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Profile

Daniel Reines PhD

  • Department of Biochemistry
    Professor Emeritus
  • (404) 727-3361
  • dreines@emory.edu
  • Pubmed
  • Lab website
  • Emory University School of Medicine
    Biochemistry
    1510 Clifton Rd., Room 4023 RRC
Head shot of Daniel Reines

Overview

The research in our lab centers on mechanisms of transcriptional regulation of gene expression. We are studying the transcription elongation and termination and factors that assist RNA polymerase II in transcription.

We have exploited yeast strains that show a novel regulatory mechanism of gene control that has shed light on the recently discovered world of transcripts that are unstable across genomes of many organisms. An unusual regulatory pathway determines where transcription of IMD2 starts as a function of the cellular GTP concentration. When GTP is abundant, transcription starts with a guanine nucleotide but the transcript terminates yielding a short non-coding RNA that is degraded; no Imd2 is made. When GTP is scarce, and Imd2 protein is needed, this start site is not used as transcription starts downstream from the termination site that yields the non-coding RNA. (Two opinion pieces describing our work and this mechanism are: B. Dichtl, 2008, Molec. Cell 31, 617 & Corden, 2008, EMBO Rep. 9:1084.) This termination mechanism is a specialized termination reaction used for small, often non-coding RNAs that employs RNA binding proteins and a helicase.

Using genetic assays, we have identified a region of an essential yeast protein, Nab3, that stitches together a complex of proteins that bind RNA and regulates expression at IMD2. Interestingly, this low complexity domain (it is almost 30% glutamine), has the aabilty to form amyloid polymers, a property of prions and other proteins that self-assemble and can cause disease in humans such as Alzheimers Disease, Huntingons Disease, and Lou Gehrigs Disease (Amyotrophic Lateral Sclerosis). We have found that there are subcategories of low complexity domains that can perform this function when they replace the native domain of Nab3. Current work focuses on why RNA binding proteins require this assembly domain and how polymerization is involved in its function.

Academic Appointment

  • Professor of Biochemistry, Emory University School of Medicine

Education

Degrees

  • Doctor of Philosophy from Albert Einstein College of Medicine
  • Bachelor of Science from University of Rochester

Research

Focus

  • Biochemistry & Molecular Biology of Gene Expression.

