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Journal articles on the topic 'Transcription initiation sites'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Lynch, M. "The Evolution of Transcription-Initiation Sites." Molecular Biology and Evolution 22, no. 4 (2005): 1137–46. http://dx.doi.org/10.1093/molbev/msi100.

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2

Means, A. L., and P. J. Farnham. "Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site." Molecular and Cellular Biology 10, no. 2 (1990): 653–61. http://dx.doi.org/10.1128/mcb.10.2.653.

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We have identified a sequence element that specifies the position of transcription initiation for the dihydrofolate reductase gene. Unlike the functionally analogous TATA box that directs RNA polymerase II to initiate transcription 30 nucleotides downstream, the positioning element of the dihydrofolate reductase promoter is located directly at the site of transcription initiation. By using DNase I footprint analysis, we have shown that a protein binds to this initiator element. Transcription initiated at the dihydrofolate reductase initiator element when 28 nucleotides were inserted between it

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3

Means, A. L., and P. J. Farnham. "Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site." Molecular and Cellular Biology 10, no. 2 (1990): 653–61. http://dx.doi.org/10.1128/mcb.10.2.653-661.1990.

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We have identified a sequence element that specifies the position of transcription initiation for the dihydrofolate reductase gene. Unlike the functionally analogous TATA box that directs RNA polymerase II to initiate transcription 30 nucleotides downstream, the positioning element of the dihydrofolate reductase promoter is located directly at the site of transcription initiation. By using DNase I footprint analysis, we have shown that a protein binds to this initiator element. Transcription initiated at the dihydrofolate reductase initiator element when 28 nucleotides were inserted between it

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4

Kaplan, C. D. "Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites." Science 301, no. 5636 (2003): 1096–99. http://dx.doi.org/10.1126/science.1087374.

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5

Howcroft, T. Kevin, Aparna Raval, Jocelyn D. Weissman, Anne Gegonne, and Dinah S. Singer. "Distinct Transcriptional Pathways Regulate Basal and Activated Major Histocompatibility Complex Class I Expression." Molecular and Cellular Biology 23, no. 10 (2003): 3377–91. http://dx.doi.org/10.1128/mcb.23.10.3377-3391.2003.

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ABSTRACT Transcription of major histocompatibility complex (MHC) class I genes is regulated by both tissue-specific (basal) and hormone/cytokine (activated) mechanisms. Although promoter-proximal regulatory elements have been characterized extensively, the role of the core promoter in mediating regulation has been largely undefined. We report here that the class I core promoter consists of distinct elements that are differentially utilized in basal and activated transcription pathways. These pathways recruit distinct transcription factor complexes to the core promoter elements and target disti

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6

Steinthorsdottir, Valgerdur, Hreinn Stefansson, Shyamali Ghosh, et al. "Multiple novel transcription initiation sites for NRG1." Gene 342, no. 1 (2004): 97–105. http://dx.doi.org/10.1016/j.gene.2004.07.029.

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7

Geng, Y., and L. F. Johnson. "Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter." Molecular and Cellular Biology 13, no. 8 (1993): 4894–903. http://dx.doi.org/10.1128/mcb.13.8.4894.

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The mouse thymidylate synthase promoter lacks a TATA box and initiates transcription at many sites across a 90-nucleotide initiation window. We showed previously that wild-type promoter activity is maintained with a promoter that extends only 13 nucleotides upstream of the first start site. G/A-rich and G/C-rich promoter elements were identified in the vicinity of the first transcriptional start site. The goals of the present study were to determine whether there are additional promoter elements in the initiation window and to determine why transcription initiates across such a broad region. M

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8

Geng, Y., and L. F. Johnson. "Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter." Molecular and Cellular Biology 13, no. 8 (1993): 4894–903. http://dx.doi.org/10.1128/mcb.13.8.4894-4903.1993.

