Cultivating DNA Sequencing Technology After the Human Genome Project

When the Human Genome Project was completed in 2003, automated Sanger DNA sequencing with fluorescent dye labels was the dominant technology. Several nascent alternative methods based on older ideas that had not been fully developed were the focus of technical researchers and companies. Funding agencies recognized the dynamic nature of technology development and that, beyond the Human Genome Project, there were growing opportunities to deploy DNA sequencing in biological research. Consequently, the National Human Genome Research Institute of the National Institutes of Health created a program-widely known as the Advanced Sequencing Technology Program-that stimulated all stages of development of new DNA sequencing methods, from innovation to advanced manufacturing and production testing, with the goal of reducing the cost of sequencing a human genome first to $100,000 and then to $1,000. The events of this period provide a powerful example of how judicious funding of academic and commercial partners can rapidly advance core technology developments that lead to profound advances across the scientific landscape.

Publisher Correction: DNA sequencing at 40: past, present and future

In this Review, the year of publication of reference 54 should be 2005, not 2015. In Box 2, "1982: GenBank ( https://www.ncbi.nlm.nih.gov/genbank/statistics/ )" should read "1982: Genbank/ENA/DDBJ" and "2007: NCBI Short Read Archive" should read "2007: NCBI and ENA Short Read Archives"; this is because the launches of these American, European and Japanese databases were coordinated. These errors have not been corrected.

The NIH Human Microbiome Project

The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites from each of at least 250 "normal" volunteers; (2) to determine whether there are associations between changes in the microbiome and health/disease by studying several different medical conditions; and (3) to provide both a standardized data resource and new technological approaches to enable such studies to be undertaken broadly in the scientific community. The ethical, legal, and social implications of such research are being systematically studied as well. The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome. The history and implementation of this new program are described here.

The challenges of sequencing by synthesis

DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

The potential and challenges of nanopore sequencing

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.

Normal Chlamydomonas nuclear gene structure on linkage group XIX

The unusual Chlamydomonas linkage group XIX-called the uni linkage group for the uni mutants that lack one of the paired flagellae of wild-type cells—has been reported to be physically located exclusively at the basal bodies. To learn whether the structure of genes on this linkage group differs from the structure of nuclear genes in this organism, we determined the primary structure of a gene that maps to linkage group XIX. This analysis reveals the presence of nine intervening sequences; the nucleotides at exon/intron boundaries conform with nuclear gene intron junction sequences. Also typical for C. reinhardtii nuclear genes are the position and sequence of the putative polyadenylation signal. These findings suggest that transcripts from linkage group XIX are likely to be processed in the nucleus. The open reading frame, which displays weak but easily detected Chlamydomonas codon bias, potentially encodes a protein similar to a membrane anchor for cytoskeletal proteins. The observation that expression of this gene is regulated during interphase and in gametes is not consistent with the hypothesis that linkage group XIX may be expressed only during mitotic and meiotic processes.

A Chlamydomonas gene encodes a G protein beta subunit-like polypeptide

A Chlamydomonas gene encodes a protein that shows sequence similarity with the beta subunit of guanine nucleotide binding proteins from mammals, fruit fly and yeast. In addition to amino acid sequences similarity, each of these proteins contains a segmented repeat structure in which certain amino acids form a consensus sequence. Thus this gene product has been designated a Chlamydomonas beta subunit-like polypeptide (Cblp). The mRNA is constitutively expressed during the cell cycle and during flagellar regeneration.

Structural organization, DNA sequence, and expression of the calmodulin gene

Calmodulin is encoded in Chlamydomonas reinhardtii by a single gene that 1) has multiple intervening sequences, 2) has 5' structural motifs that are phylogenetically conserved, 3) contains 5' sequences that are similar to those found in genes of some transforming, cytoskeletal, and stress-response proteins, and 4) produces at both life cycle stages, a single size class of mRNA and proteins that are identical in amino acid sequence. Based on the amino acid sequence of calmodulin from the vegetative phase of the life cycle, synthetic oligonucleotide probes, containing inosine in order to reduce codon redundancy, were used to detect and isolate cloned cDNAs coding for the gametic phase calmodulin. The complete DNA sequence was elucidated and shown to code for a protein identical to the vegetative phase protein. Analysis of the production of calmodulin mRNA indicates that protein production is under quantitative regulation and possibly coupled with the synthesis of other proteins in the flagellar apparatus. The full length cDNA was used to isolate overlapping genomic clones that include the entire calmodulin transcriptional unit and 5' regulatory sequences. The complete DNA sequence of the gene, including all intron sequences, was elucidated. The DNA sequence of the coding regions shows some phylogenetic conservation. Finally, there are regions of 5' sequence reminiscent of sequence motifs recently identified as binding sites of transcriptional regulatory proteins. Overall, these studies suggest possible molecular genetic relationships between calmodulin, a transducer of intracellular calcium signals, and other proteins involved in eukaryotic cell structure, motility, and homeostasis.

