3,400 new expressed sequence tags identify diversity of transcripts in human brain

Adams, Alexandra; Kerlavage, Anthony R.; Fields, Chris; Venter, J. Craig

doi:10.1038/ng0793-256

Cited by 282 publications

(114 citation statements)

References 27 publications

Supporting

Mentioning

112

Contrasting

Order By: Relevance

“…Many of these sequences are homologous to proteins from other organisms and many of them may contain protein-coding regions that represent novel gene families [16]. We reasoned that such a cDNA sequence encoding a mammalian homologue for the trp gene might exist in the database.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, we used the deduced amino acid sequence of the Drosophila trp as a query to search the Genbank database using TBLASTN, a program that allows comparison of a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames. A human EST (EST05093) was found to encode an amino acid sequence that shares similarity with the Drosophila trp sequence from Glu 33 to Asn s° as follows: The 297 nucleotide sequence of this EST was determined from a cDNA clone isolated from a fetal human brain cDNA library and was deposited in GenBank by Adams et al [16]. The deduced peptide sequence of EST05093 was then compared with the protein sequences of the Drosophila trpl and a C. elegans trp homologue (ZC21.2, Genbank accession #L16685).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Molecular cloning of a widely expressed human homologue for the Drosophila trp gene

et al. 1995

View full text Add to dashboard Cite

The Drosophila transient receptor potential (trp) gene and its homologue, trpl, have been suggested to mediate calcium entry during the insect's phototransduction process. We isolated human cDNA, human trp-1 (Htrp-1), encoding a polypeptide .f 793 amino acids that is 37% identical (62% similar) to Drosophila trp and trpl. Northern analysis showed that the Htrp-1 transcript is approximately 5.5 kb and expressed in most human tissues, with higher amounts in ovary, testis, heart, and brain.Isolation of Htrp-I suggests that a trp-type protein is present in mammals and should provide a useful tool in studying calciumdepletion induced calcium influx processes.:~ey words': Transient receptor potential; Calcium influx , hannel; Ca 2+ signaling ~. IntroductionCalcium regulation plays an important role in many cellular 0rocesses. In non-excitable mammalian cells, activation of i~hosphoinositide-specific phospholipase C (PLC) produces ~nositol 1,4,5-trisphosphate (IP3), which in turn causes the reease of intracellular calcium from its storage pools in the endo~lasmic reticulum. This results in a transient elevation of cyosolic-free Ca 2+, which is normally followed by a Ca 2+ influx 'rom the extracellular space. By refilling the pools, Ca 2+ influx )lays an important role in prolonging the Ca 2+ signal, allowing or localized signaling, and maintaining Ca 2÷ oscillations [1].Calcium influx in non-excitable cells is thought to occur hrough plasma membrane channels which, in contrast to the voltage-dependent Ca 2+ channels in excitable cells, are operated lot by changes of membrane potentials but rather by how full he internal Ca 2+ stores are [2]. Although studies using either luorescent Ca 2+ indicators or electrophysiological techniques lave suggested that multiple types of Ca 2+ permeant channels nay be involved in different cell types to fulfill the influx funcion, the molecular structure of the channels and the mechalism that regulates the influx have remained unclear and reprerent one of the major unanswered questions of cellular Ca -,+ !lomeostasis [3][4][5].Candidates involved in voltage-independent Ca 2+ entry into [9]. A detailed analysis of the trpl sequence showed that it shares moderate homology with voltage-dependent Ca 2+ and Na ÷ channels at their putative transmembrane regions. However, in clear contrast with the voltage-dependent channels, it lacks the positively charged amino acid residues at the presumed $4 segment which are thought to act as voltage sensors that promote gating in response to changes in membrane potentials. The structural homology to Ca 2+ and Na + channels together with the absence of charged residues in trpl and trp suggested that these proteins may form voltage-independent ion channels. This was demonstrated recently by expression of the cDNAs for trp and trpl in insect Sf9 cells using the baculovirus system. It was fount that trp forms a Ca 2÷ permeable cation channel which is activated by store depletion with thapsigargin [10] whereas trpl forms a Ca -'+ permeable non-selec...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Molecular cloning of a widely expressed human homologue for the Drosophila trp gene

