a non-homologous vector (e.g., a Bacillus subtilis vector) for cDNA clones of low-abundance mRNAs. Species as infrequent as 0.003% can be readily detected by colony hybridization.

Syrian hamster female protein: analysis of female protein primary structure and gene expression

The concentration in plasma of the female protein (FP) of the golden Syrian hamster is regulated by sex steroids and by mediators of the acute-phase response to tissue injury or inflammation. A complementary DNA (cDNA) clone corresponding to FP was isolated from a hamster liver cDNA library and used to determine the nucleotide sequence and derived amino acid sequence of native FP. The primary sequence of FP is 69 percent identical to human serum amyloid P component and 50 percent identical to human C-reactive protein. Evidence showed that sex-limited and acute-phase control of the FP gene is pretranslational. The FP protein is thus a useful model for investigating dual regulation of expression of a single gene.

Characterization of the messenger RNA population coding for components of viperid snake venom

Total polyadenylated messenger RNA was prepared from the milked venom glands of the South African puff adder (Bitis arietans) and translated in an in vitro translation system. The products of cell free synthesis were immunoprecipitable with puff adder venom antiserum. Treatment of these cell free products with a dog pancreas microsomal membrane preparation demonstrated the presence of signal peptides. Northern blot hybridization of total puff adder venom gland mRNA to its complementary single stranded copy DNA revealed two discrete mRNA populations coding for the major components of puff adder venom. The relative amounts of these polyadenylated mRNA sequences changed during the onset of venom synthesis, suggesting mRNA deadenylation, general endonucleolytic RNA degradation and selective degradation of high molecular weight message components.

Expression of the alpha-fetoprotein gene in pluripotent and committed cells

We have studied the structure and expression of the alpha-fetoprotein gene in various cell types which differ in their capacity to synthesize alpha-fetoprotein. In all cells and tissues examined the levels of alpha-fetoprotein RNA found in the nucleus and cytoplasm were consistent with the hypothesis that alpha-fetoprotein expression is transcriptionally regulated. The alpha-fetoprotein gene was insensitive to deoxyribonuclease I in both undifferentiated embryonal carcinoma cells and in differentiated tissues which do not express alpha-fetoprotein, whereas in endoderm cells derived from the embryonal carcinoma cells and in alpha-fetoprotein-producing tissues the gene was sensitive to deoxyribonuclease I.

Isolation and characterization of a cDNA clone for bovine cytochrome c oxidase subunit IV

We have isolated a cDNA clone for the precursor to subunit IV of bovine cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1). A cDNA library was constructed from poly(A)+ RNA of adult beef liver by insertion of cDNA into the plasmid vector pBR322. Transformants were screened by colony hybridization with two mixtures of [32P]-labeled synthetic oligodeoxyribonucleotides. We screened 20,000 transformants with a mixture of heptadecamers complementary to all 16 possible sequences encoding amino acids 98-103 and obtained two cDNA clones encoding subunit IV amino acid sequences. We determined the DNA sequence of the larger (416 base-pair) insert, which contains the coding sequence for amino acids 1-107 of the mature protein and an NH2-terminal extension (presequence). The deduced amino acid sequence of the mature protein is identical with the previously determined protein sequence: the sequence of the NH2-terminal extension contains a potential initiator methionine at amino acid -22 from the NH2-terminus of the processed protein. The presequence is quite basic and contains several arginines, including one at the processing site. No hydrophobic region analogous to that found in bacterial and eukaryotic signal peptides is present, but there are homologies with other mitochondrial protein presequences, which may include a common signal for their destination and processing.

