A transcript finishing initiative for closing gaps in the human transcriptome

Mari Cleide Sogayar, Anamaria A. Camargo, Fabiana Bettoni, Dirce Maria Carraro, Lilian C. Pires, Raphael B. Parmigiani, Elisa N. Ferreira, E. de Sá Moreira, D. Do Rosário, O. Latorre, J. G. Simpson, Luciana Oliveira Cruz, Theri Leica Degaki, Fernanda Festa, Katlin B. Massirer, Fernando Camargo Filho, Luiz Paulo Camargo, Marco A.V. Cunha, Sandro J. De Souza, Maria Faria Junior & 76 others Silvana Giuliatti, Leonardo Kopp, Paulo S.L. de Oliveira, Paulo B. Paiva, Anderson A. Pereira, Daniel G. Pinheiro, Renato D. Puga, Jorge Estefano S. de Souza, Dulcineia M. Albuquerque, Luís E.C. Andrade, Gilson S. Baia, Marcelo R.S. Briones, Ana M.S. Cavaleiro-Luna, Janete M. Cerutti, Fernando F. Costa, Eugenia Costanzi-Strauss, Enilza M. Espreafico, Adriana C. Ferrasi, Emer S. Ferro, Joelma R.F. Furchi, Daniel Giannella-Neto, Gustavo H. Goldman, Maria H.S. Goldman, Arthur Gruber, Gustavo S. Guimarães, Christine Hackel, Flavio Henrique-Silva, Edna T. Kimura, Suzana G. Leoni, Cláudia Macedo, Bettina Malnic, Carina V. Manzini B., Suely K.N. Marie, Nilce M. Martinez-Rossi, Marcelo Menossi, Elisabete C. Miracca, Maria A. Nagai, Francisco G. Nobrega, Marina P. Nobrega, Sueli M. Oba-Shinjo, Márika K. Oliveira, Guilherme M. Orbana, Audrey Y. Otsuka, Maria L. Paço-Larson, Beatriz M.C. Paixão, Jose R.C. Pandolfi, Maria I.M.C. Pardini, Maria R. Passos Bueno, Geraldo A.S. Passos A.S., Joao B. Pesquero, Juliana G. Pessoa, Paula Rahal, Cláudia A. Rainho, Caroline P. Reis, Tatiana I. Ricca, Vanderlei Rodrigues, Silvia R. Rogatto, Camila M. Romano, Janaína G. Romeiro, Antonio Rossi, Renata G. Sá, Magaly M. Sales, Simone C. Sant'Anna, Patría L. Santarosa, Fernando Segato, Wilson A. Silva, Ismael D.C.G. Silva, Neusa P. Silva, Andrea Soares-Costa, Maria F. Sonati, Bryan E. Strauss, Eloiza H. Tajara, Sandro R. Valentini, Fabiola E. Villanova, Laura S. Ward, Dalila L. Zanette

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

Original languageEnglish (US)
Pages (from-to)1413-1423
Number of pages11
JournalGenome research
Volume14
Issue number7
DOIs
StatePublished - Jul 1 2004