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The mouse thymidylate synthase promoter lacks a TATA box and initiates transcription at many sites across a 90-nucleotide initiation window. We showed previously that wild-type promoter activity is maintained with a promoter that extends only 13 nucleotides upstream of the first start site. G/A-rich and G/C-rich promoter elements were identified in the vicinity of the first transcriptional start site. The goals of the present study were to determine whether there are additional promoter elements in the initiation window and to determine why transcription initiates across such a broad region. M

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9

Travis, A., J. Hagman, and R. Grosschedl. "Heterogeneously initiated transcription from the pre-B- and B-cell-specific mb-1 promoter: analysis of the requirement for upstream factor-binding sites and initiation site sequences." Molecular and Cellular Biology 11, no. 11 (1991): 5756–66. http://dx.doi.org/10.1128/mcb.11.11.5756.

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The mb-1 gene, encoding a membrane immunoglobulin-associated protein, is developmentally regulated and expressed specifically in pre-B and mature B lymphocytes. Analysis of the TATA-less mb-1 promoter indicated that it directs initiation of transcription from multiple sites. Promoter sequences between -68 and +70 conferred the correct pattern of cell type-specific transcription upon a heterologous gene. Two nuclear factor-binding sites that are important for promoter function were identified between -59 and -38. Both sites interacted with ubiquitous nuclear factors in vitro. One of these facto

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10

Travis, A., J. Hagman, and R. Grosschedl. "Heterogeneously initiated transcription from the pre-B- and B-cell-specific mb-1 promoter: analysis of the requirement for upstream factor-binding sites and initiation site sequences." Molecular and Cellular Biology 11, no. 11 (1991): 5756–66. http://dx.doi.org/10.1128/mcb.11.11.5756-5766.1991.

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The mb-1 gene, encoding a membrane immunoglobulin-associated protein, is developmentally regulated and expressed specifically in pre-B and mature B lymphocytes. Analysis of the TATA-less mb-1 promoter indicated that it directs initiation of transcription from multiple sites. Promoter sequences between -68 and +70 conferred the correct pattern of cell type-specific transcription upon a heterologous gene. Two nuclear factor-binding sites that are important for promoter function were identified between -59 and -38. Both sites interacted with ubiquitous nuclear factors in vitro. One of these facto

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11

Barthelemy, I., M. Salas, and R. P. Mellado. "In vivo transcription of bacteriophage phi 29 DNA: transcription initiation sites." Journal of Virology 60, no. 3 (1986): 874–79. http://dx.doi.org/10.1128/jvi.60.3.874-879.1986.

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12

HAYNES, L., and L. ROTHMANDENES. "N4 virion RNA polymerase sites of transcription initiation." Cell 41, no. 2 (1985): 597–605. http://dx.doi.org/10.1016/s0092-8674(85)80032-5.

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13

Blank, Martin, and Reba Goodman. "Electromagnetic initiation of transcription at specific DNA sites." Journal of Cellular Biochemistry 81, no. 4 (2001): 689–92. http://dx.doi.org/10.1002/jcb.1102.

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14

Binder, S., and A. Brennicke. "Transcription initiation sites in mitochondria of Oenothera berteriana." Journal of Biological Chemistry 268, no. 11 (1993): 7849–55. http://dx.doi.org/10.1016/s0021-9258(18)53035-0.

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15

Nussinov, Ruth. "Compilation of eukaryotic sequences around transcription initiation sites." Journal of Theoretical Biology 120, no. 4 (1986): 479–87. http://dx.doi.org/10.1016/s0022-5193(86)80041-8.

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16

Bucher, Philipp, and Edward N. Trifonov. "On Nussinov's compilation of eukaryotic transcription initiation sites." Journal of Theoretical Biology 126, no. 3 (1987): 373–75. http://dx.doi.org/10.1016/s0022-5193(87)80243-6.

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17

Abravaya, Klara, and Lucia B. Rothman-Denes. "N4 RNA polymerase II sites of transcription initiation." Journal of Molecular Biology 211, no. 2 (1990): 359–72. http://dx.doi.org/10.1016/0022-2836(90)90357-r.

