Molecular characterization of Drosophila NELF

Wu, Chwen Huey; Lee, Chanhyo; Fan, Ruopeng; Smith, Meghan J.; Yamaguchi, Yuki; Handa, Hiroshi; Gilmour, David S.

doi:10.1093/nar/gki274

Cited by 47 publications

(41 citation statements)

References 38 publications

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“…Previous in vivo studies in human and Drosophila systems corroborate the RNAPII-stalling function of NELF in gene regulation (Wu et al, , 2005aAiyar et al, 2004).…”

Section: Discussionmentioning

confidence: 60%

Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells

et al. 2006

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“…Previous in vivo studies in human and Drosophila systems corroborate the RNAPII-stalling function of NELF in gene regulation (Wu et al, , 2005aAiyar et al, 2004).…”

Section: Discussionmentioning

confidence: 60%

Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells

et al. 2006

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“…We observed in HIV-1-infected cells expressing RON that there was more NELF, DSIF, and Pcf11 associated with the LTR, suggesting that these factors are participating in establishing RON-dependent Pol II pausing and premature termination. NELF and DSIF are associated with the Pol II complex and inhibit transcription elongation by pausing Pol II (42,(47)(48)(49). The inhibitory action of these two proteins is overcome by P-TEFb (42,50).…”

Section: Discussionmentioning

confidence: 99%

The Receptor Tyrosine Kinase RON Represses HIV-1 Transcription by Targeting RNA Polymerase II Processivity

Klatt

Zhang

Hankey

et al. 2008

The Journal of Immunology

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Efficient HIV-1 transcription requires the induction of cellular transcription factors, such as NF-κB, and the viral factor Tat, which through the recruitment of P-TEFb enhances processive transcription. However, whether cellular signals repress HIV-1 transcription to establish proviral latency has not been well studied. Previously, it has been shown that the receptor tyrosine kinase RON inhibits HIV transcription. To gain insights into the biochemical mechanisms by which RON inhibits transcription we examined the binding of transcription factors to the HIV provirus long terminal repeat using chromatin immunoprecipitation. RON expression decreased basal levels of NF-κB and RNA polymerase II (Pol II) binding to the HIV provirus long terminal repeat but did not prevent the induction of these complexes following treatment with cytokines. However, RON did decrease efficient transcription elongation because reduced RNA Pol II was associated with HIV-1 genomic sequences downstream of the transcriptional start site. There was a correlation between RON expression and increased binding of factors that negatively regulate transcription elongation, NELF, Spt5, and Pcf11. Furthermore, the ability of RON to inhibit HIV-1 transcription was sensitive to a histone deacetylase inhibitor and was associated with nucleosome remodeling. These results indicate that RON represses HIV transcription at multiple transcriptional check points including initiation, elongation and chromatin organization and are the first studies to show that cellular signaling pathways target Pol II pausing to repress gene expression.

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“…Whsc2 is a mammalian homolog of the Drosophila NELFA gene (Wright et al, 1999;Wu et al, 2005), which complexes with other Nelf proteins and can repress transcription by pausing RNA Polymerase II elongation (Wu et al, 2005). In Drosophila and mammals, it has been reported to be expressed ubiquitously (Wright et al, Yamaguchi et al, 1999;Mariotti et al, 2000).…”

Section: Genes With Spotted Expression Patterns (Spot-in-colony Pattern)mentioning

confidence: 99%

An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells

Carter

Stagg

Falco

et al. 2008

Gene Expression Patterns

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We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out highthroughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures. KeywordsES cells; EC cells; pluripotent stem cells; heterogeneous gene expression; homogeneous gene expression; Zscan4; Pou5f1; Oct4; Oct3/4; Krt8; EndoA; Whsc2; Nelfa; Rhox9; Zfp42; Rex1; Rest; Zfp42; Rex1; Rest; Atf4; Pa2g4; E2f2; Nanog; Dppa3; Pgc7; Stella; Esrrb; Fscn1 &Corresponding author: Minoru S.H. Ko, M.D., Ph.D., Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, Triad Technology Center, suite 3000, 333 Cassell Drive, Baltimore, MD 21224, USA, Phone: (410) 558-8359; Fax: (410) 558-8331, E-mail: kom@mail.nih.gov. # Current Address: Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut, 06269 $ Current Address: Stem Cell and Drug Discovery Institute, Kyoto 600-8813, Japan @ Current Address: Nagoya University Graduate School of Medicine, Aichi 466-8550, Japan * Equal contribution Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. (Falco et al., 2007). We suspect the existence of other transcription-regulating genes that show similar expression patterns. NIH Public AccessThe goals of this study are to find additional evidence for heterogeneous cell populations within undifferentiated ES cell cultures by identifying such genes and characterizing their expression patte...

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Molecular characterization of Drosophila NELF

Cited by 47 publications

References 38 publications

Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells

Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells

The Receptor Tyrosine Kinase RON Represses HIV-1 Transcription by Targeting RNA Polymerase II Processivity

An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells

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