Mapping flagellar genes in Chlamydomonas using restriction fragment length polymorphisms

To correlate cloned nuclear DNA sequences with previously characterized mutations in Chlamydomonas and, to gain insight into the organization of its nuclear genome, we have begun to map molecular markers using restriction fragment length polymorphisms (RFLPs). A Chlamydomonas reinhardtii strain (CC-29) containing phenotypic markers on nine of the 19 linkage groups was crossed to the interfertile species Chlamydomonas smithii. DNA from each member of 22 randomly selected tetrads was analyzed for the segregation of RFLPs associated with cloned genes detected by hybridization with radioactive DNA probes. The current set of markers allows the detection of linkage to new molecular markers over approximately 54% of the existing genetic map. This study focused on mapping cloned flagellar genes and genes whose transcripts accumulate after deflagellation. Twelve different molecular clones have been assigned to seven linkage groups. The alpha-1 tubulin gene maps to linkage group III and is linked to the genomic sequence homologous to pcf6-100, a cDNA clone whose corresponding transcript accumulates after deflagellation. The alpha-2 tubulin gene maps to linkage group IV. The two beta-tubulin genes are linked, with the beta-1 gene being approximately 12 cM more distal from the centromere than the beta-2 gene. A clone corresponding to a 73-kD dynein protein maps to the opposite arm of the same linkage group. The gene corresponding to the cDNA clone pcf6-187, whose mRNA accumulates after deflagellation, maps very close to the tightly linked pf-26 and pf-1 mutations on linkage group V.

Tubulin gene expression in the Chlamydomonas reinhardtii cell cycle: elimination of environmentally induced artifacts and the measurement of tubulin mRNA levels

To investigate the involvement of tubulin gene expression in controlling cell division events in Chlamydomonas reinhardtii we have measured tubulin mRNA levels during the cell cycle under different environmental conditions. In C. reinhardtii cells grown under the synchronizing conditions of 14 h of light followed by 10 h of darkness, mRNAs for tubulin and associated flagellar proteins were found to accumulate periodically with a peak just prior to cell division. This was not seen when previously synchronized cells were transferred to constant environmental conditions in a turbidostat, suggesting that dramatic changes in tubulin mRNA levels are not required for successful completion of the cell cycle. A hypothesis to explain the patterns of tubulin mRNA accumulation found under different environmental conditions is presented.

Protein synthesis is required for rapid degradation of tubulin mRNA and other deflagellation-induced RNAs in Chlamydomonas reinhardi

After flagellar detachment in Chlamydomonas reinhardi, there is a rapid synthesis and accumulation of mRNAs for tubulin and other flagellar proteins. Maximum levels of these mRNAs (flagellar RNAs) are reached within 1 h after deflagellation, after which they are rapidly degraded to their predeflagellation levels. The degradation of alpha- and beta-tubulin RNAs was shown to be due to the shortening of their half-lives after accumulation (Baker et al., J. Cell Biol. 99:2074-2081, 1984). Deflagellation in the presence of protein synthesis inhibitors results in the accumulation of tubulin and other flagellar mRNAs by kinetics similar to those of controls. However, unlike controls, in which the accumulated mRNAs are rapidly degraded, these mRNAs are stabilized in cycloheximide. The stabilization by cycloheximide is specific for the flagellar mRNAs accumulated after deflagellation, since there is no change in the levels of flagellar mRNAs in nondeflagellated (uninduced) cells in the presence of cycloheximide. The kinetics of flagellar mRNA synthesis after deflagellation are shown to be the same in cycloheximide-treated and control cells by in vivo labeling and in vitro nuclear runoff experiments. These results show that protein synthesis is not required for the induced synthesis of flagellar mRNAs, and that all necessary transcriptional control factors are present in the cell before deflagellation, but that protein synthesis is required for the accelerated degradation of the accumulated flagellar mRNAs. Since cycloheximide prevents the induced synthesis and accumulation of flagellar proteins, it is possible that the product(s) of protein synthesis required for the accelerated decay of these mRNAs is a flagellar protein(s). The possibility that one or more flagellar proteins autoregulate the stability of the flagellar mRNAs is discussed.