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Transcriptome
Expressed Sequence Tags
Complementary DNA
Genes
Exons
Protein Isoforms
Software
Databases
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Sogayar, M. C., Camargo, A. A., Bettoni, F., Carraro, D. M., Pires, L. C., Parmigiani, R. B., ... Zanette, D. L. (2004). A transcript finishing initiative for closing gaps in the human transcriptome. Genome research, 14(7), 1413-1423. https://doi.org/10.1101/gr.2111304
Sogayar, Mari Cleide ; Camargo, Anamaria A. ; Bettoni, Fabiana ; Carraro, Dirce Maria ; Pires, Lilian C. ; Parmigiani, Raphael B. ; Ferreira, Elisa N. ; de Sá Moreira, E. ; Do Rosário, D. ; Latorre, O. ; Simpson, J. G. ; Cruz, Luciana Oliveira ; Degaki, Theri Leica ; Festa, Fernanda ; Massirer, Katlin B. ; Filho, Fernando Camargo ; Camargo, Luiz Paulo ; Cunha, Marco A.V. ; De Souza, Sandro J. ; Junior, Maria Faria ; Giuliatti, Silvana ; Kopp, Leonardo ; de Oliveira, Paulo S.L. ; Paiva, Paulo B. ; Pereira, Anderson A. ; Pinheiro, Daniel G. ; Puga, Renato D. ; de Souza, Jorge Estefano S. ; Albuquerque, Dulcineia M. ; Andrade, Luís E.C. ; Baia, Gilson S. ; Briones, Marcelo R.S. ; Cavaleiro-Luna, Ana M.S. ; Cerutti, Janete M. ; Costa, Fernando F. ; Costanzi-Strauss, Eugenia ; Espreafico, Enilza M. ; Ferrasi, Adriana C. ; Ferro, Emer S. ; Furchi, Joelma R.F. ; Giannella-Neto, Daniel ; Goldman, Gustavo H. ; Goldman, Maria H.S. ; Gruber, Arthur ; Guimarães, Gustavo S. ; Hackel, Christine ; Henrique-Silva, Flavio ; Kimura, Edna T. ; Leoni, Suzana G. ; Macedo, Cláudia ; Malnic, Bettina ; Manzini B., Carina V. ; Marie, Suely K.N. ; Martinez-Rossi, Nilce M. ; Menossi, Marcelo ; Miracca, Elisabete C. ; Nagai, Maria A. ; Nobrega, Francisco G. ; Nobrega, Marina P. ; Oba-Shinjo, Sueli M. ; Oliveira, Márika K. ; Orbana, Guilherme M. ; Otsuka, Audrey Y. ; Paço-Larson, Maria L. ; Paixão, Beatriz M.C. ; Pandolfi, Jose R.C. ; Pardini, Maria I.M.C. ; Passos Bueno, Maria R. ; Passos A.S., Geraldo A.S. ; Pesquero, Joao B. ; Pessoa, Juliana G. ; Rahal, Paula ; Rainho, Cláudia A. ; Reis, Caroline P. ; Ricca, Tatiana I. ; Rodrigues, Vanderlei ; Rogatto, Silvia R. ; Romano, Camila M. ; Romeiro, Janaína G. ; Rossi, Antonio ; Sá, Renata G. ; Sales, Magaly M. ; Sant'Anna, Simone C. ; Santarosa, Patría L. ; Segato, Fernando ; Silva, Wilson A. ; Silva, Ismael D.C.G. ; Silva, Neusa P. ; Soares-Costa, Andrea ; Sonati, Maria F. ; Strauss, Bryan E. ; Tajara, Eloiza H. ; Valentini, Sandro R. ; Villanova, Fabiola E. ; Ward, Laura S. ; Zanette, Dalila L. / A transcript finishing initiative for closing gaps in the human transcriptome. In: Genome research. 2004 ; Vol. 14, No. 7. pp. 1413-1423.
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abstract = "We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1{\%} was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21{\%} of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2{\%} of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.",
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Sogayar, MC, Camargo, AA, Bettoni, F, Carraro, DM, Pires, LC, Parmigiani, RB, Ferreira, EN, de Sá Moreira, E, Do Rosário, D, Latorre, O, Simpson, JG, Cruz, LO, Degaki, TL, Festa, F, Massirer, KB, Filho, FC, Camargo, LP, Cunha, MAV, De Souza, SJ, Junior, MF, Giuliatti, S, Kopp, L, de Oliveira, PSL, Paiva, PB, Pereira, AA, Pinheiro, DG, Puga, RD, de Souza, JES, Albuquerque, DM, Andrade, LEC, Baia, GS, Briones, MRS, Cavaleiro-Luna, AMS, Cerutti, JM, Costa, FF, Costanzi-Strauss, E, Espreafico, EM, Ferrasi, AC, Ferro, ES, Furchi, JRF, Giannella-Neto, D, Goldman, GH, Goldman, MHS, Gruber, A, Guimarães, GS, Hackel, C, Henrique-Silva, F, Kimura, ET, Leoni, SG, Macedo, C, Malnic, B, Manzini B., CV, Marie, SKN, Martinez-Rossi, NM, Menossi, M, Miracca, EC, Nagai, MA, Nobrega, FG, Nobrega, MP, Oba-Shinjo, SM, Oliveira, MK, Orbana, GM, Otsuka, AY, Paço-Larson, ML, Paixão, BMC, Pandolfi, JRC, Pardini, MIMC, Passos Bueno, MR, Passos A.S., GAS, Pesquero, JB, Pessoa, JG, Rahal, P, Rainho, CA, Reis, CP, Ricca, TI, Rodrigues, V, Rogatto, SR, Romano, CM, Romeiro, JG, Rossi, A, Sá, RG, Sales, MM, Sant'Anna, SC, Santarosa, PL, Segato, F, Silva, WA, Silva, IDCG, Silva, NP, Soares-Costa, A, Sonati, MF, Strauss, BE, Tajara, EH, Valentini, SR, Villanova, FE, Ward, LS & Zanette, DL 2004, 'A transcript finishing initiative for closing gaps in the human transcriptome', Genome research, vol. 14, no. 7, pp. 1413-1423. https://doi.org/10.1101/gr.2111304