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18

Blake, M. C., R. C. Jambou, A. G. Swick, J. W. Kahn, and J. C. Azizkhan. "Transcriptional initiation is controlled by upstream GC-box interactions in a TATAA-less promoter." Molecular and Cellular Biology 10, no. 12 (1990): 6632–41. http://dx.doi.org/10.1128/mcb.10.12.6632.

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Numerous genes contain TATAA-less promoters, and the control of transcriptional initiation in this important promoter class is not understood. We have determined that protein-DNA interactions at three of the four proximal GC box sequence elements in one such promoter, that of the hamster dihydrofolate reductase gene, control initiation and relative use of the major and minor start sites. Our results indicate that although the GC boxes are apparently equivalent with respect to factor binding, they are not equivalent with respect to function. At least two properly positioned GC boxes were requir

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19

Blake, M. C., R. C. Jambou, A. G. Swick, J. W. Kahn, and J. C. Azizkhan. "Transcriptional initiation is controlled by upstream GC-box interactions in a TATAA-less promoter." Molecular and Cellular Biology 10, no. 12 (1990): 6632–41. http://dx.doi.org/10.1128/mcb.10.12.6632-6641.1990.

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Numerous genes contain TATAA-less promoters, and the control of transcriptional initiation in this important promoter class is not understood. We have determined that protein-DNA interactions at three of the four proximal GC box sequence elements in one such promoter, that of the hamster dihydrofolate reductase gene, control initiation and relative use of the major and minor start sites. Our results indicate that although the GC boxes are apparently equivalent with respect to factor binding, they are not equivalent with respect to function. At least two properly positioned GC boxes were requir

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20

Chang, D. D., J. E. Hixson, and D. A. Clayton. "Minor transcription initiation events indicate that both human mitochondrial promoters function bidirectionally." Molecular and Cellular Biology 6, no. 1 (1986): 294–301. http://dx.doi.org/10.1128/mcb.6.1.294.

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Human mitochondrial DNA is transcribed from two distinct, strand-specific promoters located in the displacement loop region of the genome. The transcriptional control sequences identified by deletion mapping and site-directed mutagenesis studies span short regions surrounding the initiation sites and bear no obvious sequence homology to any nuclear or procaryotic promoters. In vitro transcription analyses also revealed several minor initiation sites that are characterized by a pyrimidine-rich region followed by a purine-rich region, a feature that is shared by the two major promoters. In this

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21

Chang, D. D., J. E. Hixson, and D. A. Clayton. "Minor transcription initiation events indicate that both human mitochondrial promoters function bidirectionally." Molecular and Cellular Biology 6, no. 1 (1986): 294–301. http://dx.doi.org/10.1128/mcb.6.1.294-301.1986.

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Human mitochondrial DNA is transcribed from two distinct, strand-specific promoters located in the displacement loop region of the genome. The transcriptional control sequences identified by deletion mapping and site-directed mutagenesis studies span short regions surrounding the initiation sites and bear no obvious sequence homology to any nuclear or procaryotic promoters. In vitro transcription analyses also revealed several minor initiation sites that are characterized by a pyrimidine-rich region followed by a purine-rich region, a feature that is shared by the two major promoters. In this

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22

Sasaki, Takayo, Sunita Ramanathan, Yukiko Okuno, Chiharu Kumagai, Seemab S. Shaikh, and David M. Gilbert. "The Chinese Hamster Dihydrofolate Reductase Replication Origin Decision Point Follows Activation of Transcription and Suppresses Initiation of Replication within Transcription Units." Molecular and Cellular Biology 26, no. 3 (2006): 1051–62. http://dx.doi.org/10.1128/mcb.26.3.1051-1062.2006.

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ABSTRACT Chinese hamster ovary (CHO) cells select specific replication origin sites within the dihydrofolate reductase (DHFR) locus at a discrete point during G1 phase, the origin decision point (ODP). Origin selection is sensitive to transcription but not protein synthesis inhibitors, implicating a pretranslational role for transcription in origin specification. We have constructed a DNA array covering 121 kb surrounding the DHFR locus, to comprehensively investigate replication initiation and transcription in this region. When nuclei isolated within the first 3 h of G1 phase were stimulated

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23

Li, W. Z., and F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 2 (1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666.

