The Mouse Gene Encoding the Testis-Specific Isoform of Poly(A) Binding Protein (Pabp2) Is an Expressed Retroposon: Intimations That Gene Expression in Spermatogenic Cells Facilitates the Creation of New Genes

1998 ◽  
Vol 47 (3) ◽  
pp. 275-281 ◽  
Author(s):  
Kenneth C. Kleene ◽  
Evan Mulligan ◽  
Daniel Steiger ◽  
Kevin Donohue ◽  
Mary-Ann Mastrangelo
Keyword(s):  
Gene Expression ◽  
Binding Protein ◽  
Mouse Gene ◽  
Spermatogenic Cells ◽  
Gene Encoding ◽  
New Genes ◽  
The Creation

P VII.20 UV-irradiation induces the expression of a mouse gene encoding a nuclear DNA-binding protein akin to E. coli RecA protein

1997 ◽  
Vol 379 (1) ◽  
pp. S52
Author(s):  
P. Kannouche ◽  
A. Tissier ◽  
G. Pinon-Lataillade ◽  
D.S.F. Biard ◽  
Ph. Mauffrey ◽  
...  
Keyword(s):  
Dna Binding ◽  
Uv Irradiation ◽  
Nuclear Dna ◽  
Binding Protein ◽  
Reca Protein ◽  
Dna Binding Protein ◽  
Mouse Gene ◽  
Gene Encoding ◽  
E Coli

scholarly journals A direct role for C/EBP and the AP-I-binding site in gene expression linked to adipocyte differentiation.

1989 ◽  
Vol 9 (12) ◽  
pp. 5331-5339 ◽  
Author(s):  
R Herrera ◽  
H S Ro ◽  
G S Robinson ◽  
K G Xanthopoulos ◽  
B M Spiegelman
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Adipocyte Differentiation ◽  
Binding Protein ◽  
Point Mutations ◽  
Chloramphenicol Acetyltransferase ◽  
Lipid Binding ◽  
Direct Role ◽  
New Genes ◽  
Chloramphenicol Acetyltransferase Gene

Adipocyte differentiation is accompanied by the transcriptional activation of many new genes, including the gene encoding adipocyte P2 (aP2), an intracellular lipid-binding protein. Using specific deletions and point mutations, we have shown that at least two distinct sequence elements in the aP2 promoter contribute to the expression of the chloramphenicol acetyltransferase gene in chimeric constructions transfected into adipose cells. An AP-I site at -120, shown earlier to bind Jun- and Fos-like proteins, serves as a positive regulator of chloramphenicol acetyltransferase gene expression in adipocytes but is specifically silenced by adjacent upstream sequences in preadipocytes. Sequences upstream of the AP-I site at -140 (termed AE-1) can function as an enhancer in both cell types when linked to a viral promoter but can stimulate expression only in fat cells in the intact aP2 promoter. The AE-1 sequence binds an adipocyte protein identical or very closely related to an enhancer-binding protein (C/EBP) that has been previously implicated in the regulation of several liver-specific genes. A functional role for C/EBP in the regulation of the aP2 gene is indicated by the facts that C/EBP mRNA is induced during adipocyte differentiation and the aP2 promoter is transactivated by cotransfection of a C/EBP expression vector into preadipose cells. These results indicate that sequences that bind C/EBP and the Fos-Jun complex play major roles in the expression of the aP2 gene during adipocyte differentiation and demonstrate that C/EBP can directly regulate cellular gene expression.

scholarly journals Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome

2019 ◽  
Author(s):  
Jason Talkish ◽  
Haller Igel ◽  
Rhonda J. Perriman ◽  
Lily Shiue ◽  
Sol Katzman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Isoforms ◽  
Yeast Genome ◽  
Protein Coding ◽  
Coding Sequences ◽  
New Genes ◽  
Eukaryotic Genes ◽  
Non Coding Rnas ◽  
The Creation ◽  
New Protein