Isolation and characterization of a cDNA clone for human ferritin heavy chain

Ferritin, the main iron-storage protein, is composed of two partially homologous subunits, heavy (H) and light (L), with MrS of 21,000 and 19,000, respectively. We have isolated a cDNA clone for human ferritin H chains by screening a human lymphocyte cDNA library with synthetic oligodeoxyribonucleotides. The oligonucleotide sequences were derived from two pentapeptides found in human spleen ferritin. The selected clone hybridized to both probes and selected H-chain mRNA, but not L-chain mRNA, when hybridized to HeLa cell mRNA. These results indicate that the cloned DNA codes for a H chain of human ferritin. Since the amino acid sequence derived from the cloned DNA was almost identical to the partial amino acid sequence of a minor component found in human spleen ferritin, we conclude that the minor sequence found in human spleen ferritin must be a H subunit. Genomic analysis gives a complex pattern that suggests that ferritin H chains are encoded by a multigene family or have an unusually large number of exons.

The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus

The complete nucleotide sequence of the coding region of foot and mouth disease virus RNA (strain A1061) is presented. The sequence extends from the primary initiation site, approximately 1200 nucleotide from the 5' end of the genome, in an open translational reading frame of 6,999 nucleotides to a termination codon 93 nucleotides from the 3' terminal poly (A). Available amino acid sequence data correlates with that predicted from the nucleotide sequence. The amino acid sequence around cleavage sites in the polyprotein shows no consistency, although a number of the virus-coded protease cleavage sites are between glutamate and glycine residues.

Inter-locus and intra-allelic polymorphisms of HLA class I antigen gene mRNA

We have constructed cDNA clone libraries from two lymphoblastoid cell lines, JY (HLA-A2, B7, C untypeable) and LB (HLA-A28, B40, Cw3), and isolated clones encoding class I HLA antigens. We have characterized short oligonucleotide probes derived from the coding region of the HLA class I antigens which are specific for the HLA-A and -B loci. These probes have been used to subdivide the class I cDNA clones into subclasses. DNA sequencing of several HLA-A and -B related clones has allowed us to extend the primary structural characterization of these cell-surface antigens. This analysis has also detected a sequence polymorphism at the HLA-A locus, indicating that the previously considered homozygous typing cell line LB expresses two alleles of similar, although not identical, serological specificity.

Identification and isolation of transcribed human X chromosome DNA sequences

A human X chromosome specific phage library has been used as a source of X-specific genomic DNA clones which hybridize with cellular RNA. Random cDNA clones were mapped for X chromosome sequence localization and 8 were identified as hybridizing to X chromosome Hind III fragments. All eight also hybridized with autosomal Hind III fragments. The X chromosome genomic sequences corresponding to two of these cDNA clones were isolated from a phage library constructed with the Hind III endonuclease digest products of X enriched DNA. One genomic DNA segment, localized to the short area of the X, shared sequence homology with at least one region of the human Y chromosome. The methodology developed represents a rapid means to obtain a specific genomic DNA clone from a single chromosome when multiple different genomic loci homologous to an expressed DNA sequence exist.

Partial cDNA sequence to a hamster gene corrects defect in Escherichia coli pyrB mutant

The first three enzymes of pyrimidine biosynthesis (carbamoyl-phosphate synthetase, aspartate carbamoyl-transferase, and dihydro-orotase) are carried on a multifunctional protein in mammalian cells and are on separate proteins in bacteria. A plasmid containing a cDNA sequence corresponding to 80% of a hamster mRNA for this protein was transformed into Escherichia coli mutants lacking aspartate carbamoyltransferase (pyrB) or dihydro-orotase (pyrC). Only pyrB transformants were able to grow in the absence of uracil. Plasmid recovered from primary transformants was similar in size to the original plasmid and could yield prototrophs after secondary transformation of E. coli pyrB mutants. When cell extracts were prepared from pyrB transformants, high levels of aspartate carbamoyltransferase activity were found, and the enzyme had properties identical to the mammalian enzyme, including lack of allosteric regulation, precipitation by antiserum specific to the hamster multifunctional protein, and presence of a strong aggregation center. These results demonstrate that (i) a partial hamster protein can complement E. coli defective in pyrimidine biosynthesis, (ii) the order of the enzyme domains of the multifunctional protein is likely to be NH2-dihydro-orotase-carbamoyl-phosphate synthetase-aspartate carbamoyltransferase-COOH, and (iii) the enzyme domains appear to be self-contained at the DNA and protein levels. The protocol described here may be a general means for studying the domains of multifunctional proteins and for isolating other mammalian genes for which bacterial mutants have been prepared. It also permits study of the structure and function of the same gene in both prokaryotic and eukaryotic cells and may provide new insight into the evolution of complex genes.

