An Introduction to Transcription and Gene Regulation

Geiduschek, E. Peter

doi:10.1074/jbc.x110.143867

Cited by 4 publications

(2 citation statements)

References 49 publications

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“…These ORFs were on opposite strands, and did not overlap. It was not possible to ascertain which was the correct gene product, and it is a distinct possibility that both strands were transcribed 38 . A slightly different situation arose when both the ORFs were on the same strand 39 , as in the case of the transcript C54995_G6_I2.…”

Section: Resultsmentioning

confidence: 99%

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

et al. 2015

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The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

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Section: Resultsmentioning

confidence: 99%

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

et al. 2015

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“…The elegant systems by which T4 hijacks the host RNAP offer insight into the basic mechanisms of transcription [reviewed in ( 1 , 74 )]. For example, the activation of T4 middle promoters through the process of σ appropriation highlights the importance of σ 70 Region 4/H5 for contacting the DNA, RNAP core, and regulatory factors.…”

Section: Discussionmentioning

confidence: 99%

Visualizing the phage T4 activated transcription complex of DNA andE. coliRNA polymerase

et al. 2016

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The ability of RNA polymerase (RNAP) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. However, there is only one crystallized structure of a complete activator/RNAP/DNA complex. In a process called σ appropriation, bacteriophage T4 activates a class of phage promoters using an activator (MotA) and a co-activator (AsiA), which function through interactions with the σ70 subunit of RNAP. We have developed a holistic, structure-based model for σ appropriation using multiple experimentally determined 3D structures (Escherichia coli RNAP, the Thermus aquaticus RNAP/DNA complex, AsiA /σ70 Region 4, the N-terminal domain of MotA [MotANTD], and the C-terminal domain of MotA [MotACTD]), molecular modeling, and extensive biochemical observations indicating the position of the proteins relative to each other and to the DNA. Our results visualize how AsiA/MotA redirects σ, and therefore RNAP activity, to T4 promoter DNA, and demonstrate at a molecular level how the tactful interaction of transcriptional factors with even small segments of RNAP can alter promoter specificity. Furthermore, our model provides a rational basis for understanding how a mutation within the β subunit of RNAP (G1249D), which is far removed from AsiA or MotA, impairs σ appropriation.

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The Enzymology of Transcriptional Regulation: the Work of E. Peter Geiduschek

Kresge¹,

Simoni²,

Hill³

2010

Journal of Biological Chemistry

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E. Peter Geiduschek was born in Vienna, Austria in 1928. He attended Columbia University and graduated with a degree in chemistry in 1945, after which he enrolled at Harvard University, intending to study physical chemistry. However, instead he joined Paul Doty's biophysical chemistry laboratory where he studied the interactions between macromolecules. Geiduschek earned his doctoral degree in 1952 and then left Cambridge for New Haven, where he had been offered an instructorship in chemistry at Yale University. At the end of his first year of teaching, Geiduschek began two years of military service, during which he was posted to the biochemistry department at the Walter Reed Hospital in Washington, D.C. He returned to Yale and later did a brief stint at the University of Michigan. In 1959, he moved again, this time to Chicago to accept a position in the Committee on Biophysics at the University of Chicago, where he was first introduced to enzymology and phage. In 1970, Geiduschek joined the biology department at the University of California, San Diego, where he has remained since. Geiduschek's research has dealt primarily with the enzymology of transcriptional regulation in phage-infected bacteria, eukaryotes, and archaea. One topic he has researched extensively is the regulation of the late genes of bacteriophage T4. The story of how Geiduschek came to that subject can be found in his Journal of Biological Chemistry (JBC) Reflections (1). By 1978, when Geiduschek's first JBC Classic was published, it was known that after infecting Escherichia coli, the T4 bacteriophage made different proteins at different times of the viral infection cycle. The genes for these proteins were referred to as early, middle, and late genes. It also was known that the late genes required T4 DNA replication for their transcription and that the RNA polymerase that functioned in T4-infected cells during the late period of infection was an extensively modified host enzyme, containing ADP-ribosylation and T4specific subunits gp33 and gp55.

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An Introduction to Transcription and Gene Regulation

Cited by 4 publications

References 49 publications

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

Visualizing the phage T4 activated transcription complex of DNA andE. coliRNA polymerase

The Enzymology of Transcriptional Regulation: the Work of E. Peter Geiduschek

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