et al. 1995

View full text Add to dashboard Cite

show abstract

“…The high-throughput single-pass partial sequencing of cDNAs to generate ESTs has proven to be a powerful and successful way to assemble a profile of genes expressed in a particular organism, tissue, or cell type [18][19][20][22][23][24]34]. Libraries of short cDNA fragments corresponding to the 3Ј or 5Ј end regions of the mRNA have offered advantages to accelerate gene discovery and gene mapping.…”

Section: Discussionmentioning

confidence: 99%

“…Large-scale, single-pass sequencing of cDNA clones randomly picked from libraries has proven to be a powerful approach to discovering genes and novel members of gene families as well as an expressed gene profile [18][19][20][21][22][23][24][25][26]. The NCBI EST database (dbEST) has become one of the fastest growing segments of the public DNA databases [27].…”

mentioning

confidence: 99%

Gene Expression Profile of Human Bone Marrow Stromal Cells: High-Throughput Expressed Sequence Tag Sequencing Analysis

et al. 2002

View full text Add to dashboard Cite

Human bone marrow stromal cells (HBMSC) are pluripotent cells with the potential to differentiate into osteoblasts, chondrocytes, myelosupportive stroma, and marrow adipocytes. We used high-throughput DNA sequencing analysis to generate 4258 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5Ј (97) and 3Ј (4161) ends of human cDNA clones from a HBMSC cDNA library. Our goal was to obtain tag sequences from the maximum number of possible genes and to deposit them in the publicly accessible database for ESTs (dbEST of the National Center for Biotechnology Information). Comparisons of our EST sequencing data with nonredundant human mRNA and protein databases showed that the ESTs represent 1860 gene clusters. The EST sequencing data analysis showed 60 novel genes found only in this cDNA library after BLAST analysis against 3.0 million ESTs in NCBI's dbEST database. The BLAST search also showed the identified ESTs that have close homology to known genes, which suggests that these may be newly recognized members of known gene families. The gene expression profile of this cell type is revealed by analyzing both the frequency with which a message is encountered and the functional categorization of expressed sequences. Comparing an EST sequence with the human genomic sequence database enables assignment of an EST to a specific chromosomal region (a process called digital gene localization) and often enables immediate partial determination of intron/exon boundaries within the genomic structure. It is expected that high-throughput EST sequencing and data mining analysis will greatly promote our understanding of gene expression in these cells and of growth and development of the skeleton.Key Words: human bone marrow stromal cells, EST sequencing analysis, novel genes, gene expression profile, data mining them potentially useful for cell and gene therapy [2][3][4]. After extensive proliferation in vitro, the HBMSC population includes precursor cells for at least four types of connective tissue: bone, cartilage, hematopoiesis-supporting stroma, and associated adipocytes [5][6][7][8]. When single bone marrow stromal cells develop into individual HBMSC colonies, they show different morphologies and rates of proliferation. HBMSC strains derived from individual colonies also vary widely in their ability to form bone and the hematopoietic microenvironment after in vivo transplantation [9]. Despite efforts to understand the biology of HBMSC through studies 8Article doi:10.1006/geno.2001.6683, available online at http://www.idealibrary.com on IDEAL at different levels, the study of genes and proteins important to the biological phenotypes of HBMSC is still in its infancy. Well-known exceptions include STRO1 [10,11], THY1 [12,13], and SCA1 [14]. Determining the genetic expression profile of this specific cell type is key to rapid advances in understanding skeletal growth and development. The ability to peer into HBMSC and read their molecular signature will enable us to identify more preci...