Rapid changes in tubulin RNA synthesis and stability induced by deflagellation in Chlamydomonas

Detachment of the flagella of Chlamydomonas induces a rapid accumulation of mRNAs for tubulin and other flagellar proteins. Measurement of the rate of alpha and beta tubulin RNA synthesis during flagellar regeneration shows that deflagellation elicits a rapid, 4-7-fold burst in tubulin RNA synthesis. The synthesis rate peaks within 10-15 min, then declines back to the predeflagellation rate. Redeflagellation of cells at times before the first flagellar regeneration is completed (and when cells have already accumulated elevated levels of tubulin RNA) induces another burst in tubulin RNA synthesis which is identical to the first in magnitude and duration. This finding indicates that the induction signal may act to simply reprogram the tubulin genes for a transient burst of maximal synthesis. Evidence is presented that the stability of the tubulin RNAs changes during regeneration. Stability changes include both an apparent stabilization during regeneration and accelerated decay following regeneration.

The two beta-tubulin genes of Chlamydomonas reinhardtii code for identical proteins

The two beta-tubulin genes of the unicellular green alga Chlamydomonas reinhardtii are expressed coordinately after deflagellation and produce two transcripts of 2.1 and 2.0 kilobases. Full-length cDNA clones corresponding to the transcript of each gene were isolated. DNA sequences were obtained from the cDNA clones and from cloned tubulin gene fragments. Both genes contained 1,332 base pairs of coding sequence, with only 19 nucleotide differences between the genes. Because all the differences occurred at the third base position of a codon and did not change the predicted amino acid sequence, we concluded that both beta-tubulin genes code for the same protein of 443 amino acids. The predicted amino acid sequence is 89 and 72% homologous with beta-tubulins from chicken and yeast cells, respectively. Each gene had three intervening sequences, which occurred at identical positions. Although the first two intervening sequences were not conserved between the two genes, the nucleotide sequence of the third intervening sequence was 89% conserved between the genes. The codon usage in the tubulin genes of C. reinhardtii was very biased: only 37 different codons were used. Striking differences occurred between the codons used in these nuclear genes and C. reinhardtii chloroplast genes.

Subroutines in the programme of Chlamydomonas gene expression induced by flagellar regeneration

The unicellular green alga Chlamydomonas reinhardtii possesses two anterior flagella that are rapidly replaced if they are lost. A cytoplasmic pool of flagellar precursors supports regeneration of partial length flagella, but complete regeneration requires de novo synthesis of flagellar proteins. This increase in protein synthesis is transient and is programmed by changes in the physical abundance of a set of RNAs. These changes were measured using cloned cDNAs. The curves that were generated with probes for a number of different RNAs were variations-on-the-theme of a rapid accumulation following deflagellation of the cells, followed by similarly rapid degradation. Differences in the characteristics of the accumulation curves suggest that several 'subroutines' for RNA metabolism appear to run concurrently during flagellar regeneration. A significant portion of the mRNA abundance regulation occurs at the transcriptional level. A group of cDNAs that encode mRNAs whose abundance remains at constant levels during regeneration provides an important internal control for the abundance and transcription measurements. Flagella contain over 200 different proteins, so the possibility exists that the cells coordinately and rapidly alter the transcription of the same number of genes. Chlamydomonas flagellar regeneration thus provides an opportunity to study cellular mechanisms for coordinating the expression of a large set of genes, and correlating these changes with an easily monitored morphogenetic process.

Subroutines in the programme of Chlamydomonas gene expression induced by flagellar regeneration

The unicellular green alga Chlamydomonas reinhardtii possesses two anterior flagella that are rapidly replaced if they are lost. A cytoplasmic pool of flagellar precursors supports regeneration of partial length flagella, but complete regeneration requires de novo synthesis of flagellar proteins. This increase in protein synthesis is transient and is programmed by changes in the physical abundance of a set of RNAs. These changes were measured using cloned cDNAs. The curves that were generated with probes for a number of different RNAs were variations-on-the-theme of a rapid accumulation following deflagellation of the cells, followed by similarly rapid degradation. Differences in the characteristics of the accumulation curves suggest that several ‘subroutines’ for RNA metabolism appear to run concurrently during flagellar regeneration. A significant portion of the mRNA abundance regulation occurs at the transcriptional level. A group of cDNAs that encode mRNAs whose abundance remains at constant levels during regeneration provides an important internal control for the abundance and transcription measurements. Flagella contain over 200 different proteins, so the possibility exists that the cells coordinately and rapidly alter the transcription of the same number of genes. Chlamydomonas flagellar regeneration thus provides an opportunity to study cellular mechanisms for coordinating the expression of a large set of genes, and correlating these changes with an easily monitored morphogenetic process.