The isolation of a clone for human alpha 1-antitrypsin and the detection of alpha 1-antitrypsin in mRNA from liver and leukocytes

A recombinant clone containing an insert complementary to alpha 1-antitrypsin (alpha 1-AT) mRNA has been isolated from a human adult liver cDNA library. The clone was selected by direct screening of recombinants with a synthetic oligodeoxynucleotide 17 bases in length corresponding to the known partial DNA sequence of the gene. The insert size of the clone is 250 base pairs. The DNA sequence of the clone has been determined and agrees with the published partial DNA sequence. There is one nucleotide difference from the published sequence, causing a single amino acid change at position 376 where aspartate replaces glutamate. The clone has been used to detect alpha 1-AT mRNA sequences in human liver and in a mixed leukocyte population containing monocytes and lymphocytes. A single mRNA approximately 1,400 nucleotides in length is observed in both leukocytes and liver. Leukocytes contain only 0.15% as much alpha 1-AT mRNA as liver.

Quantitative analysis of mRNA synthesis during early cortisol action on rat thymocytes: restricted size of a possible hormone response

Complete inhibition of cortisol-induced pycnosis was seen by actinomycin D and cycloheximide only when added during the initial period of hormone action. This phenomenon, being a characteristic of steroid hormone effects in general, is often taken as indirect evidence for early steroid-induced mRNA synthesis. The lack of direct evidence for this theory has been tested for significance. Approximately 133 newly synthesized mRNA molecules were found to accumulate in the cytoplasm/min/cell, suggesting an average synthesis rate for individual mRNA species of about 1 copy/h/cell. Electrophoretic fractionation of double labelled RNA failed to reveal any changes of the isotope ratio of single fractions during the first 15-45 min of cortisol action, within an experimental error corresponding to +/- 2- +/- 20 molecules/cell. Possible effects of cortisol are thus restricted to changes in the range of constitutive mRNA synthesis rates. In contrast, the RNA labelling pattern was differentially changed after 45 min treatment with 10(-5) M cycloheximide.

Molecular cloning of complementary DNA: preparation of a plasmid vector with low transformation background

A simple method that allows the rapid preparation of oligo dG-tailed plasmid vectors is presented. The procedure involves purification of the tailed molecules by hybridization to oligo dC-cellulose followed by a stepwise thermal elution. The resulting plasmid is virtually devoid of transformation activity in the absence of oligo dC-tailed DNA fragments. It allows construction of cDNA libraries with as low as 1% of colonies harboring wild-type plasmids.

The effects of lectin transformation on cytoplasmic polyadenylated RNA from human lymphocytes

The translational activity of cytoplasmic poly(A)+ RNA from resting human lymphocytes was approximately 20% of that from phytohemagglutinin-transformed lymphocytes in a rabbit reticulocyte lysate assay. Translation assays in the presence of cap analogues suggested that the mRNA from resting cells was relatively deficient in functional 5'-terminal cap structures. Neither mRNA fraction inhibited the translation of globin mRNA in the cell-free assay, and both preparations were essentially pure as shown by hybridisation with [3H]poly(U). The size distribution and poly(A) tail length of poly(A)+ RNA was similar in the resting and transformed cell and both preparations directed the synthesis of peptides of molecular weight 15 000 to 90 000. Two dimensional gels of total proteins from resting and transformed lymphocytes showed predominantly quantitative changes. However cross-hydridising cDNA and mRNA from resting and transformed cells after the common sequences have been removed by hydroxylapatite chromatography showed that about 4% of the cytoplasmic poly(A)+ RNA from transformed lymphocytes was not present in resting cells. This difference may result from transformation-specific gene expression.

