scholarly journals SINE Retrotransposons Import Polyadenylation Signals to 3’UTRs in Dog (Canis familiaris)

2020 ◽  
Author(s):  
Jessica D. Choi ◽  
Lelani A. Del Pinto ◽  
Nathan B. Sutter
Keyword(s):  
Messenger Rna ◽  
Consensus Sequence ◽  
Domestic Dog ◽  
Untranslated Regions ◽  
Nuclear Retention ◽  
Sense Strand ◽  
Sine Insertion ◽  
Gene Transcripts ◽  
Human Ortholog ◽  
Polyadenylation Signals

AbstractBackgroundMessenger RNA 3’ untranslated regions (3’UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3’UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy number. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may help terminate transcript in some dog genes.ResultsDog 3’UTRs have several peaks of AATAAA PAS frequency within 40 bp of the 3’UTR end, including four bp-interval peaks at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. While density of antisense-oriented Can-SINEs in 3’UTRs is fairly constant with distances from 3’end, sense-oriented Can-SINEs are common at the 3’end but nearly absent farther upstream. There are nine Can-SINE sub-types in the dog genome and the consensus sequence sense strands (head to tail) all carry at least three PASs while antisense strands usually have none. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp for target site duplications (TSDs). We find that all Can-SINE types favor integration at TSDs beginning with A(4). The count of AATAAA PASs differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3’UTR ends are very likely to carry AATAAA on the mRNA sense strand while those farther upstream are not. We also identified loci where Can-SINE insertion has truncated or altered a dog 3’UTR compared to the human ortholog.ConclusionDog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3’UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3’UTR regions but are retained at the far downstream end of 3’UTRs, which we infer reflects their role as termination sequences for these transcripts.

Messenger RNA in Dormant Cells of Sterkiella histriomuscorum (Oxytrichidae): Identification of Putative Regulatory Gene Transcripts

Protist ◽  
1999 ◽  
Vol 150 (2) ◽  
pp. 137-147 ◽  
Author(s):  
Anne Baroin Tourancheau ◽  
Loic Morin ◽  
Tie Yang ◽  
Roland Perasso
Keyword(s):  
Messenger Rna ◽  
Regulatory Gene ◽  
Dormant Cells ◽  
Gene Transcripts

Improved superoxide-generating ability by interferon γ due to splicing pattern change of transcripts in neutrophils from patients with a splice site mutation inCYBB gene

Blood ◽  
2001 ◽  
Vol 98 (2) ◽  
pp. 436-441 ◽  
Author(s):  
Fuminari Ishibashi ◽  
Tomoyuki Mizukami ◽  
Shiro Kanegasaki ◽  
Lena Motoda ◽  
Ryota Kakinuma ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Present Report ◽  
Interferon Γ ◽  
Silent Mutation ◽  
Site Mutation ◽  
Splicing Pattern ◽  
Cybb Gene ◽  
Gene Transcripts ◽  
Ifn Γ ◽  
Neutrophil Superoxide

Chronic granulomatous disease (CGD) is an inherited disorder of host defense against microbial infections caused by defective activity of the phagocyte NADPH oxidase. Based on an increase of neutrophil superoxide-generating ability in response to interferon γ (IFN-γ) in a single patient with CGD, multicentered group studies demonstrated a beneficial effect of prophylactic IFN-γ. However, no apparent increase of the phagocyte superoxide generation was found in patients enrolled in these studies. The present report offers an additional kindred in whom an IFN-γ–dependent increase in neutrophil superoxide production was observed in 3 affected patients. The defect in the CYBB gene for gp91-phox was identified as an otherwise silent mutation adjacent to the third intron of theCYBB gene that alters messenger RNA splicing. By molecular analysis, significant differences were found in the splicing pattern ofCYBB gene transcripts in patient neutrophils between 1 and 25 days after administration of IFN-γ. Furthermore, a complete transcript containing the missing exons could be detected in all specimens after the treatment. The changes in the splicing pattern of the transcripts and the prolonged effect on superoxide-generating ability of patient neutrophils indicate that IFN-γ induced a partial correction of the abnormal splicing of CYBB gene transcripts in myeloid progenitor cells.

scholarly journals Characterization of Specific Nucleotide Substitutions in DtxR-Specific Operators of Corynebacterium diphtheriae That Dramatically Affect DtxR Binding, Operator Function, and Promoter Strength