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Functional TATA elements in the 5' untranslated region of the CYC1 gene in the yeast Saccharomyces cerevisiae have been defined by transcriptional analysis of site-directed mutations. Five sites previously suggested to contain functional TATA elements were altered individually and in all possible combinations. The results indicated that only two elements are required for transcription at the normal level and the normal start sites. The two functional TATA elements are located at sites -178 and -123, where the A of the ATG start codon is assigned nucleotide position +1. They direct initiation w

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24

Li, W. Z., and F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 2 (1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666-676.1991.

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Functional TATA elements in the 5' untranslated region of the CYC1 gene in the yeast Saccharomyces cerevisiae have been defined by transcriptional analysis of site-directed mutations. Five sites previously suggested to contain functional TATA elements were altered individually and in all possible combinations. The results indicated that only two elements are required for transcription at the normal level and the normal start sites. The two functional TATA elements are located at sites -178 and -123, where the A of the ATG start codon is assigned nucleotide position +1. They direct initiation w

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25

Kelly, S., S. Kramer, A. Schwede, P. K. Maini, K. Gull, and M. Carrington. "Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes." Open Biology 2, no. 4 (2012): 120033. http://dx.doi.org/10.1098/rsob.120033.

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The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated

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26

Yadon, Adam N., Daniel Van de Mark, Ryan Basom, Jeffrey Delrow, Iestyn Whitehouse, and Toshio Tsukiyama. "Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription." Molecular and Cellular Biology 30, no. 21 (2010): 5110–22. http://dx.doi.org/10.1128/mcb.00602-10.

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ABSTRACT Nucleosome-free regions (NFRs) at the 5′ and 3′ ends of genes are general sites of transcription initiation for mRNA and noncoding RNA (ncRNA). The presence of NFRs within transcriptional regulatory regions and the conserved location of transcription start sites at NFRs strongly suggest that the regulation of NFRs profoundly affects transcription initiation. To date, multiple factors are known to facilitate transcription initiation by positively regulating the formation and/or size of NFRs in vivo. However, mechanisms to repress transcription by negatively regulating the size of NFRs

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27

Healy, A. M., T. L. Helser, and R. S. Zitomer. "Sequences required for transcriptional initiation of the Saccharomyces cerevisiae CYC7 genes." Molecular and Cellular Biology 7, no. 10 (1987): 3785–91. http://dx.doi.org/10.1128/mcb.7.10.3785.

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A series of BAL 31 deletions were constructed in the upstream region of the Saccharomyces cerevisiae CYC7 gene to determine sequences required for transcriptional initiation. These deletions identified the TATA box as an alternating A-T sequence at -160 and the initiation sequences as well as the spatial relationship between them. The TATA box was necessary for wild-type levels of expression of the CYC7 gene. Decreasing the distance between the TATA sequence and the initiation site did not alter gene expression, but the site of transcription was shifted 3'-ward. In most cases, transcription in

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28

Healy, A. M., T. L. Helser, and R. S. Zitomer. "Sequences required for transcriptional initiation of the Saccharomyces cerevisiae CYC7 genes." Molecular and Cellular Biology 7, no. 10 (1987): 3785–91. http://dx.doi.org/10.1128/mcb.7.10.3785-3791.1987.

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A series of BAL 31 deletions were constructed in the upstream region of the Saccharomyces cerevisiae CYC7 gene to determine sequences required for transcriptional initiation. These deletions identified the TATA box as an alternating A-T sequence at -160 and the initiation sequences as well as the spatial relationship between them. The TATA box was necessary for wild-type levels of expression of the CYC7 gene. Decreasing the distance between the TATA sequence and the initiation site did not alter gene expression, but the site of transcription was shifted 3'-ward. In most cases, transcription in

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29

Sakurai, H., T. Ohishi, and T. Fukasawa. "Two alternative pathways of transcription initiation in the yeast negative regulatory gene GAL80." Molecular and Cellular Biology 14, no. 10 (1994): 6819–28. http://dx.doi.org/10.1128/mcb.14.10.6819.

