Alan G. Hinnebusch, Ph.D.

NIH Distinguished Investigator

Section on Nutrient Control of Gene Expression


6 230


Research Topics

The goal of research in the Section on Nutrient Control of Gene Expression is to elucidate fundamental molecular mechanisms of eukaryotic gene regulation. Saccharomyces cerevisiae is employed as a model organism, allowing genetics and biochemistry to be combined in dissecting processes of gene transcription and mRNA translation crucial in living cells. Much work focuses on the general amino acid control, wherein amino acid biosynthetic genes in multiple pathways are induced by transcriptional activator Gcn4 in response to limitation for any amino acid. Gcn4 is one of the best-understood transcription factors regarding the structure of its activation domain, co-activator targets, and activation mechanism, its transcriptome, and pathways regulating its synthesis, function, and degradation. This knowledge base, combined with the large battery of mutants, plasmids, and antibodies generated over the years, and new technologies based on next-generation sequencing, can be applied to dissect numerous aspects of transcriptional control of general importance in eukaryotic cells. Recent accomplishments of the group include uncovering overlapping functions of histone acetyltransferase (HAT) complexes SAGA and NuA4, and opposing activities of multiple histone deacetylase (HDA) complexes, in nucleosome disassembly and transcription elongation by RNA Polymerase II (Pol II). They have enhanced understanding of the mechanism of phosphorylation of the C-terminal domain (CTD) of Pol II subunit Rpb1 and its role in coactivator recruitment by (i) uncovering the contribution of cyclin-dependent kinase (Cdk) Bur1/Bur2 to CTD phosphorylation on Ser2 and the role of Cdk Kin28 in Bur1/Bur2 recruitment, (ii) identifying contributions of Kin28, Bur1/Bur2 and yeast DSIF (Spt4/Spt5) to recruitment of elongation factor Paf1C via phosphorylated Pol II CTD and C-terminal repeats in Spt5; and they identified a “two-stage” recruitment mechanism for both HDA complexes and HAT complex NuA4 via phosphorylated Pol II CTD and methylated histone tails. More recently, they uncovered genome-wide functional cooperation among the HAT complex SAGA, chromatin remodeling complex SWI/SNF, and protein chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation. Similarly, they showed that SWI/SNF cooperates with the RSC remodeling complex to both evict and reposition promoter nucleosomes at the most highly expressed yeast genes. They found unexpectedly that most of the occupied Gcn4 binding sites in the genome reside inside coding sequences rather than upstream of promoters; and that such non-canonical binding events frequently induce bidirectional transcription from within the coding sequences in addition to the conventional full-length mRNA transcripts of the gene.