2000 ◽  
Vol 182 (2) ◽  
pp. 432-438 ◽  
Author(s):  
John H. Lee ◽  
Randall K. Holmes
Keyword(s):  
Consensus Sequence ◽  
Corynebacterium Diphtheriae ◽  
Promoter Strength ◽  
Negative Effects ◽  
Nucleotide Substitutions ◽  
Mobility Shift ◽  
Diphtheria Toxin Repressor ◽  
Sense Strand ◽  
Gel Mobility Shift ◽  
The Cost

ABSTRACT The diphtheria toxin repressor (DtxR) of Corynebacterium diphtheriae uses Fe2+ as a corepressor. Holo-DtxR inhibits transcription from the iron-regulated promoters (IRPs) designated IRP1 through IRP5 as well as from the promoters for thetox and hmuO genes. DtxR binds to 19-bp operators with the consensus sequence 5′-TTAGGTTAGCCTAACCTAA-3′, a perfect 9-bp palindrome interrupted by a single C · G base pair. Among the seven known DtxR-specific operators, IRP3 exhibits the weakest binding to DtxR. The message (sense) strand of the IRP3 operator (5′-TTAGGTGAGACGCACCCAT-3′ [nonconsensus nucleotides underlined]) overlaps by 2 nucleotides at its 5′ end with the putative −10 sequence of the IRP3 promoter. The underlined C at position +7 from the center of the IRP3 operator [C(+7)] is unique, because T is conserved at that position in other DtxR-specific operators. The present study examined the effects of nucleotide substitutions at position +7 or −7 in the IRP3 operator. In gel mobility shift assays, only the change of C(+7) to the consensus nucleotide T caused a dramatic increase in the binding of DtxR, whereas other nucleotide substitutions for C(+7) or replacements for A(−7) had only small positive or negative effects on DtxR binding. All substitutions for C(+7) or A(−7) except for A(−7)C dramatically decreased IRP3 promoter strength. In contrast, the A(−7)C variant caused increased promoter strength at the cost of nearly eliminating repressibility by DtxR. The message (sense) strand of the IRP1 operator (5′-TTAGGTTAGCCAAACCTTT-3′) includes the −35 region of the IRP3 promoter. A T(+7)C variant of the IRP1 operator was also constructed, and it was shown to exhibit decreased binding to DtxR, decreased repressibility by DtxR, and increased promoter strength. The nucleotides at positions +7 and −7 in DtxR-specific operators are therefore important determinants of DtxR binding and repressibility of transcription by DtxR, and they also have significant effects on promoter activity for IRP3 and IRP1.

Unique effects of zinc protoporphyrin on HO-1 induction and apoptosis

Blood ◽  
2001 ◽  
Vol 97 (5) ◽  
pp. 1306-1313 ◽  
Author(s):  
Guang Yang ◽  
Xuandai Nguyen ◽  
Judy Ou ◽  
Prasad Rekulapelli ◽  
David K. Stevenson ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Cultured Cells ◽  
Consensus Sequence ◽  
Nuclear Proteins ◽  
Zinc Protoporphyrin ◽  
Activator Protein 1 ◽  
Signaling Mechanism ◽  
Disease States ◽  
Mrna Induction ◽  
Dnase I Footprinting

Zinc protoporphyrin (ZnPP), a naturally occurring molecule, is increased in iron deficiency and lead intoxication. ZnPP can also induce heme oxygenase (HO-1), the enzyme it competitively inhibits. In cultured cells (HA-1), ZnPP was the strongest HO-1 inducer of any metalloporphyrin (MP) tested. This was not due to increased oxidative stress, enhanced binding at metal response element, nor increased binding at activator protein-1 (AP-1) or SP-1 sites on HO-1. Only ZnPP, however, increased binding of nuclear proteins to early growth response-1 (Egr-1) protein consensus sequence. Pretreatment of HA-1 with cycloheximide inhibited ZnPP-induced HO-1 messenger RNA (mRNA) by 55%. Incubation with antisense Egr-1 oligomers decreased ZnPP-induced HO-1 expression by 47%. Furthermore, the level of HO-1 mRNA induction by ZnPP was 2-fold less in Egr-1–deficient fibroblasts than in wild-type cells. Because no Egr-1 binding site was previously identified on the HO-1 promoter, HA-1 cells were transfected with HO-1 CAT constructs containing segments of a 12.5-kb enhancer region of HO-1. A 196-bp fragment (RH) located approximately 9.5 kb upstream of the transcription start site mediated HO-1 induction by ZnPP alone. DNase I footprinting analysis further revealed that nuclear proteins bound to a 50-bp sequence in the RH. Within this sequence, a novel 9-bp region with 78% homology to the Egr-1 consensus sequence was identified further suggesting that Egr-1 partially mediates HO-1 induction by ZnPP. Lastly, increased apoptosis and nuclear localization were only seen with ZnPP, suggesting that increased ZnPP in disease states may serve as a cellular signaling mechanism.