AbstractIntrons are a prevalent feature of eukaryotic genomes, yet their origins and contributions to genome function and evolution remain mysterious. In budding yeast, repression of the highly transcribed intron-containing ribosomal protein genes (RPGs) globally increases splicing of non-RPG transcripts through reduced competition for the spliceosome. We show that under these “hungry spliceosome” conditions, splicing occurs at more than 150 previously unannotated locations we call protointrons that do not overlap known introns. Protointrons use a less constrained set of splice sites and branchpoints than standard introns, including in one case AT-AC in place of GT-AG. Protointrons are not conserved in all closely related species, suggesting that most are not under selection. Some are found in non-coding RNAs (e. g. CUTs and SUTs), where they may contribute to the creation of new genes. Others are found across boundaries between noncoding and coding sequences, or within coding sequences, where they offer pathways to the creation of new protein variants, or new regulatory controls for existing genes. We define protointrons as (1) nonconserved intron-like sequences that are (2) infrequently spliced, and importantly (3) are not currently understood to contribute to gene expression or regulation in the way that standard introns function. A very few protointrons in S. cerevisiae challenge this classification by their increased splicing frequency and potential function, consistent with the proposed evolutionary process of “intronization”, whereby new standard introns are created. This snapshot of intron evolution highlights the important role of the spliceosome in the expansion of transcribed genomic sequence space, providing a pathway for the rare events that may lead to the birth of new eukaryotic genes and the refinement of existing gene function.Author SummaryThe protein coding information in eukaryotic genes is broken by intervening sequences called introns that are removed from RNA during transcription by a large protein-RNA complex called the spliceosome. Where introns come from and how the spliceosome contributes to genome evolution are open questions. In this study, we find more than 150 new places in the yeast genome that are recognized by the spliceosome and spliced out as introns. Since they appear to have arisen very recently in evolution by sequence drift and do not appear to contribute to gene expression or its regulation, we call these protointrons. Protointrons are found in both protein-coding and non-coding RNAs and are not efficiently removed by the splicing machinery. Although most protointrons are not conserved, a few are spliced more efficiently, and are located where they might begin to play functional roles in gene expression, as predicted by the proposed process of intronization. The challenge now is to understand how spontaneously appearing splicing events like protointrons might contribute to the creation of new genes, new genetic controls, and new protein isoforms as genomes evolve.

A direct role for C/EBP and the AP-I-binding site in gene expression linked to adipocyte differentiation

1989 ◽  
Vol 9 (12) ◽  
pp. 5331-5339
Author(s):  
R Herrera ◽  
H S Ro ◽  
G S Robinson ◽  
K G Xanthopoulos ◽  
B M Spiegelman
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Adipocyte Differentiation ◽  
Binding Protein ◽  
Point Mutations ◽  
Chloramphenicol Acetyltransferase ◽  
Lipid Binding ◽  
Direct Role ◽  
New Genes ◽  
Chloramphenicol Acetyltransferase Gene

Adipocyte differentiation is accompanied by the transcriptional activation of many new genes, including the gene encoding adipocyte P2 (aP2), an intracellular lipid-binding protein. Using specific deletions and point mutations, we have shown that at least two distinct sequence elements in the aP2 promoter contribute to the expression of the chloramphenicol acetyltransferase gene in chimeric constructions transfected into adipose cells. An AP-I site at -120, shown earlier to bind Jun- and Fos-like proteins, serves as a positive regulator of chloramphenicol acetyltransferase gene expression in adipocytes but is specifically silenced by adjacent upstream sequences in preadipocytes. Sequences upstream of the AP-I site at -140 (termed AE-1) can function as an enhancer in both cell types when linked to a viral promoter but can stimulate expression only in fat cells in the intact aP2 promoter. The AE-1 sequence binds an adipocyte protein identical or very closely related to an enhancer-binding protein (C/EBP) that has been previously implicated in the regulation of several liver-specific genes. A functional role for C/EBP in the regulation of the aP2 gene is indicated by the facts that C/EBP mRNA is induced during adipocyte differentiation and the aP2 promoter is transactivated by cotransfection of a C/EBP expression vector into preadipose cells. These results indicate that sequences that bind C/EBP and the Fos-Jun complex play major roles in the expression of the aP2 gene during adipocyte differentiation and demonstrate that C/EBP can directly regulate cellular gene expression.

Cloning and characterization of the mouse gene encoding mammary-derived growth inhibitor/heart-fatty acid-binding protein

Gene ◽  
1994 ◽  
Vol 147 (2) ◽  
pp. 237-242 ◽  
Author(s):  
Mike Treuner ◽  
Christine A. Kozak ◽  
Daniel Gallahan ◽  
Richard Grosse ◽  
Thomas Müller
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Binding Protein ◽  
Binding Protein ◽  
Growth Inhibitor ◽  
Mouse Gene ◽  
Gene Encoding ◽  
Fatty Acid Binding ◽  
Acid Binding Protein

scholarly journals ArabidopsisHAF2 Gene Encoding TATA-binding Protein (TBP)-associated Factor TAF1, Is Required to Integrate Light Signals to Regulate Gene Expression and Growth