mRNA abundance changes during flagellar regeneration in Chlamydomonas reinhardtii

Flagellar amputation in Chlamydomonas reinhardtii induces the accumulation of a specific set of RNAs, many of which encode flagellar proteins. We prepared a cDNA clone bank from RNA isolated from cells undergoing flagellar regeneration. From this bank, we selected clones that contain RNA sequences that display several different patterns of abundance regulation. Based on quantitation of the relative amounts of labeled, cloned cDNAs hybridizing to dots of RNA on nitrocellulose filters, the cloned sequences were divided into five regulatory classes: class I RNAs remain at constant abundance during flagellar regeneration; classes II, III, and IV begin to increase in abundance within a few minutes after deflagellation, reach maximal abundance at successively later times during regeneration, and return to control cell levels within 2 to 3 h; and class V RNA abundance decreases during flagellar regeneration. Alpha- and beta-tubulin mRNAs are included in regulatory class IV. The abundance kinetics of alpha-tubulin mRNAs differ slightly from those of beta-tubulin mRNAs. The availability of these clones makes possible studies on the mechanisms controlling the abundance of a wide variety of different RNA species during flagellar regeneration in Chlamydomonas.

Transcription of alpha- and beta-tubulin genes in vitro in isolated Chlamydomonas reinhardi nuclei

Removal of the flagella of Chlamydomonas results in increases in both flagellar protein synthesis and tubulin messenger RNA accumulation. These observations led us to examine whether flagellar protein gene sequences are transcribed differentially in nuclei isolated before and after deflagellation. A nuclear isolation protocol was developed using the cell wall-less strain of Chlamydomonas, CW 15, after cell lysis with 0.5% Nonidet P-40. Transcriptional activity of isolated nuclei was determined by incorporating [32P]UTP into TCA-precipitable and phenol-extractable RNA, and by hybridizing newly transcribed RNA to complementary DNA clones containing alpha- and beta-tubulin sequences. Nuclei from deflagellated cells are more active in transcribing sequences that hybridize with alpha- and beta-tubulin complementary DNA probes than are nuclei from nondeflagellated cells. In addition, while total [32P]UTP incorporation is inhibited 45% by alpha-amanitin concentrations of 1.0 micrograms/ml, tubulin RNA synthesis in this system is completely inhibited by this concentration of alpha-amanitin. This demonstration of differential transcription in nuclei before and after cell deflagellation provides the means to study in vitro the mechanisms that signal and regulate flagellar protein gene activity.

Microfilaments and tropomyosin of cultured mammalian cells: isolation and characterization

Microfilaments were isolated from cultured mammalian cells, utilizing procedures similar to those for isolation of "native" thin filaments from muscle. Isolated microfilaments from rat embryo, baby hamster kidney (BHK- 21), and Swiss mouse 3T3 cells appeared structurally similar to muscle thin filaments, exhibiting long, 6 nm Diam profiles with a beaded, helical substructure. An arrowhead pattern was observed after reaction of isolated microfilaments with rabbit skeletal muscle myosin subfragment 1. Under appropriate conditions, isolated microfilaments will aggregate into a form that resembles microfilament bundles seen in situ cultured cells. Isolated microfilaments represent a complex of proteins including actin. Some of these components have been tentatively identified, based on coelectrophoresis with purified proteins, as myosin, tropomyosin, and a high molecular weight actin-binding protein. The tropomyosin components of isolated microfilaments were unexpected; polypeptides comigrated on SDS-polyacrylamide gels with both muscle and nonmuscle types of tropomyosin. In order to identify more specifically these subunits, we isolated and partially characterized tropomyosin from three cell types. BHK-21 cell tropomyosin was similar to other nonmuscle tropomyosins, as judged by several criteria. However, tropomyosin isolated from rate embryo and 3T3 cells contained subunits that comigrated with both skeletal muscle and nonmuscle types of myosin, whereas the BHK cell protein consistently contained a minor muscle-like subunit. The array of tropomyosin subunits present in a cell culture was reflected in the polypeptide chain pattern seen on SDS-polyacrylamide gels of microfilaments isolated from that culture. These studies provide a starting point for correlating changes in the ultrastructural organization of microfilaments with alterations in their protein composition.