Publications

  • Nab3 nuclear granule accumulation is driven by respiratory capacity.
    Curr Genet Volume: 68 Page(s): 581 - 591
    12/01/2022 Authors: Hutchinson KM; Hunn JC; Reines D
  • Variable penetrance of Nab3 granule accumulation quantified by a new tool for high-throughput single-cell granule analysis.
    Curr Genet Volume: 68 Page(s): 467 - 480
    08/01/2022 Authors: Hunn JC; Hutchinson KM; Kelley JB; Reines D
  • Recent advances in understanding RNA polymerase II structure and function.
    Fac Rev Volume: 9 Page(s): 11
    01/01/2020 Authors: Reines D
  • A fluorescent assay for the genetic dissection of the RNA polymerase II termination machinery.
    Methods Volume: 159-160 Page(s): 124 - 128
    04/15/2019 Authors: Reines D
  • Compositional complexity of rods and rings.
    Mol Biol Cell Volume: 29 Page(s): 2303 - 2316
    09/15/2018 Authors: Schiavon CR; Griffin ME; Pirozzi M; Parashuraman R; Zhou W; Jinnah HA; Reines D; Kahn RA
  • Nab3's localization to a nuclear granule in response to nutrient deprivation is determined by its essential prion-like domain.
    PLoS One Volume: 13 Page(s): e0209195
    01/01/2018 Authors: Loya TJ; O'Rourke TW; Simke WC; Kelley JB; Reines D
  • The hnRNP-like Nab3 termination factor can employ heterologous prion-like domains in place of its own essential low complexity domain.
    PLoS One Volume: 12 Page(s): e0186187
    01/01/2017 Authors: Loya TJ; O'Rourke TW; Reines D
  • Recent advances in understanding transcription termination by RNA polymerase II.
    F1000Res Volume: 5
    01/01/2016 Authors: Loya TJ; Reines D
  • Determinants of Amyloid Formation for the Yeast Termination Factor Nab3.
    PLoS One Volume: 11 Page(s): e0150865
    01/01/2016 Authors: O'Rourke TW; Reines D
  • RNA editing of non-coding RNA and its role in gene regulation.
    Biochimie Volume: 117 Page(s): 22 - 27
    10/01/2015 Authors: Daniel C; Lagergren J; hman M
  • Termination of Transcription of Short Noncoding RNAs by RNA Polymerase II.
    Volume: 84 Page(s): 381 - 404
    01/01/2015 Authors: Arndt KM; Reines D
  • Amyloid-like assembly of the low complexity domain of yeast Nab3.
    Prion Volume: 9 Page(s): 34 - 47
    01/01/2015 Authors: O'Rourke TW; Loya TJ; Head PE; Horton JR; Reines D
  • A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination.
    J Biol Chem Volume: 288 Page(s): 34158 - 34167
    11/22/2013 Authors: Loya TJ; O'Rourke TW; Degtyareva N; Reines D
  • Yeast Nab3 protein contains a self-assembly domain found in human heterogeneous nuclear ribonucleoprotein-C (hnRNP-C) that is necessary for transcription termination.
    J Biol Chem Volume: 288 Page(s): 2111 - 2117
    01/25/2013 Authors: Loya TJ; O'Rourke TW; Reines D
  • A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3.
    Nucleic Acids Res Volume: 40 Page(s): 7476 - 7491
    08/01/2012 Authors: Loya TJ; O'Rourke TW; Reines D
  • Decapping goes nuclear.
    Mol Cell Volume: 46 Page(s): 241 - 242
    05/11/2012 Authors: Reines D
  • Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast.
    Mol Cell Biol Volume: 28 Page(s): 3883 - 3893
    06/01/2008 Authors: Jenks MH; O'Rourke TW; Reines D
  • Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts.
    Mol Cell Biol Volume: 27 Page(s): 2821 - 2829
    04/01/2007 Authors: Kopcewicz KA; O'Rourke TW; Reines D
  • Transcription, translation and fragile X syndrome.
    Curr Opin Genet Dev Volume: 16 Page(s): 270 - 275
    06/01/2006 Authors: Garber K; Smith KT; Reines D; Warren ST
  • The gene encoding the fragile X RNA-binding protein is controlled by nuclear respiratory factor 2 and the CREB family of transcription factors.
    Nucleic Acids Res Volume: 34 Page(s): 1205 - 1215