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The yeast GAL80 gene, encoding a negative regulatory protein of galactose-inducible genes, shows both constitutive and galactose-inducible expression. The inducible transcription is under the control of Gal4p, a common activator for the galactose-inducible genes, which binds to an upstream activation sequence, called UASG, spanning between -105 and -89 in the 5'-flanking region of GAL80. Here we demonstrate that the constitutive transcription started at +1, whereas the inducible transcription occurs from a set of downstream sites at +37, +47, +56, and +67. Both transcriptions were enhanced 10-

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30

Sakurai, H., T. Ohishi, and T. Fukasawa. "Two alternative pathways of transcription initiation in the yeast negative regulatory gene GAL80." Molecular and Cellular Biology 14, no. 10 (1994): 6819–28. http://dx.doi.org/10.1128/mcb.14.10.6819-6828.1994.

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The yeast GAL80 gene, encoding a negative regulatory protein of galactose-inducible genes, shows both constitutive and galactose-inducible expression. The inducible transcription is under the control of Gal4p, a common activator for the galactose-inducible genes, which binds to an upstream activation sequence, called UASG, spanning between -105 and -89 in the 5'-flanking region of GAL80. Here we demonstrate that the constitutive transcription started at +1, whereas the inducible transcription occurs from a set of downstream sites at +37, +47, +56, and +67. Both transcriptions were enhanced 10-

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31

Wang, Kevin L. C., and Jonathan R. Warner. "Positive and Negative Autoregulation ofREB1 Transcription in Saccharomyces cerevisiae." Molecular and Cellular Biology 18, no. 7 (1998): 4368–76. http://dx.doi.org/10.1128/mcb.18.7.4368.

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ABSTRACT Reb1p is a DNA binding protein of Saccharomyces cerevisiae that has been implicated in the activation of transcription by polymerase (Pol) II, in the termination of transcription by Pol I, and in the organization of nucleosomes. Studies of the transcriptional control of the REB1 gene have led us to identify three Reb1p binding sites in the 5′ region of the its gene, termed A, B, and C, at positions −110, −80, and +30 with respect to transcription initiation. In vitro, Reb1p binds to the three sites with the relative affinity of A ≥ C > B. Kinetic parameters suggest that when both A

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32

Shah, N. P., O. N. Witte, and C. T. Denny. "Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines." Molecular and Cellular Biology 11, no. 4 (1991): 1854–60. http://dx.doi.org/10.1128/mcb.11.4.1854.

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The t(9;22) Philadelphia chromosome translocation fuses 5' regulatory and coding sequences of the BCR gene to the c-ABL proto-oncogene. This results in the formation of hybrid BCR-ABL mRNAs and proteins. The shift in ABL transcriptional control to the BCR promoter may play a role in cellular transformation mediated by this rearrangement. We have functionally localized the BCR promoter to a region 1 kb 5' of BCR exon 1 coding sequences by using a chloramphenicol acetyltransferase reporter gene assay. Nucleotide sequence analysis of this region revealed many consensus binding sequences for trans

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33

Shah, N. P., O. N. Witte, and C. T. Denny. "Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines." Molecular and Cellular Biology 11, no. 4 (1991): 1854–60. http://dx.doi.org/10.1128/mcb.11.4.1854-1860.1991.

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The t(9;22) Philadelphia chromosome translocation fuses 5' regulatory and coding sequences of the BCR gene to the c-ABL proto-oncogene. This results in the formation of hybrid BCR-ABL mRNAs and proteins. The shift in ABL transcriptional control to the BCR promoter may play a role in cellular transformation mediated by this rearrangement. We have functionally localized the BCR promoter to a region 1 kb 5' of BCR exon 1 coding sequences by using a chloramphenicol acetyltransferase reporter gene assay. Nucleotide sequence analysis of this region revealed many consensus binding sequences for trans

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34

Auchincloss, Andrea H., and Gregory G. Brown. "Soybean mitochondrial transcripts capped in vitro with guanylyltransferase." Biochemistry and Cell Biology 67, no. 6 (1989): 315–19. http://dx.doi.org/10.1139/o89-049.