Organization of actin gene sequences in the sea urchin: molecular cloning of an intron-containing DNA sequence coding for a cytoplasmic actin

Southern transfer and solution hybridization experiments, using as probe a DNA fragment that encodes for Drosophila actin, demonstrate cross hybridization to DNA from the sea urchin Strongylocentrotus purpuratus. Recombinant DNA clones that contained sea urchin genomic DNA fragments were constructed and screened for the presence of actin-encoding DNA sequences by colony hybridization with the Drosophila actin sequence. Two different putative actin-encoding clones were identified and were shown to specifically hybridize actin-encoding mRNA from a complex mRNA population. Southern blot hybridization experiments with both the Drosophila actin sequence and one of the cloned sea urchin sequences, in conjunction with solution hybridization data, suggest an actin gene copy number of 5-20 per haploid genome. DNA sequence analysis of one of the cloned sequences indicates that this fragment codes for a cytoplasmic form of actin and contains an intervening sequence of at least 200 nucleotides beginning immediately after amino acid 121 in the protein sequence.

Isolation of a high molecular weight actin-binding protein from baby hamster kidney (BHK-21) cells

A high molecular weight protein (HMWP) with properties similar to those of both actin-binding protein (ABP) and filamin has been isolated from cultured baby hamster kidney (BHK-21) cells. The protein was present in an actomyosin-depleted sucrose extract of the cells and was eluted, upon gel chromatography on Sepharose 4B, near the void volume. The subunit migration on sodium dodecyl sulfate/polyacrylamide gels and the amino acid composition of HMWP were similar to those of ABP and filamin. HMWP bound to and crosslinked F-actin from rabbit muscle, as shown by the formation of a gel that was sedimented with low-speed centrifugation. This interaction was insensitive to temperature and low concentrations of calcium ions, although it may depend on the presence of myosin. Observation of thin sections of the actin-HMWP gel revealed crosslinked complexes of laterally aggregated actin filaments. The axial period of the dense crosslinks was 34 nm. The HMWP may be involved in regulation of microfilament organization.

Myosin subfragment binding for the localization of actin-like microfilaments in cultured cells. A light and electron microscope study

Fluorescein-labeled heavy meromyosin subfragment-1 (F-S-1) has been purified by ion exchange chromatography and characterized in terms of its ability to bind specifically to actin. F-S-1 activates the Mg++-adenosine triphosphatase activity of rabbit skeletal muscle actin and decorates actin as shown by negative stains and thin sections of rabbit actin and rat embryo cell microfilament bundles, respectively. Binding of F-S-1 to cellular structures is prevented by pyrophosphate and by competition with excess unlabeled S-1. The F-S-1 is used in light microscope studies to determine the distribution of actin-containing structures in wnterphase and mitotic rat embryo and rat kangaroo cells. Interphase cells display the familiar pattern of fluorescent stress fibers. Chromosome-to-pole fibers are fluorescent in mitotic cells. The glycerol extraction procedures employed provide an opportunity to examine cells prepared in an identical manner by light and electron microscopy. The latter technique reveals that actin-like microfilaments are identifiable in spindles of glycerinated cells before and after addition of S-1 or HMM. In some cases, microfilaments appear to be closely associated with spindle microtubles. Comparison of the light and electron microscope results aids in the evaluation of the fluorescent myosin fragment technique and provides further evidence for possible structural and functional roles of actin in the mitotic apparatus.

Localization and organization of microfilaments and related proteins in normal and virus-transformed cells

The localization and organization of actin-like microfilaments in normal, SV-40 and adenovirus transformed cells are determined by the coordinated use of light optical, electron optical and biochemical techniques. In adenovirus-type 5 transformed hamster embryo cells, microfilament meshworks appear to be the predominant organizational form of cellular action, while in normal hamster cells, microfilament bundles are prevalent. Differences between 3T3 and SV-40 transformed 3T3 cells are less apparent and may be related to the packing and intracellular distribution of microfilament bundles. Attempts at relating these ultrastructural changes in transformed cells to the images obtained following reaction with fluorescein-labelled myosin fragments and indirect immunofluorescence with smooth muscle myosin antibody are discussed. In several instances the fluorescence microscope images to not correspond to the ultrastructural observations. The results are discussed in terms of the possible relationships between alterations in cytoplasmic contractile elements and the abnormal behavior of transformed cells.