Guolin Zhou - Academia.edu (original) (raw)

Papers by Guolin Zhou

Research paper thumbnail of Silencing of B Cell Receptor Signals in Human Naive B Cells

In an attempt to repeat the FACS analyses of surface antigens that were described as diff erentia... more In an attempt to repeat the FACS analyses of surface antigens that were described as diff erentially expressed between naive and memory B cells in our paper, we observed no or only minor diff erences for most of these molecules. A systematic reanalysis of the primary data in the laboratories of R. Küppers and M. Müschen revealed that incorrect FACS instrument compensations were responsible for the discrepancy (double stainings were performed, laboratory of M. Müschen).

Research paper thumbnail of Correct Identification of Genes from Serial Analysis of Gene Expression Tag Sequences

Genomics, 2002

When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to... more When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to overcome the life-threatening challenge? To address this issue, we performed a genome-wide transcriptome analysis in EPO (erythropoietin) deprivation-induced apoptotic erythroid cells using the SAGE method. The results show that the transcript contents for the majority of the genes remain unchanged in the apoptotic cells, including the apoptotic genes and the heat shock genes. Of the small number of genes with an altered expression, they are mainly associated with cellular structure. Our study reveals that there is no genetic reprogramming for the transcriptional machinery in the apoptotic genome. Apoptosis, as defined by programmed cell death, is not a crisis but a peaceful physiological process.

Research paper thumbnail of Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags

Proceedings of The National Academy of Sciences, 2002

The number of genes in the human genome is still a controversial issue. Whereas most of the genes... more The number of genes in the human genome is still a controversial issue. Whereas most of the genes in the human genome are said to have been physically or computationally identified, many short cDNA sequences identified as tags by use of serial analysis of gene expression (SAGE) do not match these genes. By performing experimental verification of more than 1,000 SAGE tags and analyzing 4,285,923 SAGE tags of human origin in the current SAGE database, we examined the nature of the unmatched SAGE tags. Our study shows that most of the unmatched SAGE tags are truly novel SAGE tags that originated from novel transcripts not yet identified in the human genome, including alternatively spliced transcripts from known genes and potential novel genes. Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods.

Research paper thumbnail of High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3? complementary DNAs

Genes Chromosomes & Cancer, 2002

Serial analysis of gene expression (SAGE) is a powerful technique for genome-wide analysis of gen... more Serial analysis of gene expression (SAGE) is a powerful technique for genome-wide analysis of gene expression. However, two-thirds of SAGE tags cannot be used directly for gene identification for two reasons. First, many SAGE tags match several known expressed sequences, owing to the short length of SAGE tag sequences. Second, many SAGE tags do not match any known expressed sequences, presumably because the sequences corresponding to these SAGE tags have not been identified. These two problems can be solved by extension of the SAGE tags into 3′ complementary DNAs (cDNAs) by use of the GLGI technique (generation of longer cDNA fragments from SAGE tags for gene identification). We have improved the original GLGI technique into a high-throughput procedure for simultaneous conversion of a large number of SAGE tags into corresponding 3′ cDNAs. The whole process is simple, rapid, low-cost, and highly efficient, as shown by our use of this procedure for analyzing hundreds of SAGE tags. In addition to identifying the correct gene for SAGE tags with multiple matches, GLGI can be used for large-scale identification of novel genes by converting novel SAGE tags into 3′ cDNAs. Applying this high-throughput procedure should accelerate the rate of gene identification significantly in the human and other eukaryotic genomes. © 2002 Wiley-Liss, Inc.

Research paper thumbnail of Over 20% of human transcripts might form sense-antisense pairs

Nucleic Acids Research, 2004

The major challenge to identifying natural senseantisense (SA) transcripts from public databases ... more The major challenge to identifying natural senseantisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.

Research paper thumbnail of The pattern of gene expression in human CD15+ myeloid progenitor cells

Proceedings of The National Academy of Sciences, 2001

We performed a genome-wide analysis of gene expression in primary human CD15 ؉ myeloid progenitor... more We performed a genome-wide analysis of gene expression in primary human CD15 ؉ myeloid progenitor cells. By using the serial analysis of gene expression (SAGE) technique, we obtained quantitative information for the expression of 37,519 unique SAGE-tag sequences. Of these unique tags, (i) 25% were detected at high and intermediate levels, whereas 75% were present as single copies, (ii) 53% of the tags matched known expressed sequences, 34% of which were matched to more than one known expressed sequence, and (iii) 47% of the tags had no matches and represent potentially novel genes. The correct genes were confirmed by application of the generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) technique for high-copy tags with multiple matches. A set of genes known to be important in myeloid differentiation were expressed at various levels and used different spliced forms. This study provides a normal baseline for comparison of gene expression in myeloid diseases. The strategy of using SAGE and GLGI techniques in this study has broad applications to the genome-wide identification of expressed genes.