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A method was devised which permitted the efficient labelling of soybean mitochondrial transcripts carrying initiator 5′ di- or tri-phosphate termini with [α-32P]GTP and the capping enzyme guanylyltransferase. The RNAs labelled in this manner appear to represent several different transcription initiation sites and to be present at only low to moderate abundance in soybean mtRNA preparations.Key words: transcription initiation, promoter, mitochondrial DNA, RNA processing, gene expression.

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35

Adams, T. H., and W. E. Timberlake. "Upstream elements repress premature expression of an Aspergillus developmental regulatory gene." Molecular and Cellular Biology 10, no. 9 (1990): 4912–19. http://dx.doi.org/10.1128/mcb.10.9.4912.

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The Aspergillus nidulans abaA gene regulates intermediate steps in asexual reproductive development and is itself developmentally regulated. An 822-base-pair DNA fragment from the abaA 5'-flanking region is sufficient to drive developmentally appropriate expression of the Escherichia coli lacZ gene. Deletion analysis showed that this fragment contains elements that repress transcription in vegetative cells and immature conidiophores and that activate transcription later during development. A 45-base-pair region encompassing the major and minor abaA transcription initiation sites contains direc

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36

Adams, T. H., and W. E. Timberlake. "Upstream elements repress premature expression of an Aspergillus developmental regulatory gene." Molecular and Cellular Biology 10, no. 9 (1990): 4912–19. http://dx.doi.org/10.1128/mcb.10.9.4912-4919.1990.

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The Aspergillus nidulans abaA gene regulates intermediate steps in asexual reproductive development and is itself developmentally regulated. An 822-base-pair DNA fragment from the abaA 5'-flanking region is sufficient to drive developmentally appropriate expression of the Escherichia coli lacZ gene. Deletion analysis showed that this fragment contains elements that repress transcription in vegetative cells and immature conidiophores and that activate transcription later during development. A 45-base-pair region encompassing the major and minor abaA transcription initiation sites contains direc

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37

Enríquez, José A., Patricio Fernández-Silva, Nuria Garrido-Pérez, Manuel J. López-Pérez, Acisclo Pérez-Martos, and Julio Montoya. "Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone." Molecular and Cellular Biology 19, no. 1 (1999): 657–70. http://dx.doi.org/10.1128/mcb.19.1.657.

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ABSTRACT 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 in

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38

Huo, Yi-Xin, Yuan-Tao Zhang, Yan Xiao, et al. "IHF-binding sites inhibit DNA loop formation and transcription initiation." Nucleic Acids Research 37, no. 12 (2009): 3878–86. http://dx.doi.org/10.1093/nar/gkp258.

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39

Nussinov, Ruth. "Putative elements in the vicinity of viral transcription initiation sites." International Journal of Biochemistry 20, no. 7 (1988): 721–30. http://dx.doi.org/10.1016/0020-711x(88)90168-1.

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40

Topper, J. N., and D. A. Clayton. "Identification of transcriptional regulatory elements in human mitochondrial DNA by linker substitution analysis." Molecular and Cellular Biology 9, no. 3 (1989): 1200–1211. http://dx.doi.org/10.1128/mcb.9.3.1200.

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Human mitochondrial DNA contains two major promoters, one for transcription of each strand of the helix. Previous mapping and mutagenesis data have localized these regulatory elements and have suggested regions important to their function. In order to define, at high resolution, the sequences critical for accurate and efficient transcriptional initiation, a linker substitution analysis of the entire promoter region was performed. Each promoter was shown to consist of approximately 50 base pairs comprising two functionally distinct elements. These and previous data strongly support a mode of tr

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41

Topper, J. N., and D. A. Clayton. "Identification of transcriptional regulatory elements in human mitochondrial DNA by linker substitution analysis." Molecular and Cellular Biology 9, no. 3 (1989): 1200–1211. http://dx.doi.org/10.1128/mcb.9.3.1200-1211.1989.