scholarly journals Anti-CD3 monoclonal antibody-mediated cytotoxicity occurs through an interleukin-2-independent pathway in CD3+ large granular lymphocytes

Blood ◽  
1990 ◽  
Vol 75 (4) ◽  
pp. 935-940 ◽  
Author(s):  
TP Jr Loughran ◽  
JA Aprile ◽  
FW Ruscetti
Keyword(s):  
Monoclonal Antibody ◽  
Messenger Rna ◽  
Blot Hybridization ◽  
Interleukin 2 ◽  
Northern Blot Hybridization ◽  
Binding Studies ◽  
Granule Formation ◽  
Receptor Sites ◽  
Gene Transcripts ◽  
Lgl Leukemia

Abstract The mechanism of induction of cytotoxicity produced by anti-CD3 monoclonal antibody (MoAb) was studied in four patients with CD3+ large granular lymphocyte (LGL) leukemia. Anti-CD3 MoAb treatment resulted in increased target cell binding and increased granule formation. After activation, leukemic LGL remained Tac-, with the exception of a patient with CD4+ LGL leukemia. Radiolabeled interleukin-2 (IL-2) binding studies demonstrated that treatment with anti-CD3 MoAb resulted in upregulation of the number of p75 intermediate affinity IL-2 receptor sites per cell. Northern blot hybridization analysis showed expression of gamma-interferon gene transcripts 24 to 48 hours after activation. There was no evidence for expression of IL-2 messenger RNA or secretion of IL-2 after activation. Anti-CD3 MoAb and IL-2 provide different signals for activation of CD3+ LGL. Induction of cytotoxicity produced by anti-CD3 MoAb in leukemic CD3+ LGL is not associated with IL-2 production.

scholarly journals Bunyamwera Orthobunyavirus S-Segment Untranslated Regions Mediate Poly(A) Tail-Independent Translation

2009 ◽  
Vol 83 (8) ◽  
pp. 3637-3646 ◽  
Author(s):  
Gjon Blakqori ◽  
Ingeborg van Knippenberg ◽  
Richard M. Elliott
Keyword(s):  
Rna Stability ◽  
Initiation Factor ◽  
Untranslated Regions ◽  
Luciferase Reporter ◽  
Translation Efficiency ◽  
Luciferase Reporter Gene ◽  
Viral Mrnas ◽  
Nuclear Retention ◽  
Eukaryotic Mrnas ◽  
Independent Process

ABSTRACT The mRNAs of Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family, possess a 5′ cap structure but lack a 3′ poly(A) tail, a common feature of eukaryotic mRNAs that greatly enhances translation efficiency. Viral mRNAs also contain untranslated regions (UTRs) that flank the coding sequence. Using model virus-like mRNAs that harbor the Renilla luciferase reporter gene, we found that the 3′ UTR of the BUNV small-segment mRNA mediated efficient translation in the absence of a poly(A) tail. Viral UTRs did not increase RNA stability, and polyadenylation did not significantly enhance reporter activity. Translation of virus-like mRNAs in transfected cells was unaffected by knockdown of poly(A)-binding protein (PABP) but was markedly reduced by depletion of eukaryotic initiation factor 4G, suggesting a PABP-independent process for translation initiation. In BUNV-infected cells, translation of polyadenylated but not virus-like mRNAs was inhibited. Furthermore, we demonstrate that the viral nucleocapsid protein binds to, and colocalizes with, PABP in the cytoplasm early in infection, followed by nuclear retention of PABP. Our results suggest that BUNV corrupts PABP function in order to inhibit translation of polyadenylated cellular mRNAs while its own mRNAs are translated in a PABP-independent process.

scholarly journals Structure of the constant and 3′ untranslated regions of the murine Balb/c γ2a heavy chain messenger RNA