    01/01/2006 Authors: Smith KT; Nicholls RD; Reines D
  • Dissection of the molecular basis of mycophenolate resistance in Saccharomyces cerevisiae.
    Yeast Volume: 22 Page(s): 1181 - 1190
    11/01/2005 Authors: Jenks MH; Reines D
  • Detection of the mycophenolate-inhibited form of IMP dehydrogenase in vivo.
    Proc Natl Acad Sci U S A Volume: 101 Page(s): 12171 - 12176
    08/17/2004 Authors: McPhillips CC; Hyle JW; Reines D
  • Occupancy and synergistic activation of the FMR1 promoter by Nrf-1 and Sp1 in vivo.
    Hum Mol Genet Volume: 13 Page(s): 1611 - 1621
    08/01/2004 Authors: Smith KT; Coffee B; Reines D
  • Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil.
    Yeast Volume: 21 Page(s): 241 - 248
    02/01/2004 Authors: Riles L; Shaw RJ; Johnston M; Reines D
  • Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast.
    J Biol Chem Volume: 278 Page(s): 28470 - 28478
    08/01/2003 Authors: Hyle JW; Shaw RJ; Reines D
  • Use of RNA yeast polymerase II mutants in studying transcription elongation.
    Methods Enzymol Volume: 371 Page(s): 284 - 292
    01/01/2003 Authors: Reines D
  • Histone modifications depict an aberrantly heterochromatinized FMR1 gene in fragile x syndrome.
    Am J Hum Genet Volume: 71 Page(s): 923 - 932
    10/01/2002 Authors: Coffee B; Zhang F; Ceman S; Warren ST; Reines D
  • Use of an in vivo reporter assay to test for transcriptional and translational fidelity in yeast.
    J Biol Chem Volume: 277 Page(s): 24420 - 24426
    07/05/2002 Authors: Shaw RJ; Bonawitz ND; Reines D
  • Effect of thymine glycol on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II.
    J Biol Chem Volume: 276 Page(s): 45367 - 45371
    11/30/2001 Authors: Tornaletti S; Maeda LS; Lloyd DR; Reines D; Hanawalt PC
  • Regulation of an IMP dehydrogenase gene and its overexpression in drug-sensitive transcription elongation mutants of yeast.
    J Biol Chem Volume: 276 Page(s): 32905 - 32916
    08/31/2001 Authors: Shaw RJ; Wilson JL; Smith KT; Reines D
  • Analysis of gene induction and arrest site transcription in yeast with mutations in the transcription elongation machinery.
    J Biol Chem Volume: 276 Page(s): 11531 - 11538
    04/13/2001 Authors: Wind-Rotolo M; Reines D
  • Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion.
    Mol Cell Biol Volume: 20 Page(s): 7427 - 7437
    10/01/2000 Authors: Shaw RJ; Reines D
  • Transcription elongation factor SII.
    Bioessays Volume: 22 Page(s): 327 - 336
    04/01/2000 Authors: Wind M; Reines D
  • Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA.
    J Biol Chem Volume: 274 Page(s): 24124 - 24130
    08/20/1999 Authors: Tornaletti S; Reines D; Hanawalt PC
  • Mechanism and regulation of transcriptional elongation by RNA polymerase II.
    Curr Opin Cell Biol Volume: 11 Page(s): 342 - 346
    06/01/1999 Authors: Reines D; Conaway RC; Conaway JW
  • Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells.
    Nat Genet Volume: 22 Page(s): 98 - 101
    05/01/1999 Authors: Coffee B; Zhang F; Warren ST; Reines D
  • Mutations in RNA polymerase II and elongation factor SII severely reduce mRNA levels in Saccharomyces cerevisiae.
    Mol Cell Biol Volume: 18 Page(s): 5771 - 5779
    10/01/1998 Authors: Lennon JC; Wind M; Saunders L; Hock MB; Reines D
  • Recognition of a human arrest site is conserved between RNA polymerase II and prokaryotic RNA polymerases.
    J Biol Chem Volume: 273 Page(s): 16843 - 16852
    07/03/1998 Authors: Mote J; Reines D
  • Nucleotide sequence context effect of a cyclobutane pyrimidine dimer upon RNA polymerase II transcription.
    J Biol Chem Volume: 272 Page(s): 31719 - 31724
    12/12/1997 Authors: Tornaletti S; Donahue BA; Reines D; Hanawalt PC