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Human mitochondrial DNA contains two major promoters, one for transcription of each strand of the helix. Previous mapping and mutagenesis data have localized these regulatory elements and have suggested regions important to their function. In order to define, at high resolution, the sequences critical for accurate and efficient transcriptional initiation, a linker substitution analysis of the entire promoter region was performed. Each promoter was shown to consist of approximately 50 base pairs comprising two functionally distinct elements. These and previous data strongly support a mode of tr

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42

Kasai, Y., H. Chen, and S. J. Flint. "Anatomy of an unusual RNA polymerase II promoter containing a downstream TATA element." Molecular and Cellular Biology 12, no. 6 (1992): 2884–97. http://dx.doi.org/10.1128/mcb.12.6.2884.

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The adenovirus type 2 IVa2 promoter lacks a conventional TATA element yet directs transcription from two closely spaced initiation sites. To define elements required for in vitro transcription of this promoter, IVa2 templates carrying 5' deletions or linker-scanning mutations were transcribed in HeLa whole-cell extracts and the transcripts were analyzed by primer extension. Mutation of the sequence centered on position -47, which is specifically recognized by a cellular factor, reduced the efficiency of IVa2 transcription two- to threefold, whereas mutation of the sequence centered on position

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43

Kasai, Y., H. Chen, and S. J. Flint. "Anatomy of an unusual RNA polymerase II promoter containing a downstream TATA element." Molecular and Cellular Biology 12, no. 6 (1992): 2884–97. http://dx.doi.org/10.1128/mcb.12.6.2884-2897.1992.

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The adenovirus type 2 IVa2 promoter lacks a conventional TATA element yet directs transcription from two closely spaced initiation sites. To define elements required for in vitro transcription of this promoter, IVa2 templates carrying 5' deletions or linker-scanning mutations were transcribed in HeLa whole-cell extracts and the transcripts were analyzed by primer extension. Mutation of the sequence centered on position -47, which is specifically recognized by a cellular factor, reduced the efficiency of IVa2 transcription two- to threefold, whereas mutation of the sequence centered on position

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Ponticelli, A. S., and K. Struhl. "Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription." Molecular and Cellular Biology 10, no. 6 (1990): 2832–39. http://dx.doi.org/10.1128/mcb.10.6.2832.

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The promoter region of the Saccharomyces cerevisiae his3 gene contains two TATA elements, TC and TR, that direct transcription initiation to two sites designated +1 and +13. On the basis of differences between their nucleotide sequences and their responsiveness to upstream promoter elements, it has previously been proposed that TC and TR promote transcription by different molecular mechanisms. To begin a study of his3 transcription in vitro, we used S. cerevisiae nuclear extracts together with various DNA templates and transcriptional activator proteins that have been characterized in vivo. We

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45

Ponticelli, A. S., and K. Struhl. "Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription." Molecular and Cellular Biology 10, no. 6 (1990): 2832–39. http://dx.doi.org/10.1128/mcb.10.6.2832-2839.1990.

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The promoter region of the Saccharomyces cerevisiae his3 gene contains two TATA elements, TC and TR, that direct transcription initiation to two sites designated +1 and +13. On the basis of differences between their nucleotide sequences and their responsiveness to upstream promoter elements, it has previously been proposed that TC and TR promote transcription by different molecular mechanisms. To begin a study of his3 transcription in vitro, we used S. cerevisiae nuclear extracts together with various DNA templates and transcriptional activator proteins that have been characterized in vivo. We

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46

Cano, A. "Characterization of the rat NHE3 promoter." American Journal of Physiology-Renal Physiology 271, no. 3 (1996): F629—F636. http://dx.doi.org/10.1152/ajprenal.1996.271.3.f629.

