[16] A modified method for the display of 3′-end restriction fragments of cDNAs: Molecular profiling of gene expression in neutrophils

Subrahmanyam, Y. V. B. K.; Baskaran, Namadev; Newburger, Peter E.; Weissman, Sherman M.

doi:10.1016/s0076-6879(99)03018-9

Cited by 23 publications

(23 citation statements)

References 20 publications

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“…17 Human hematopoietic stem and progenitor cell populations were isolated from peripheral blood stem cells (mobilized by granulocyte colonystimulating factor), and monocytes were prepared from peripheral blood, as previously described. [18][19][20] The University of Massachusetts Medical School and Yale University human subjects committees approved procedures and consent forms at their respective sites.…”

Section: Human Leukocyte Isolationmentioning

confidence: 99%

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

Zhang

Zheng²,

Padden

et al. 2009

Blood

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329

344

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We have identified an intergenic transcriptional activity that is located between the human HOXA1 and HOXA2 genes, shows myeloid-specific expression, and is upregulated during granulocytic differentiation. The novel gene, termed HOTAIRM1 (HOX antisense intergenic RNA myeloid 1), is transcribed antisense to the HOXA genes and originates from the same CpG island that embeds the start site of IntroductionHuman HOX gene clusters are known for the prevalence of intergenic transcription between coding genic members. 1 Similar activity has also been observed in other developmentally important or tissue-specific gene loci, such as those containing the human beta globin genes, cardiac myosin heavy chain genes, and the interleukin-4 (IL-4)/IL-13 gene cluster. [2][3][4] Extensive HOX gene cluster intergenic transcripts have been described largely as noncoding RNAs (ncRNAs), including both short microRNA (miRNA) species and long ncRNAs that are antisense to their canonical HOX neighbors. Well-defined HOX region ncRNAs include the mir-10 and mir-196 paralogs, bithoraxoid ncRNAs of the Drosophila bithorax complex, and human HOX antisense intergenic RNA (HOTAIR). [5][6][7] Intergenic regions have been proposed as locations for novel radiational and reorganizing changes that have occurred in the evolution of HOX gene clusters, which are relatively constrained in structure in the higher vertebrates. 5,8 Several recent studies have focused on expression of intergenic ncRNAs in the human HOX regions, especially the HOXA cluster, in tumor cell lines, tissues, and fibroblasts from different anatomic origins. All reported unusually active transcription within the intergenic regions, occurring in patterns coordinated with their HOX neighbors. 7,9,10 Intergenic ncRNAs in the HOXA gene cluster were usually associated with CpG islands and their expression accompanied changes in either polycomb group repressive complex binding or methylation of histones, suggesting a pattern of cis modulation of the intergenic transcripts before the activation of adjacent HOX genes. However, the HOTAIR transcript, located between HOXC11 and HOXC12, was found to function in trans to repress a distal group of homologous HOXD genes by demarcating an extended silenced domain through interaction with the polycomb group complex PRC2 histone methyltransferase 7,10,11 De novo genomic transcription mapping has revealed that intergenic ncRNA is possibly the most abundant form of transcriptional output from the genomes of humans and other higher eukaryotic organisms. 12,13 Within the human genome, the majority of intergenic ncRNA are not highly conserved at the sequence level, with long ncRNAs generally less conserved than short miRNAs. Nevertheless, their expression patterns may be conserved among tissues or along developmental axes. 14,15 More importantly, ncRNA function in gene regulation has emerged as an important mechanism in the control of many biologic processes in development and carcinogenesis. 16 In the present study, we have identified intergenic transc...

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Section: Human Leukocyte Isolationmentioning

confidence: 99%

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

Zhang

Zheng²,

Padden

et al. 2009

Blood

Self Cite

329

344

View full text Add to dashboard Cite

show abstract

“…21 All reagents, serum, buffers, and media were free of LPS (less than 0.01 ng/mL by limulus amoebocyte lysate assay [Sigma]). Monocytes were enumerated in neutrophil preparations by flow microfluorometry.…”

Section: Cell Separation and Activation By Bacteriamentioning

confidence: 99%

RNA expression patterns change dramatically in human neutrophils exposed to bacteria

Subrahmanyam

Yamaga

Prashar

et al. 2001

Blood

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123

105

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“…cDNA was then synthesized using a T-7 Sal-Oligo d(T) 32 primer as described previously. 8,18 The double-stranded cDNA was digested with 1 of 9 different restriction enzymes (ApaI, BglII, BamHI, EagI, EcoRI, HindIII, XbaI, KpnI, and SphI) and ligated to Y-shaped adaptors with a complementary overhang. DNA fragments were then amplified by PCR as described previously.…”

Section: Rna Isolation and Differential Displaymentioning

confidence: 99%

“…DNA fragments were then amplified by PCR as described previously. 8,18 PCR products were separated on a sequencing gel of 6% polyacrylamide with 7 M urea. The gel was dried and exposed to x-ray film.…”

Section: Rna Isolation and Differential Displaymentioning

confidence: 99%

“…We have used a modified polymerase chain reaction (PCR)-based cDNA differential display (DD) method in which single restriction fragments derived from the 3Ј end of cDNAs are separated on a sequencing gel. 8,9 Bands from the gel can be identified initially by sequencing, but then comparison of patterns from different samples can be made without further sequencing. This sensitive and reproducible method detects, in principle, most cDNAs regardless of whether they are represented in existing databases.…”

Section: Introductionmentioning

confidence: 99%

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Genomic and proteomic analysis of the myeloid differentiation program

Zheng

Wang

Yamaga

et al. 2001

Blood

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[16] A modified method for the display of 3′-end restriction fragments of cDNAs: Molecular profiling of gene expression in neutrophils

Cited by 23 publications

References 20 publications

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

RNA expression patterns change dramatically in human neutrophils exposed to bacteria

Genomic and proteomic analysis of the myeloid differentiation program

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