Research paper thumbnail of Silencing of B Cell Receptor Signals in Human Naive B Cells

In an attempt to repeat the FACS analyses of surface antigens that were described as diff erentia... more In an attempt to repeat the FACS analyses of surface antigens that were described as diff erentially expressed between naive and memory B cells in our paper, we observed no or only minor diff erences for most of these molecules. A systematic reanalysis of the primary data in the laboratories of R. Küppers and M. Müschen revealed that incorrect FACS instrument compensations were responsible for the discrepancy (double stainings were performed, laboratory of M. Müschen).

Research paper thumbnail of Correct Identification of Genes from Serial Analysis of Gene Expression Tag Sequences

Genomics, 2002

When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to... more When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to overcome the life-threatening challenge? To address this issue, we performed a genome-wide transcriptome analysis in EPO (erythropoietin) deprivation-induced apoptotic erythroid cells using the SAGE method. The results show that the transcript contents for the majority of the genes remain unchanged in the apoptotic cells, including the apoptotic genes and the heat shock genes. Of the small number of genes with an altered expression, they are mainly associated with cellular structure. Our study reveals that there is no genetic reprogramming for the transcriptional machinery in the apoptotic genome. Apoptosis, as defined by programmed cell death, is not a crisis but a peaceful physiological process.

Research paper thumbnail of Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags

Proceedings of The National Academy of Sciences, 2002

The number of genes in the human genome is still a controversial issue. Whereas most of the genes... more The number of genes in the human genome is still a controversial issue. Whereas most of the genes in the human genome are said to have been physically or computationally identified, many short cDNA sequences identified as tags by use of serial analysis of gene expression (SAGE) do not match these genes. By performing experimental verification of more than 1,000 SAGE tags and analyzing 4,285,923 SAGE tags of human origin in the current SAGE database, we examined the nature of the unmatched SAGE tags. Our study shows that most of the unmatched SAGE tags are truly novel SAGE tags that originated from novel transcripts not yet identified in the human genome, including alternatively spliced transcripts from known genes and potential novel genes. Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods.

Research paper thumbnail of High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3? complementary DNAs

Genes Chromosomes & Cancer, 2002

Serial analysis of gene expression (SAGE) is a powerful technique for genome-wide analysis of gen... more Serial analysis of gene expression (SAGE) is a powerful technique for genome-wide analysis of gene expression. However, two-thirds of SAGE tags cannot be used directly for gene identification for two reasons. First, many SAGE tags match several known expressed sequences, owing to the short length of SAGE tag sequences. Second, many SAGE tags do not match any known expressed sequences, presumably because the sequences corresponding to these SAGE tags have not been identified. These two problems can be solved by extension of the SAGE tags into 3′ complementary DNAs (cDNAs) by use of the GLGI technique (generation of longer cDNA fragments from SAGE tags for gene identification). We have improved the original GLGI technique into a high-throughput procedure for simultaneous conversion of a large number of SAGE tags into corresponding 3′ cDNAs. The whole process is simple, rapid, low-cost, and highly efficient, as shown by our use of this procedure for analyzing hundreds of SAGE tags. In addition to identifying the correct gene for SAGE tags with multiple matches, GLGI can be used for large-scale identification of novel genes by converting novel SAGE tags into 3′ cDNAs. Applying this high-throughput procedure should accelerate the rate of gene identification significantly in the human and other eukaryotic genomes. © 2002 Wiley-Liss, Inc.

Research paper thumbnail of Over 20% of human transcripts might form sense-antisense pairs

Nucleic Acids Research, 2004

The major challenge to identifying natural senseantisense (SA) transcripts from public databases ... more The major challenge to identifying natural senseantisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.

Research paper thumbnail of The pattern of gene expression in human CD15+ myeloid progenitor cells

Proceedings of The National Academy of Sciences, 2001

We performed a genome-wide analysis of gene expression in primary human CD15 ؉ myeloid progenitor... more We performed a genome-wide analysis of gene expression in primary human CD15 ؉ myeloid progenitor cells. By using the serial analysis of gene expression (SAGE) technique, we obtained quantitative information for the expression of 37,519 unique SAGE-tag sequences. Of these unique tags, (i) 25% were detected at high and intermediate levels, whereas 75% were present as single copies, (ii) 53% of the tags matched known expressed sequences, 34% of which were matched to more than one known expressed sequence, and (iii) 47% of the tags had no matches and represent potentially novel genes. The correct genes were confirmed by application of the generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) technique for high-copy tags with multiple matches. A set of genes known to be important in myeloid differentiation were expressed at various levels and used different spliced forms. This study provides a normal baseline for comparison of gene expression in myeloid diseases. The strategy of using SAGE and GLGI techniques in this study has broad applications to the genome-wide identification of expressed genes.