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NHE3, a transmembrane protein involved in transcellular ion transport, is expressed in the apical membrane of renal and gastrointestinal epithelia. Chronic regulation by multiple stimuli, including glucocorticoid-induced transcriptional regulation, has been demonstrated. To study the tissue-specific expression and transcriptional regulation of NHE3, the 5' flanking region of the rat NHE3 gene was cloned. Two genomic libraries were screened with the 5' end of the NHE3 cDNA. The 5' flanking region and first exon were isolated. Primer extension mapped a single transcription start site in stomach,

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47

Friedman, AD, BL Krieder, D. Venturelli, and G. Rovera. "Transcriptional regulation of two myeloid-specific genes, myeloperoxidase and lactoferrin, during differentiation of the murine cell line 32D C13." Blood 78, no. 9 (1991): 2426–32. http://dx.doi.org/10.1182/blood.v78.9.2426.bloodjournal7892426.

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The transcriptional regulation of myeloperoxidase (MPO) and lactoferrin (LF) was examined during terminal myeloid differentiation of the murine cell line 32D C13. The rates of transcription initiation for MPO and LF, determined by an in vitro nuclear run-on assay, increased approximately ninefold. The accumulation of MPO mRNA in 32D C13 cells, determined by Northern blot analysis, correlated temporally with the observed increase in MPO transcription initiation. On the other hand, accumulation of LF mRNA lagged behind the observed increase in LF transcription initiation. In mouse L cells, the L

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48

Gumina, Richard J., Nancy E. Kirschbaum, Kim Piotrowski, and Peter J. Newman. "Characterization of the Human Platelet/Endothelial Cell Adhesion Molecule-1 Promoter: Identification of a GATA-2 Binding Element Required for Optimal Transcriptional Activity." Blood 89, no. 4 (1997): 1260–69. http://dx.doi.org/10.1182/blood.v89.4.1260.

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Abstract Platelet/endothelial cell adhesion molecule-1 (PECAM-1) is a 130-kD member of the Ig gene superfamily that is expressed on platelets, endothelial cells, and certain leukocyte subsets. To examine the factors controlling vascular-specific expression of PECAM-1, we cloned the 5′-flanking region of the PECAM-1 gene and analyzed its transcriptional activity. 5′-Rapid amplification of cDNA ends (5′-RACE) analysis showed that transcription initiation occurred at several closely spaced nearby sites originating approximately 204 bp upstream from the translation start site. Analysis of the sequ

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Sement, François M., Takuma Suematsu, Liye Zhang, et al. "Transcription initiation defines kinetoplast RNA boundaries." Proceedings of the National Academy of Sciences 115, no. 44 (2018): E10323—E10332. http://dx.doi.org/10.1073/pnas.1808981115.

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Mitochondrial genomes are often transcribed into polycistronic RNAs punctuated by tRNAs whose excision defines mature RNA boundaries. Although kinetoplast DNA lacks tRNA genes, it is commonly held that in Trypanosoma brucei the monophosphorylated 5′ ends of functional molecules typify precursor partitioning by an unknown endonuclease. On the contrary, we demonstrate that individual mRNAs and rRNAs are independently synthesized as 3′-extended precursors. The transcription-defined 5′ terminus is converted into a monophosphorylated state by the pyrophosphohydrolase complex, termed the “PPsome.” C

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Bogenhagen, D. F., and B. K. Yoza. "Accurate in vitro transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters." Molecular and Cellular Biology 6, no. 7 (1986): 2543–50. http://dx.doi.org/10.1128/mcb.6.7.2543.

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The mitochondrial RNA polymerase from Xenopus laevis oocytes was partially purified by heparin-Sepharose chromatography and phosphocellulose chromatography. This RNA polymerase preparation specifically initiated the transcription of X. laevis mitochondrial DNA (mtDNA) from two bidirectional promoters contained within a 123-base-pair segment of the mtDNA between the heavy-strand replication origin and the rRNA cistrons. Transcription in vitro initiated from precisely the same start sites previously mapped as initiation sites for transcription in vivo. At each of the four sites, initiation occur

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