Isolation of cDNA clones for the human complement protein factor B, a class III major histocompatibility complex gene product

cDNA clones corresponding to a major histocompatibility class III antigen, the complement protein factor B, have been isolated from a human adult liver cDNA library. The clones, ranging in size from 1.0 to 2.3 kilobases, were identified by direct hybridization with two synthetic oligonucleotide mixtures. Two regions of the factor B amino acid sequence, each with minimal ambiguity in codon assignment, were chosen for synthesis of the oligonucleotides. The sequences of two clones have been partially determined. They contain coding information for the amino acid sequence of the Bb fragment of factor B and the entire 3' -untranslated region.

The purification of human DNA fragments containing benzpyrene adducts

DNA was isolated from human diploid lung epithelial cells treated in culture with [3H]benzpyrene. The DNA contained one covalently bound benzpyrene group per 38 kb and it was digested with a series of restriction endonucleases giving decreasing fragment sizes, and also with DNAase I to 96% acid solubility. The digests were applied to octyl-Sepharose columns under conditions which promote hydrophobic interaction of the benzpyrene groups on the DNA with the octyl groups in the column matrix. Separation of fragments without and with benzpyrene groups was achieved with successive high salt and ethanediol washes. As DNA fragment size is decreased, more DNA-associated benzpyrene is eluted with ethanediol. Under these conditions, DNA from untreated cells is totally removed in the high salt wash and free benzpyrene metabolites are retained on the column. The separation of DNA fragments with covalently-bound hydrophobic benzpyrene groups, from less modified or unmodified DNA will facilitate examination of the distribution of benzpyrene adducts in defined regions of the human genome.

Benzpyrene groups bind preferentially to the DNA of active chromatin in human lung cells

The cells of the bronchial epithelium of man are targets for benzo(a)pyrene carcinogenesis. When cultures of these cells, and of non-target fibroblasts, are exposed to [3H]-benzo(a)pyrene, we find that the epithelial cells metabolise and bind to DNA far greater amounts of benzpyrene than do fibroblasts. By analysis of nuclei of benzpyrene-treated cells for sensitivity to limited digestion with pancreatic DNase I, we have shown that benzpyrene groups bind initially to the DNA of expressed (DNase I sensitive) regions of chromatin in both cell types. Covalent binding of benzpyrene groups to non-expressed (DNase I resistant) regions follows rapidly in the target epithelial cells. These maintain high levels of carcinogen adducts in their DNA. In fibroblasts, benzpyrene group binding to non-expressed DNA occurs more slowly and active removal of adducts from the DNA is evident.

The imported preprotein of the proteolipid subunit of the mitochondrial ATP synthase from Neurospora crassa. Molecular cloning and sequencing of the mRNA

The proteolipid subunit of the mitochondrial ATP synthase from Neurospora crassa is an extremely hydrophobic protein of 81 amino acid residues, which is imported into mitochondria as a precursor of mol. wt. 15 000. The primary structure of the imported form has now been determined by isolating and analyzing cDNA clones of the preproteolipid mRNA. An initial cDNA clone was identified by hybridizing total polyadenylated RNA to pooled cDNA recombinant plasmids from an ordered clone bank and subsequent cell-free translation of hybridization-selected mRNA. Further preproteolipid clones were identified at a frequency of 0.2% by colony filter hybridization. One isolated cDNA represented the major part of the preproteolipid mRNA. The nucleotide sequence showed 243 bases corresponding to the mature proteolipid and, in addition, 178 bases coding for an amino-terminal presequence . Non-coding sequences of 48 bases at the 5' end and of 358 bases at the 3' end plus a poly(A) tail were determined. The long presequence of 66 amino acids is very polar, in contrast to the lipophilic mature proteolipid, and includes 12 basic and no acidic side chains. It is suggested that the presequence is specifically designed to solubilize the proteolipid for post-translational import into the mitochondria.