2004 ◽  
Vol 280 (2) ◽  
pp. 1465-1473 ◽  
Author(s):  
Claire Bertrand ◽  
Moussa Benhamed ◽  
You-Fang Li ◽  
Mira Ayadi ◽  
Gaëtan Lemonnier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Protein ◽  
Tata Binding Protein ◽  
Gene Encoding ◽  
Regulate Gene Expression ◽  
Associated Factor ◽  
Light Signals ◽  
Regulate Gene

An Experimental Study of Gene Expressing Profile in Human Myeloma Cell Line RPMI8226 Induced by Thalidomide.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4357-4357
Author(s):  
Mei Zhang ◽  
Ting Liu ◽  
Bingjing Yang ◽  
Pengcheng He ◽  
Mengchang Wang
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Protein Synthesis ◽  
Cell Line ◽  
Cdna Microarray ◽  
Binding Protein ◽  
Expression Profiles ◽  
Myeloma Cell ◽  
Myeloma Cell Line ◽  
Gene Encoding

Abstract Multiple myeloma (MM) is one of malignant plasmacyte neoplasm in hematopietic system. Although nearly 70% patients of myeloma response to chemotherapy, but repeated therapies will induce drug resistance soon and lead to refractory or relapsed myelomas. In recent years, thalidomide is used to treat relapsed and refractory myeloma with satisfied effects and overall therapeutic rate with thalidomide is about 60%. Furthermore, the adverse effects of thalidomide is slight without myelosuppression, hepatotoxicity and renal toxicity. So thalidomide is likely to be a prospective antitumor agent. However, the mechanism of antitumor activity of the agent is still not clear. DNA microarray technology has provided us a very useful method to detect simultaneously the expression pattern of thousands of genes for investigating the molecular antitumor mechanism of thalidomide. To investigate the genes expression profiles of multiple myeloma cell line RPMI8226 treated with thalidomide, cDNA microarray were used to detect thousands of gene expression in a chip. Two cDNA probes were prepared through reverse transcription from mRNA of RPMI8226 cells with or without thalidomide treatment. The probes were labled with Cy3 and Cy5 fluorescence dyes individually, hybridized with cDNA microarray representing 1152 different human genes. Fluorescent intensity were scanned and screened by means of differential analysis between two gene expression profiles. After 72 hrs’ co-culture of RPMI8226 cells and thalidomide in 100μmol/L concentration, the expression of 18 genes were up-regulated and 4 genes were down-regulated. The up-regulated genes(GeneBank Accession) included: 1) protein synthesis-related genes:NM_004184(WARS), NM_ 003335(UBE1L); 2) immune-related protein:NM_001465(FYB), NM_004341 (CAD), NM_002388(MCM3); 3) matabolism relatedgenes: BC008861, NM_001640(APEH), NM_020040(TUBB4Q), NM_001033(RRM1), NM_ 001976(ENO3), NM_003330 (TXNRD1); 4) cell signals and transducing proteins: NM_005167(ARHC), NM_001465(FYB); 5) other genes: NM_ 017432(PTOV1), NM_003564 (TAGLN2), NM_005053(RAD23A), NM_ 001033(RRM1), AK025983, NM_015685 (CLONE24904), NM_033158 (HYAL2). The down-regulated genes includes: 1) protein synthesis-related genes: NM_000994(RPL32); 2) immune-related proteins: NM_001551 (IGBP1); 3) other genes: NM_002983(SCYA3), NM_002421(MMP1). These genes were involved in preotein synthesis and degradation, cell signal transduction, cytoskeletal movement immune cell matabolism and regulation of anti-oncogene. WARS gene encoding tryptophanyl-tRNA synthetase was up-regulated by thalidomide, while MMP1 gene encoding matrix metalloprotein 1 was down-regulated. They may be related to the inhibition of angiogenesis caused by thalidomide. SCYA3 gene encoding macrophage inflammatory protein-1alpha was down-regulated by thalidomide, as well as IGBP1 gene which encoding immunoglobulin binding protein 1. They may play a role in the inhibition of cell proliferation caused by thalidomide. TUBB4Q gene encoding tubulinβ4, UBE1L gene encoding ubiquitin- activating enzyme E1-like protein and TXNRD1 gene encoding thioredoxin reductase 1 were up-regulated by thalidomide. They may involve in apoptosis of RPMI8226 cells induced by thalidomide. FYB gene encoding Fyn-binding protein was up regulated by thalidomide. The elevated expression of this gene may play a role in the killing of RPMI8226 cells by thalidomide.

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