  • Assays for investigating transcription by RNA polymerase II in vitro.
    Methods Volume: 12 Page(s): 192 - 202
    07/01/1997 Authors: Reines D; Dvir A; Conaway JW; Conaway RC
  • Glutamic acid-371 of the barnase homology domain in RNA polymerase II is not required for SII-activated RNA cleavage.
    Mol Gen Genet Volume: 253 Page(s): 507 - 511
    01/27/1997 Authors: Powell W; Lennon JC; Elsevier JP; Reines D
  • Elongation factor SII contacts the 3'-end of RNA in the RNA polymerase II elongation complex.
    J Biol Chem Volume: 271 Page(s): 22301 - 22304
    09/13/1996 Authors: Powell W; Bartholomew B; Reines D
  • The RNA polymerase II general elongation factors.
    Trends Biochem Sci Volume: 21 Page(s): 351 - 355
    09/01/1996 Authors: Reines D; Conaway JW; Conaway RC
  • Transcription elongation factor SII (TCEA) maps to human chromosome 3p22 --> p21.3.
    Genomics Volume: 36 Page(s): 185 - 188
    08/15/1996 Authors: DiMarco SP; Glover TW; Miller DE; Reines D; Warren ST
  • Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest.
    Proc Natl Acad Sci U S A Volume: 93 Page(s): 6935 - 6940
    07/09/1996 Authors: Gu W; Wind M; Reines D
  • Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II.
    J Biol Chem Volume: 271 Page(s): 10588 - 10594
    05/03/1996 Authors: Donahue BA; Fuchs RP; Reines D; Hanawalt PC
  • Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro.
    J Biol Chem Volume: 271 Page(s): 6866 - 6873
    03/22/1996 Authors: Powell W; Reines D
  • Purification of RNA polymerase II general transcription factors from rat liver.
    Methods Enzymol Volume: 273 Page(s): 194 - 207
    01/01/1996 Authors: Conaway RC; Reines D; Garrett KP; Powell W; Conaway JW
  • Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence.
    J Biol Chem Volume: 270 Page(s): 30441 - 30447
    12/22/1995 Authors: Gu W; Reines D
  • T7 RNA polymerase bypass of large gaps on the template strand reveals a critical role of the nontemplate strand in elongation.
    Cell Volume: 82 Page(s): 577 - 585
    08/25/1995 Authors: Zhou W; Reines D; Doetsch PW
  • Identification of a decay in transcription potential that results in elongation factor dependence of RNA polymerase II.
    J Biol Chem Volume: 270 Page(s): 11238 - 11244
    05/12/1995 Authors: Gu W; Reines D
  • TRANSCRIPTION OF DNA CONTAINING SPECIFIC LESIONS
    FASEB JOURNAL Volume: 9 Page(s): A1402 - A1402
    04/24/1995 Authors: DONAHUE BA; REINES D; HANAWALT PC
  • TRANSCRIPTION OF TEMPLATES CONTAINING A SPECIFIC DNA LESION AT A DEFINED SITE
    JOURNAL OF CELLULAR BIOCHEMISTRY Page(s): 313 - 313
    03/10/1995 Authors: DONAHUE BA; REINES D; HANAWALT PC
  • In male mouse germ cells, copper-zinc superoxide dismutase utilizes alternative promoters that produce multiple transcripts with different translation potential.
    J Biol Chem Volume: 270 Page(s): 236 - 243
    01/06/1995 Authors: Gu W; Morales C; Hecht NB
  • Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template.
    Proc Natl Acad Sci U S A Volume: 91 Page(s): 8502 - 8506
    08/30/1994 Authors: Donahue BA; Yin S; Taylor JS; Reines D; Hanawalt PC
  • A DNA minor groove-binding ligand both potentiates and arrests transcription by RNA polymerase II. Elongation factor SII enables readthrough at arrest sites.
    J Mol Biol Volume: 236 Page(s): 725 - 737
    02/25/1994 Authors: Mote J; Ghanouni P; Reines D
  • NASCENT RNA CLEAVAGE BY POLYMERASE-II DOES NOT REQUIRE UPSTREAM TRANSLOCATION OF THE ELONGATION COMPLEX ON DNA
    JOURNAL OF CELLULAR BIOCHEMISTRY Page(s): 59 - 59
    02/13/1994 Authors: GU WG; POWELL W; MOTE J; REINES D
  • MECHANISM OF SII-DEPENDENT RNA-SYNTHESIS
    JOURNAL OF CELLULAR BIOCHEMISTRY Page(s): 10 - 10
    02/13/1994 Authors: REINES D