Sequence complexity and diversity of polyadenylated RNA molecules of human normal resting, PHA-stimulated and leukemic lymphocytes

The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduced in respect to normal unstimulated lymphocytes. The differences is due to a small portion, by weight, of high complexity sequences, suggesting the involvement or nuclear, not necessarily transcriptional, events. Moreover the heterologous hybridizations show that: 1) in PHA-stimulated lymphocytes there is a set of highly abundant sequences which are represented in normal and leukemic lymphocytes at a very reduced rate; 2) the sequences abundant in normal unstimulated lymphocytes are less represented in leukemic lymphocytes; the converse also is true, but at a lower extent. On the basis of available data, it is suggested that the observed changes in the abundance pattern of PHA-stimulated lymphocytes may be related mainly to a difference in the half-life of the mRNAs, while those of leukemic lymphocytes require some transcriptional or post-transcriptional nuclear event.

The isolation, mapping and transcription in vitro of a beta 0-thalassaemia globin gene

The red blood cell precursors of a patient with homozygous beta 0-thalassaemia have previously been shown to contain nuclear, but not cytoplasmic, beta-globin-specific transcripts. We describe the isolation of a beta-globin gene from this patient as a recombinant bacteriophage chromosome. Restriction-enzyme cleavage-site mapping experiments demonstrate no detectable deletions, insertions or major rearrangements in this thalassaemia gene. Two different techniques show that the gene isolated is transcribed as efficiently in vitro as the normal beta-globin gene.

A new era in mammalian gene mapping: somatic cell genetics and recombinant DNA methodologies

Mammalian gene mapping techniques are now sufficiently advanced to contribute significantly to prenatal diagnosis and to human molecular genetics. Restriction fragment mapping can be used to place polymorphic genetic markers at random sites within the genome, and these sites used to assign genes responsible for disease conditions to a chromosomal region. Somatic cell genetic techniques can then be applied to saturate that region with additional restriction fragment markers, some of which will be closely linked to the disease gene. Closely linked restriction fragment markers, especially flanking pairs of markers, can act as predictors for the transmission of defective genes to offspring. A series of tightly linked flanking restriction markers might in addition contribute to the eventual isolation and cloning of the disease gene itself.

There are approximately 20 actin gene in the human genome

By three different lines of evidence there are approximately 20 copies of actin genes in the human genome. Firstly, the rate of hybridisation of a mouse actin probe to human DNA indicates that there are a minimum of 20 complementary copies of the actin sequence per genome. Secondly, this probe hybridises to 17-20 bands in Southern blots of restriction enzyme digests of total human DNA. Most of these bands hybridise with both 3' and 5' fragments of the cDNA and are therefore likely to contain the entire gene sequence. Thirdly, we have picked 12 actin recombinants from a genomic library, and at the level of restriction enzymes mapping these represent nine different genes. Probability calculations indicate that these recombinants were picked from a pool of at least 20 different genes.

The occurrence of families of repetitive sequences in a library of cloned cDNA from human lymphocytes

A library of cloned cDNAs representative of lymphocyte total poly(A)+ RNA was screened with total DNA probes at high clone density. 10% of the recombinants showed the presence of sequences which are repeated in the genome. Further analysis of six such isolated cDNA clones indicated that they contain different families of repetitive sequences with reiteration frequencies of between 150 and 45,000 copies per haploid genomes. Five of the six clones were found to contain single copy sequences as well as a repetitive sequence. cDNA clones containing repetitive sequences have been found to be derived from high, intermediate and low abundance classes of lymphocyte poly(A)+ RNA.