1980 ◽  
Vol 8 (14) ◽  
pp. 3143-3156 ◽  
Author(s):  
Jean-Louis Sikorav ◽  
Charles Auffray ◽  
François Rougeon
Keyword(s):  
Heavy Chain ◽  
Messenger Rna ◽  
Untranslated Regions

Regulation of the expression of histone H3.3 by differential polyadenylation

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 503-510 ◽  
Author(s):  
Rongrong Feng ◽  
Xiaoying Tang ◽  
Angela Becker ◽  
Anja Berger ◽  
Jing Ye ◽  
...  
Keyword(s):  
Germ Line ◽  
Evolutionary Conservation ◽  
Untranslated Regions ◽  
Histone Genes ◽  
Marker Protein ◽  
Male Germ Line ◽  
Histone H3.3 ◽  
Polyadenylation Sites ◽  
Functional Relevance ◽  
Polyadenylation Signals

Previously we have shown that the 3' untranslated regions (UTRs) of the replacement histone genes H3.3.A and H3.3B of Drosophila melanogaster differ in their nucleotide sequences and have different polyadenylation sites. To understand their functional relevance, which might explain the presence and evolutionary conservation of 2 different H3.3 genes, green flourescent protein (GFP) constructs with different 3' UTR sections were studied by the expression of GFP as a marker protein. Here we show that the polyadenylation signals modify the cell-specific translation of the histone replacement variants in testes and ovaries. The H3.3A gene may be required to provide postmeiotic histone H3.3 in the male germ line in transition to chromatin packaging in sperm.Key words: histone H3.3, polyadenylation, oogenesis, spermatogenesis, histone translation.

scholarly journals Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyeon-Mu Cho ◽  
Se-Hee Choe ◽  
Young-Hyun Kim ◽  
Hye-Ri Park ◽  
Hee-Eun Lee ◽  
...  
Keyword(s):  
Computational Analysis ◽  
World Monkey ◽  
Consensus Sequence ◽  
Alternative Polyadenylation ◽  
Mrna Isoforms ◽  
Reading Frame ◽  
Exon Splicing ◽  
Human Genes ◽  
Gene Transcripts ◽  
Polyadenylation Sites

AbstractTransposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3′ end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented AluYRa1. In conclusion, AluYRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3′UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.

Messenger RNA profiling of human platelets by microarray hybridization

2003 ◽  
Vol 90 (10) ◽  
pp. 738-748 ◽  
Author(s):  
Alex Dugrillon ◽  
Ayse Günaydin ◽  
Hermann Eichler ◽  
Harald Klüter ◽  
Peter Bugert
Keyword(s):  
Messenger Rna ◽  
De Novo ◽  
Rna Isolation ◽  
Human Platelets ◽  
Buffy Coat ◽  
Microarray Hybridization ◽  
Rt Pcr ◽  
Rna Profiling ◽  
Human Genes ◽  
Gene Transcripts

SummaryPlatelets are generally believed to be inactive in terms of de novo protein synthesis. On the other hand, the presence of ribosomes and mRNA molecules is well established. Many studies have used reverse transcriptase (RT) -PCR for detection of gene transcripts in platelets. As RT-PCR is a very sensitive method, any leukocyte contamination of platelet preparations can lead to false results. We performed three filtration procedures to minimize leukocyte contamination of pooled buffy-coat platelet concentrates prior to RNA isolation. Furthermore, by applying a genomic PCR approach with 50 amplification cycles we demonstrated that nucleated cells were not detectable. Microarray hybridization was used to analyze 9,850 individual human genes in RNA from purified platelets. In total we identified 1,526 (15.5%) positive genes. The data were confirmed in six individual experiments each performed on a PC pooled from four individual blood donations. Genes specific for nucleated blood cells such as CD4, CD83 and others were negative and verified the purity of PC. Overrepresentation of positive genes was found in the functional categories of glycoproteins/integrins (22.6% vs. 15.5%, p=0.029) and receptors (20.7% vs. 15.5%, p<0.001). Gene transcripts encoding RANTES, GRO-α, MIP-1α, MIP-1β, and others were found at high levels of signal intensity and confirmed literature data. This work provides a mRNA profile of human platelets and a complete list of results can be downloaded from the website of our institute www.ma.uni-heidelberg.de/inst/iti/plt_array.xls. The knowledge about gene transcripts may have an impact on the characterization of novel proteins and their functions in platelets.

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