Accès ouvert
2026
article
OpenAlex
Zarmik Moqtaderi, Joseph V. Geisberg, Kevin Struhl
The poly(A) profile of a typical yeast gene comprises ∼50 poly(A) sites corresponding to distinct 3' mRNA isoforms. Poly(A) profiles are shifted upstream in strains with slow RNA polymerase II (Pol II) elongation rates resulting from Pol II mutations or from depletion …
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Accès ouvert
2024
article
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
Expression of a typical yeast gene results in ∼50 3' mRNA isoforms that are distinguished by the locations of poly(A) sites within the 3' untranslated regions (3' UTRs). The location of poly(A) sites with respect to the translational termination codon varies considerably …
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Accès ouvert
2024
article
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
The RNA polymerase II (Pol II) elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization. In yeast, depletion of either of the histone chaperones FACT or Spt6 causes …
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Accès ouvert
2023
article
OpenAlex
Alexandra Khitun, Christian Brion, Zarmik Moqtaderi, Joseph V. Geisberg et autres
Yeast mRNAs are polyadenylated at multiple sites in their 3' untranslated regions (3' UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites, and fast …
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Accès ouvert
2023
article
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
Alternative polyadenylation generates numerous 3' mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3' untranslated regions (3'UTRs). Here, we examine how environmental conditions affect 3' mRNA …
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Accès ouvert
2022
article
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Nova Fong, Benjamin Erickson et autres
Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' untranslated regions. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et al., …
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Accès ouvert
2022
peer-review
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Nova Fong, Benjamin Erickson et autres
Cleavage/polyadenylation, the process generating mRNA 3' ends, is linked at the nucleotide level to the position of RNA polymerase II, indicating a spatial coupling so polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.
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Accès ouvert
2022
preprint
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Nova Fong, Benjamin Erickson et autres
ABSTRACT Alternative polyadenylation yields many mRNA isoforms whose 3’ termini occur disproportionately in clusters within 3’ UTRs. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et., 2020). …
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Accès ouvert
2022
article
OpenAlex
Kai Hin Lui, Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
The 3' ends of eukaryotic mRNAs are generated by cleavage of nascent transcripts followed by polyadenylation, which occurs at numerous sites within 3' untranslated regions (3' UTRs) but rarely within coding regions. An individual gene can yield many 3'-mRNA isoforms with distinct …
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Accès ouvert
2022
article
OpenAlex
Zarmik Moqtaderi, Joseph V. Geisberg, Kevin Struhl
Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and messenger RNA (mRNA) turnover in the cytoplasm. On a …
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Accès ouvert
2021
preprint
OpenAlex
Zarmik Moqtaderi, Susan J. Brown, Welcome Bender
Eukaryotic genomes typically show a uniform G + C content among chromosomes, but on smaller scales, many species have a G + C density that fluctuates with a characteristic wavelength. This oscillation is evident in many insect species, with wavelengths ranging between …
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Accès ouvert
2020
article
OpenAlex
Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
Yeast cells undergoing the diauxic response show a striking upstream shift in poly(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3' mRNA isoforms for most genes. This altered poly(A) pattern is extremely similar to that observed in …
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