  • SII INDUCES CLEAVAGE OF NASCENT TRANSCRIPTS ARRESTED BY A CYCLOBUTANE PYRIMIDINE DIMER ON THE TEMPLATE DNA STRAND
    JOURNAL OF CELLULAR BIOCHEMISTRY Page(s): 58 - 58
    02/13/1994 Authors: DONAHUE BA; REINES D; HANAWALT PC
  • Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA.
    J Biol Chem Volume: 268 Page(s): 25604 - 25616
    12/05/1993 Authors: Gu W; Powell W; Mote J; Reines D
  • FMR1 protein: conserved RNP family domains and selective RNA binding.
    Science Volume: 262 Page(s): 563 - 566
    10/22/1993 Authors: Ashley CT; Wilkinson KD; Reines D; Warren ST
  • Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein.
    Proc Natl Acad Sci U S A Volume: 90 Page(s): 1917 - 1921
    03/01/1993 Authors: Reines D; Mote J
  • Transcription elongation by RNA polymerase II: mechanism of SII activation.
    Cell Mol Biol Res Volume: 39 Page(s): 331 - 338
    01/01/1993 Authors: Reines D; Ghanouni P; Gu W; Mote J; Powell W
  • The RNA polymerase II elongation complex. Factor-dependent transcription elongation involves nascent RNA cleavage.
    J Biol Chem Volume: 267 Page(s): 15516 - 15522
    08/05/1992 Authors: Reines D; Ghanouni P; Li QQ; Mote J
  • Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II.
    J Biol Chem Volume: 267 Page(s): 3795 - 3800
    02/25/1992 Authors: Reines D
  • Purification of RNA using an anti-RNA monoclonal antibody.
    Anal Biochem Volume: 196 Page(s): 367 - 372
    08/01/1991 Authors: Reines D
  • RNA polymerase II elongation complex. Elongation complexes purified using an anti-RNA antibody do not contain initiation factor alpha.
    J Biol Chem Volume: 266 Page(s): 10510 - 10517
    06/05/1991 Authors: Reines D
  • INHIBITION OF TRANSCRIPTION BY OXIDATIVE DNA DAMAGE PRODUCTS
    FASEB JOURNAL Volume: 5 Page(s): A439 - A439
    03/11/1991 Authors: BYRD S; REINES D; DOETSCH PW
  • Purified elongation factor SII is sufficient to promote read-through by purified RNA polymerase II at specific termination sites in the human histone H3.3 gene.
    J Biol Chem Volume: 265 Page(s): 14554 - 14560
    08/25/1990 Authors: SivaRaman L; Reines D; Kane CM
  • Transcription initiated by RNA polymerase II and purified transcription factors from liver. Cooperative action of transcription factors tau and epsilon in initial complex formation.
    J Biol Chem Volume: 265 Page(s): 7552 - 7558
    05/05/1990 Authors: Conaway JW; Reines D; Conaway RC
  • Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro.
    J Biol Chem Volume: 264 Page(s): 10799 - 10809
    06/25/1989 Authors: Reines D; Chamberlin MJ; Kane CM
  • Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences.
    J Mol Biol Volume: 196 Page(s): 299 - 312
    07/20/1987 Authors: Reines D; Wells D; Chamberlin MJ; Kane CM
  • TRANSCRIPTIONAL ELONGATION BY PURIFIED RNA POLYMERASE-II
    FEDERATION PROCEEDINGS Volume: 45 Page(s): 1777 - 1777
    05/01/1986 Authors: KANE CM; DEDRICK RM; REINES D; CHAMBERLIN MJ
  • TRANSCRIPTION TERMINATION BY CALF THYMUS RNA POLYMERASE-II
    JOURNAL OF CELLULAR BIOCHEMISTRY Page(s): 172 - 172
    01/01/1986 Authors: KANE CM; DEDRICK RL; REINES D; CHAMBERLIN MJ
  • Immunochemical analysis of the supramolecular structure of myosin in contractile cytoskeletons of Dictyostelium amoebae.
    J Biol Chem Volume: 260 Page(s): 14248 - 14254
    11/15/1985 Authors: Reines D; Clarke M
  • Quantitative immunochemical studies of myosin in Dictyostelium discoideum.
    J Biol Chem Volume: 260 Page(s): 1133 - 1140
    01/25/1985 Authors: Reines D; Clarke M
  • QUANTITATIVE IMMUNOCHEMICAL STUDIES OF MYOSIN IN DICTYOSTELIUM DISCOIDEUM
    JOURNAL OF CELL BIOLOGY Volume: 99 Page(s): A35 - A35
    01/01/1984 Authors: REINES D; CLARKE M
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