The pathway for inducing Gcn4 synthesis is also a focal point of research, as this represents one branch of a dual mechanism of translational control, conserved throughout eukaryotes, mobilized by nutrient starvation or stress to achieve both general and gene-specific changes in protein synthesis. The intricate mechanism governing GCN4 translation involves multiple initiation factors (eIFs) and a signaling pathway that attenuates the function of eIF2 through its phosphorylation by protein kinase Gcn2. Mutants altering GCN4 translation have been identified that affect assembly of initiation complexes, and complementary selections are used to uncover mutations that alter the fidelity of selecting AUG as the initiation codon. Analyzing the biochemical effects of such mutations in a yeast reconstituted in vitro system, in collaboration with Jon Lorsch’s group in NICHD, is illuminating in vivo mechanisms involved in recruitment of initiator tRNAMet and mRNA to ribosomes and recognition of start codons during ribosomal scanning. Our collaboration with Venki Ramakrishnan’s group (MRC, Cambridge) is providing high-resolution structures of translation preinitiation complexes (PICs) in different states that inform our interpretations of previous findings and reveal new aspects of the initiation process that can be interrogated with genetics and biochemistry. Recent accomplishments of the group include identifying functional domains of eukaryotic initiation factors (eIFs) 1, 1A, 2, 3c, and 5, and of initiator tRNAi, 18S rRNA, and ribosomal proteins uS7/Rps5 and uS3/Rps3, involved in accurate and efficient AUG recognition during scanning; and contributing to elucidation of conformational transitions in the PIC through FRET analysis, chemical modification, and cryo-EM analyses of reconstituted PICs in different functional states. The group has identified multiple elements in yeast eIF4G involved in activating mRNA for translation initiation and functional domains in yeast eIF4B that enhance PIC attachment to mRNA, implicated eIF4B in eIFG∙eIF4A assembly, and defined distinct roles of DEAD-box helicases eIF4A and Ded1 in modulating translational efficiencies of mRNAs genome-wide by facilitating ribosome attachment and subsequent scanning of the 5' untranslated leaders of mRNAs--particularly when the 5'UTRs are burdened with secondary structures. They have uncovered the functions of ABCE proteins Rli1/ABCE1 and Arb1 in PIC assembly and ribosome biogenesis, respectively, and, in collaboration with Rachel Greens's lab established that Rli1 is required in vivo for efficient ribosome recycling and to prevent aberrant translation of 3’ untranslated regions (3' UTR) by unrecycled 80S ribosomes. Recently, in collaboration with Nicholas Guydosh and Sergey Dmitriev, they demonstrated that the Tma64/Tma20/Tma22 proteins carry out the second step of ribosome recycling in vivo, acting after release of the 60S subunit by Rli1 in the dissociation of 40S post-termination complexes; and that these proteins are needed to prevent unscheduled reinitiation events in mRNA 3'UTRs by unrecycled 40S subunits.


Dr. Alan G. Hinnebusch received his B.S. in Biology from the University of Dayton, Ohio, in 1975 and his Ph.D. in Biochemistry and Molecular Biology from Harvard University in 1980. He studied as a postdoctoral fellow in the laboratory of Dr. Gerald R. Fink at Cornell University and the Massachusetts Institute of Technology from 1980 to 1983. He joined the NICHD as a Senior Staff Fellow in 1983 and became Chief of the Laboratory of Eukaryotic Gene Regulation in 1995. In 2000, he was appointed as Chief of the Laboratory of Gene Regulation and Development and Head of the Section on Nutrient Control of Gene Regulation. In 2007, he was named Head of the Program in Cellular Regulation and Metabolism. Dr. Hinnebusch has served on the editorial boards of Genetics, Microbiological Reviews, Molecular Microbiology, Journal of Biological Chemistry, and Molecular & Cellular Biology, and is currently a member of the editorial boards of Genes & Development, eLife, and Genetics. He was co-organizer of the Cold Spring Harbor Laboratory Meeting on Translational Control from 2000 to 2010. He has published more than 200 research articles in peer-reviewed journals and more than 50 review articles and book chapters pertaining to his field of research. In 1994 he was named Maryland's Outstanding Young Scientist and was elected as a Fellow of the American Academy of Microbiology. In 2009 he was elected as a Fellow of the American Association for the Advancement of Science and as a Fellow of the American Academy of Arts and Sciences, and in 2015 he was elected to the National Academy of Sciences.

Selected Publications

  1. Rawal Y, Chereji RV, Valabhoju V, Qiu H, Ocampo J, Clark DJ, Hinnebusch AG. Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast. Mol Cell. 2018;70(2):297-311.e4.

  2. Rawal Y, Chereji RV, Qiu H, Ananthakrishnan S, Govind CK, Clark DJ, Hinnebusch AG. SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast. Genes Dev. 2018;32(9-10):695-710.

  3. Dong J, Aitken CE, Thakur A, Shin BS, Lorsch JR, Hinnebusch AG. Rps3/uS3 promotes mRNA binding at the 40S ribosome entry channel and stabilizes preinitiation complexes at start codons. Proc Natl Acad Sci U S A. 2017;114(11):E2126-E2135.

  4. Sen ND, Zhou F, Ingolia NT, Hinnebusch AG. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Res. 2015;25(8):1196-205.

  5. Saini AK, Nanda JS, Lorsch JR, Hinnebusch AG. Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome. Genes Dev. 2010;24(1):97-110.

This page was last updated on October 22nd, 2018