A tridecamer DNA sequence supports human mitochondrial RNA 3'-end formation in vitro.

Christianson, Thomas; Clayton, David A.

doi:10.1128/mcb.8.10.4502

Cited by 86 publications

(63 citation statements)

References 16 publications

(23 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another potential mechanism to regulate the mRNA/rRNA ratio could be by influencing mTERF-dependent transcription termination. The function of mTERF requires its specific binding to an mtDNA motif at the boundary between the rRNA and mRNA genes (6,12,21,25). Therefore, we also analyzed the footprinting pattern of the mtDNA area containing the mTERF binding site in organelles isolated from euthyroid and hypothyroid animals, in the latter case with and without the addition of T 3 to the incubation medium (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Two models have been proposed to explain the independent regulation of mRNA and rRNA syntheses in mammalian mitochondria. One model is based on the identification of the 5Ј end of the transcripts synthesized on a partially reconstructed in vitro transcription system (6,13), and it proposes that the synthesis of both polycistrons starts at a single initiation site, upstream of the tRNA Phe gene. The polymerase transcribes the rRNA genes more frequently stopping at the 3Ј end of 16S rRNA due to the binding to mtDNA of a mitochondrial transcription termination factor (mTERF) (6,12,21,25).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone

Enríquez

Fernández‐Silva

Garrido-Pérez

et al. 1999

Molecular and Cellular Biology

145

View full text Add to dashboard Cite

We have analyzed the influence of in vivo treatment and in vitro addition of thyroid hormone on in organello mitochondrial DNA (mtDNA) transcription and, in parallel, on the in organello footprinting patterns at the mtDNA regions involved in the regulation of transcription. We found that thyroid hormone modulates mitochondrial RNA levels and the mRNA/rRNA ratio by influencing the transcriptional rate. In addition, we found conspicuous differences between the mtDNA dimethyl sulfate footprinting patterns of mitochondria derived from euthyroid and hypothyroid rats at the transcription initiation sites but not at the mitochondrial transcription termination factor (mTERF) binding region. Furthermore, direct addition of thyroid hormone to the incubation medium of mitochondria isolated from hypothyroid rats restored the mRNA/rRNA ratio found in euthyroid rats as well as the mtDNA footprinting patterns at the transcription initiation area. Therefore, we conclude that the regulatory effect of thyroid hormone on mitochondrial transcription is partially exerted by a direct influence of the hormone on the mitochondrial transcription machinery. Particularly, the influence on the mRNA/rRNA ratio is achieved by selective modulation of the alternative H-strand transcription initiation sites and does not require the previous activation of nuclear genes. These results provide the first functional demonstration that regulatory signals, such as thyroid hormone, that modify the expression of nuclear genes can also act as primary signals for the transcriptional apparatus of mitochondria.Thyroid hormone regulates the expression of key nucleus encoded mitochondrial genes (23,37,38,47) and the steadystate concentration of all mitochondrial DNA (mtDNA)-encoded mRNAs (mt-mRNAs) (15-17, 32, 44). In rat liver, changes in mt-mRNA levels in response to in vivo treatment with thyroid hormones were well correlated with amounts of the corresponding polypeptides, while mtDNA copy number remained unmodified (33,47). Based on these observations, transcriptional control has been tentatively proposed as the main mechanism to explain the thyroid hormone effect on mt-mRNA steady-state levels and protein synthesis (33-36).Two alternative potential mechanisms for the regulation of mtDNA transcription by thyroid hormone have been suggested: through activation of mitochondrial transcription factor A (mtTFA) expression (18, 45), or by a direct action of the hormone through mitochondrial receptors (48). The second alternative is supported by earlier (42, 43) and recent (1, 48) reports that have proposed the existence of T 3 (3,3,5-triiodo-L-thyronine) binding proteins in mitochondria, which could interact with cis elements of mtDNA (7, 48). However, the lack of experimental evidence showing thyroid hormone-mediated transcription regulation in the absence of nuclear gene expression prevents any definitive conclusion about whether direct regulation of mtDNA transcription by this hormone occurs (38). Presently it is more generally believed that this transcripti...