A transcript finishing initiative for closing gaps in the human transcriptome. / Sogayar, Mari Cleide; Camargo, Anamaria A.; Bettoni, Fabiana; Carraro, Dirce Maria; Pires, Lilian C.; Parmigiani, Raphael B.; Ferreira, Elisa N.; de Sá Moreira, E.; Do Rosário, D.; Latorre, O.; Simpson, J. G.; Cruz, Luciana Oliveira; Degaki, Theri Leica; Festa, Fernanda; Massirer, Katlin B.; Filho, Fernando Camargo; Camargo, Luiz Paulo; Cunha, Marco A.V.; De Souza, Sandro J.; Junior, Maria Faria; Giuliatti, Silvana; Kopp, Leonardo; de Oliveira, Paulo S.L.; Paiva, Paulo B.; Pereira, Anderson A.; Pinheiro, Daniel G.; Puga, Renato D.; de Souza, Jorge Estefano S.; Albuquerque, Dulcineia M.; Andrade, Luís E.C.; Baia, Gilson S.; Briones, Marcelo R.S.; Cavaleiro-Luna, Ana M.S.; Cerutti, Janete M.; Costa, Fernando F.; Costanzi-Strauss, Eugenia; Espreafico, Enilza M.; Ferrasi, Adriana C.; Ferro, Emer S.; Furchi, Joelma R.F.; Giannella-Neto, Daniel; Goldman, Gustavo H.; Goldman, Maria H.S.; Gruber, Arthur; Guimarães, Gustavo S.; Hackel, Christine; Henrique-Silva, Flavio; Kimura, Edna T.; Leoni, Suzana G.; Macedo, Cláudia; Malnic, Bettina; Manzini B., Carina V.; Marie, Suely K.N.; Martinez-Rossi, Nilce M.; Menossi, Marcelo; Miracca, Elisabete C.; Nagai, Maria A.; Nobrega, Francisco G.; Nobrega, Marina P.; Oba-Shinjo, Sueli M.; Oliveira, Márika K.; Orbana, Guilherme M.; Otsuka, Audrey Y.; Paço-Larson, Maria L.; Paixão, Beatriz M.C.; Pandolfi, Jose R.C.; Pardini, Maria I.M.C.; Passos Bueno, Maria R.; Passos A.S., Geraldo A.S.; Pesquero, Joao B.; Pessoa, Juliana G.; Rahal, Paula; Rainho, Cláudia A.; Reis, Caroline P.; Ricca, Tatiana I.; Rodrigues, Vanderlei; Rogatto, Silvia R.; Romano, Camila M.; Romeiro, Janaína G.; Rossi, Antonio; Sá, Renata G.; Sales, Magaly M.; Sant'Anna, Simone C.; Santarosa, Patría L.; Segato, Fernando; Silva, Wilson A.; Silva, Ismael D.C.G.; Silva, Neusa P.; Soares-Costa, Andrea; Sonati, Maria F.; Strauss, Bryan E.; Tajara, Eloiza H.; Valentini, Sandro R.; Villanova, Fabiola E.; Ward, Laura S.; Zanette, Dalila L.

In: Genome research, Vol. 14, No. 7, 01.07.2004, p. 1413-1423.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A transcript finishing initiative for closing gaps in the human transcriptome

AU - Sogayar, Mari Cleide

AU - Camargo, Anamaria A.