show abstract

“…Because these were inactivating mutations, it was clear that this protein, aptly given the name sclerostin, functioned either directly or indirectly as an inhibitor of bone formation. During this same general time period, large-scale cDNA/ expressed sequence tag (EST) (10)(11)(12) and genomic DNA sequencing efforts were being made in academia and industry to rapidly identify new human genes. A novel secreted protein of unknown function, which turned out to be sclerostin, was discovered by computational mining of large DNA sequence databases using either homology-based programs (eg, BLAST) (13,14) or a special CxGxC-class cystine-knot search pattern (C Paszty, unpublished) (15) designed to identify new families of cystine-knot proteins.…”

mentioning

confidence: 99%

Sclerostin: A gem from the genome leads to bone-building antibodies

Pászty

Turner

Robinson

2010

Journal of Bone and Mineral Research

113

View full text Add to dashboard Cite

Discovery of SclerostinG enomics technologies and DNA sequencing have had a transformative impact on biological research, giving us unprecedented access to the genomes of numerous organisms and ushering in such new fields as systems biology (1) and, more recently, synthetic biology. (2,3) In the 1990s, the advent of highthroughput sequencing spurred application of this powerful new technology to the challenging endeavor of trying to understand the genetic basis of various inherited human diseases. One such disease was sclerosteosis, a very rare, recessively inherited highbone-mass disorder that was thought to be caused primarily by excessive osteoblast-mediated bone formation rather than by defective osteoclast-mediated bone resorption. (4,5) Within the realm of inherited high-bone-mass disorders, (6) it was the hope for a discovery in the area of osteoblast biology that made sclerosteosis particularly interesting.Indeed, the identification of new bone-building pathways that might yield novel anabolic agents had been a long-standing goal in bone biology, with hopes for therapeutic application in fracture healing, orthopedic procedures, and low-bone-mass conditions such as osteoporosis. Against this backdrop came the exciting news, independently from Mary Brunkow's group at Celltech R&D, Inc., (7,8) and from Wim Van Hul's group at the University of Antwerp, (9) that sclerosteosis was caused by mutations in a single gene (SOST) encoding a novel secreted protein. Because these were inactivating mutations, it was clear that this protein, aptly given the name sclerostin, functioned either directly or indirectly as an inhibitor of bone formation. During this same general time period, large-scale cDNA/ expressed sequence tag (EST) (10)(11)(12) and genomic DNA sequencing efforts were being made in academia and industry to rapidly identify new human genes. A novel secreted protein of unknown function, which turned out to be sclerostin, was discovered by computational mining of large DNA sequence databases using either homology-based programs (eg, BLAST) (13,14) or a special CxGxC-class cystine-knot search pattern (C Paszty, unpublished) (15) designed to identify new families of cystine-knot proteins. (16,17) Thus sclerostin emerged during an exciting era of gene discovery that was fueled, in part, by the development of important genomics technologies and the advent of high-throughput DNA sequencing.Similar to sclerostin inactivation in humans, mice with a targeted deletion of the sclerostin gene (SOST knockout mice) were found to have high bone mass, demonstrating evolutionary conservation of sclerostin's function as a negative regulator of bone formation. (18) Analysis of bones from these mice revealed that bone formation was markedly increased on each of the key skeletal surfaces where new bone is normally formed (surface of trabecular bone and internal and external surfaces of cortical bone). Consistent with the increases in bone formation and bone mass, robust increases in bone strength also were found in these anima...

show abstract

3,400 new expressed sequence tags identify diversity of transcripts in human brain

Cited by 282 publications

References 27 publications

Molecular cloning of a widely expressed human homologue for the Drosophila trp gene

Molecular cloning of a widely expressed human homologue for the Drosophila trp gene

Gene Expression Profile of Human Bone Marrow Stromal Cells: High-Throughput Expressed Sequence Tag Sequencing Analysis

Sclerostin: A gem from the genome leads to bone-building antibodies

Contact Info

Product

Resources

About