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone

Enríquez

Fernández‐Silva

Garrido-Pérez

et al. 1999

Molecular and Cellular Biology

145

View full text Add to dashboard Cite

show abstract

“…Fig. 1 shows that the L-strand and H-strand primers ND1 (position 2761-2740) and 16S (position 2542-2563) detected a region of 15 bp (position 2659 -2673) containing hypermethylated and undermethylated bases; almost all the involved residues (7 on the L-strand and 3 on the H-strand) were comprised in the conserved tridecamer sequence block (8,34), which contains the binding site for mTERF. To estimate the protein occupancy at each region of DMS-altered reactivity, the relative level of methylation protection was measured; it can be considered equivalent to the percentage of the sites bound continuously by the protein or to the percentage of the time in which all the available sites were bound.…”

Section: Dms Footprinting In Isolated Ratmentioning

confidence: 99%

Identification by in Organello Footprinting of Protein Contact Sites and of Single-stranded DNA Sequences in the Regulatory Region of Rat Mitochondrial DNA

Cantatore

Daddabbo

Fracasso

et al. 1995

Journal of Biological Chemistry

View full text Add to dashboard Cite

Footprinting studies with the purine-modifying reagent dimethyl sulfate and with the single-stranded DNA probing reagent potassium permanganate were carried out in isolated mitochondria from rat liver. Dimethyl sulfate footprinting allowed the detection of protein-DNA interactions within the rat analogues of the human binding sites for the transcription termination factor mTERF and for the transcription activating factor mt-TFA. Although mTERF contacts were localized only at the boundary between the 16S rRNA/tRNA Leu UUR genes, multiple mtTFA contacts were detected. Contact sites were located in the light and the heavy strand promoters and, in agreement with in vitro footprinting data on human mitochondria, between the conserved sequence blocks (CSB) 1 and 2 and inside CSB-1. Potassium permanganate footprinting allowed detection of a 25-base pair region entirely contained in CSB-1 in which both strands were permanganate-reactive. No permanganate reactivity was associated with the other regions of the D-loop, including CSB-2 and -3, and with the mTERF contact site. We hypothesize that the single-stranded DNA at CSB-1 may be due to a profound helix distortion induced by mtTFA binding or be associated with a RNA polymerase pause site. In any case the location in CSB-1 of the 3 end of the most abundant replication primer and of the 5 end of the prominent D-loop DNA suggests that protein-induced DNA conformational changes play an important role in directing the transition from transcription to replication in mammalian mitochondria.The majority of mammalian mitochondrial (mt) 1 DNA molecules possess a triple helix structure called D-loop due to the displacement of the parental H-strand by short nascent Hstrand chains. The D-loop region, that is the main noncoding region and the most variable part of vertebrate mt genomes, contains the origin of H-strand DNA replication (O H ) and the promoters for H and L-strand transcription (for review see Refs. 1-3). The two promoters (HSP and LSP) hold the binding sites for the transcription factor mtTFA (4), which activates Hand L-strand in vitro transcription. The H-strand transcripts initiate in two points. One, I HR , located few bases upstream of the tRNA Phe gene, is responsible for the synthesis of the two rRNAs 16S and 12S and of 2 tRNAs; the other, I HT , located near the 5Ј end of the 12S rRNA gene, directs the synthesis of 12 mRNAs and of 12 tRNAs (5-7). The L-strand is entirely transcribed as a single transcription unit, starting from a point that in humans is located 216 bp upstream of O H . It has a low informational content, because it directs only the synthesis of the primer for H-strand replication, of 1 mRNA and of 8 tRNAs.The contrast between the complete L-strand transcription and its low informational content is not yet fully understood. Moreover, despite many studies in different laboratories, the molecular mechanisms that regulate the production of the mature Hand L-strand transcripts are not yet completely known. They likely involve protein factors and nucl...

show abstract

“…Mitochondrial genes for proteins and tRNAs are located on both the heavy and light strands of the genome, which are transcribed as large polycistronic transcripts covering almost the entire length of each strand (Aloni and Attardi 1971;Murphy et al 1975;Montoya et al 1981;Mercer et al 2011). A third transcript covering the start of the heavy strand and the two rRNA genes is also produced (Christianson and Clayton 1988). These long precursor mitochondrial transcripts undergo processing to form functional RNAs .…”

Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

Rackham

Shearwood²,

Mercer³

et al. 2011

RNA

283

221

View full text Add to dashboard Cite

Human mitochondrial long noncoding RNAs (lncRNAs) have not been described to date. By analysis of deep-sequencing data we have identified three lncRNAs generated from the mitochondrial genome and confirmed their expression by Northern blotting and strand-specific qRT-PCR. We show that the abundance of these lncRNAs is comparable to their complementary mRNAs and that nuclear-encoded mitochondrial proteins involved in RNA processing regulate their expression. We also identify the 59 and 39 transcript ends of the three lncRNAs and show that mitochondrial RNase P protein 1 (MRPP1) is important for the processing of these transcripts. Finally, we show that mitochondrial lncRNAs form intermolecular duplexes and that their abundance is cell-and tissue-specific, suggesting a functional role in the regulation of mitochondrial gene expression.

show abstract

A tridecamer DNA sequence supports human mitochondrial RNA 3'-end formation in vitro.

Cited by 86 publications

References 16 publications

Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone

Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone

Identification by in Organello Footprinting of Protein Contact Sites and of Single-stranded DNA Sequences in the Regulatory Region of Rat Mitochondrial DNA

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

Contact Info

Product

Resources

About