AU - Bettoni, Fabiana

AU - Carraro, Dirce Maria

AU - Pires, Lilian C.

AU - Parmigiani, Raphael B.

AU - Ferreira, Elisa N.

AU - de Sá Moreira, E.

AU - Do Rosário, D.

AU - Latorre, O.

AU - Simpson, J. G.

AU - Cruz, Luciana Oliveira

AU - Degaki, Theri Leica

AU - Festa, Fernanda

AU - Massirer, Katlin B.

AU - Filho, Fernando Camargo

AU - Camargo, Luiz Paulo

AU - Cunha, Marco A.V.

AU - De Souza, Sandro J.

AU - Junior, Maria Faria

AU - Giuliatti, Silvana

AU - Kopp, Leonardo

AU - de Oliveira, Paulo S.L.

AU - Paiva, Paulo B.

AU - Pereira, Anderson A.

AU - Pinheiro, Daniel G.

AU - Puga, Renato D.

AU - de Souza, Jorge Estefano S.

AU - Albuquerque, Dulcineia M.

AU - Andrade, Luís E.C.

AU - Baia, Gilson S.

AU - Briones, Marcelo R.S.

AU - Cavaleiro-Luna, Ana M.S.

AU - Cerutti, Janete M.

AU - Costa, Fernando F.

AU - Costanzi-Strauss, Eugenia

AU - Espreafico, Enilza M.

AU - Ferrasi, Adriana C.

AU - Ferro, Emer S.

AU - Furchi, Joelma R.F.

AU - Giannella-Neto, Daniel

AU - Goldman, Gustavo H.

AU - Goldman, Maria H.S.

AU - Gruber, Arthur

AU - Guimarães, Gustavo S.

AU - Hackel, Christine

AU - Henrique-Silva, Flavio

AU - Kimura, Edna T.

AU - Leoni, Suzana G.

AU - Macedo, Cláudia

AU - Malnic, Bettina

AU - Manzini B., Carina V.

AU - Marie, Suely K.N.

AU - Martinez-Rossi, Nilce M.

AU - Menossi, Marcelo

AU - Miracca, Elisabete C.

AU - Nagai, Maria A.

AU - Nobrega, Francisco G.

AU - Nobrega, Marina P.

AU - Oba-Shinjo, Sueli M.

AU - Oliveira, Márika K.

AU - Orbana, Guilherme M.

AU - Otsuka, Audrey Y.

AU - Paço-Larson, Maria L.

AU - Paixão, Beatriz M.C.

AU - Pandolfi, Jose R.C.

AU - Pardini, Maria I.M.C.

AU - Passos Bueno, Maria R.

AU - Passos A.S., Geraldo A.S.

AU - Pesquero, Joao B.

AU - Pessoa, Juliana G.

AU - Rahal, Paula

AU - Rainho, Cláudia A.

AU - Reis, Caroline P.

AU - Ricca, Tatiana I.

AU - Rodrigues, Vanderlei

AU - Rogatto, Silvia R.

AU - Romano, Camila M.

AU - Romeiro, Janaína G.

AU - Rossi, Antonio

AU - Sá, Renata G.

AU - Sales, Magaly M.

AU - Sant'Anna, Simone C.

AU - Santarosa, Patría L.

AU - Segato, Fernando

AU - Silva, Wilson A.

AU - Silva, Ismael D.C.G.

AU - Silva, Neusa P.

AU - Soares-Costa, Andrea

AU - Sonati, Maria F.

AU - Strauss, Bryan E.

AU - Tajara, Eloiza H.

AU - Valentini, Sandro R.

AU - Villanova, Fabiola E.

AU - Ward, Laura S.

AU - Zanette, Dalila L.

PY - 2004/7/1

Y1 - 2004/7/1

N2 - We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

AB - We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

UR - http://www.scopus.com/inward/record.url?scp=3543131342&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=3543131342&partnerID=8YFLogxK

U2 - 10.1101/gr.2111304

DO - 10.1101/gr.2111304

M3 - Article

VL - 14

SP - 1413

EP - 1423

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 7

ER -

Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB et al. A transcript finishing initiative for closing gaps in the human transcriptome. Genome research. 2004 Jul 1;14(7):1413-1423. https://doi.org/10.1101/gr.2111304