Robert E. Kingston

Last updated
Robert E. Kingston
Alma mater Harvard College, University of California, Berkeley
Known forNucleosome biology
Scientific career
Institutions Massachusetts General Hospital
Doctoral advisor Michael Chamberlin
Other academic advisors Phillip Sharp
Notable students Geeta Narlikar

Robert E. Kingston (born in 1954) is an American biochemist and geneticist who studies the functional and regulatory role nucleosomes play in gene expression, specifically during early development. [1] After receiving his PhD (1981) and completing post-doctoral research, Kingston became an assistant professor at Massachusetts General Hospital (1985), where he started a research laboratory focused on understanding chromatin's structure with regards to transcriptional regulation. [1] As a Harvard graduate himself, Kingston has served his alma mater through his leadership. [1]

Contents

He was the head of the Harvard's Biological and Biomedical Sciences PhD program from 2004 to 2007, the chair of the molecular biology department at Massachusetts General Hospital from 2005 to 2023, the vice-chair of the department of genetics at Harvard Medical School, and the chair of the executive committee on research at Massachusetts General Hospital from 2012 to 2015. [2] [1] In November 2022, he was appointed as the inaugural Chief Academic Officer and Senior Vice President for Research and Education for Massachusetts General Hospital effective January 2023. [3]

In addition to being a professor of genetics at Harvard Medical School, Kingston frequently organizes conferences and performs editorials on his research interests. [1] In 2016, he was elected by his peers to be a member of the National Academy of Sciences. [2]

Education

Kingston graduated from Harvard College in 1976. [1] Four years later, he completed his PhD on bacterial regulatory mechanisms at the University of California, Berkeley, while under the mentorship of Michael Chamberlin. [1] He then performed postdoctoral research on mammalian post-transcriptional mechanisms at the Massachusetts Institute of Technology under the supervision of Dr. Philip Sharp. [1]

Research

Kingston's research continues to have a significant impact on developmental biology and epigenetics, as it focuses on an important feature of eukaryotic gene expression: chromatin remodeling. [2] His research can be applied to the field of gene therapy, specifically principles surrounding chromatin regulation. [2]

nusA protein

In 1981, Kingston received his PhD after working on a number of research initiatives surrounding genome regulation and expression. Through an in vitro study that mapped termination sites dependent on the nusA protein, he discovered that in vivo rRNA transcription is regulated by turnstile attenuation, a mechanism that terminates rrnB chains in the leader region. [4] He found that this happens because of the specific presence and location of pause sites, located 90 and 91 bases from the P1 promoter, which are sensitive to the presence of nusA protein and concentration of regulatory nucleotide guanosine tetraphosphate. [4]

Heat shock protein 70 (HSP70)

After recognizing that the myc gene was involved with tumor formation, Kingston drew a parallel between the presence of the myc gene and the increased genomic expression of HSP70. [5] He also found that the genomic expression of HSP70 is also dependent on physiological stresses.5 Analyzing the gene sequences showed that heat shock, cadmium induction, and metallothionein II responsiveness are needed for HSP70 gene expression during the primary level of transcription. [6] He observed that while the physiological factors have a role on one domain (distal) of the HSP70 promoter, the other domain (proximal) is more responsive to serum stimulation. [6] After conducting in vitro transcription experiments, Kingston found that there is a heat-shock transcription factor (HSTF) that allows the interactions with the heat shock element (HSE), and that the HSP70 gene promoter also depends on a CCAAT-box-binding transcription factor (CTF) for CCAAT-box-dependent transcription. [7] In vitro cell-free systems that have heat-induced activation of human heat-shock factor (HSF) were used to determine that at 43 °C, HSF undergoes post-translational modification to where it can then bind to a specific DNA sequence, HSE. [8]

SWI/SNF subunits of chromatin remodeling

Kingston's primary research interests surround chromatin remodeling, and his breakthroughs within the field began when he discovered the functional subunit responsibilities of SWI/SNF, a chromatin remodeling complex that causes specific transcription factors to bind to nucleosomal DNA. [9] He defined that two SWI/SNF subunits, BRG1 and BAF155, along with EKLF zinc-finger DNA binding domains (DBDs) can be used to remodel chromatin, meaning that these specific domains of SWI/SNF have an effect on transcription factor-directed nucleosome remodeling. [9] He was also able to conclude that different domains of transcription factors target SWI/SNF complexes to chromatin in a gene-selective way. [9] His work on nucleosomal DNA extends to his findings on TATA-binding protein (TPB), specifically how dynamic remodeling of chromatin can allow for TPB to bind onto the TATA sequence. His work on SWI/SNF led him to conclude that these two subunits are responsible for an “activation” function related to transcription. [10] This is because a purified human SWI/SNF complex mediated the ATP-dependent disruption of a nucleosomal barrier, resulting in SWI/SNF activators (GAL4-VP16 and GAL 4-AH) binding onto the nucleosome core. [11] Since the TATA sequence is inside a nucleosome, adding ATP will cause human SWI/SNF to recognize its chromatin structure and alter the nucleosomal DNA sequence so that the TPB can access and bind to it. [10] From a broader perspective, this allows for more eukaryotic gene expression, since a variety of eukaryotic promoters will be regulated. [10]

Advancements in biotechnology

Because Polycomb repressive complex 1 (PRC1) contains a number of proteins that work together to repress SWI/SNF complex chromatin remodeling, Kingston refined a method to reconstitute a stable complex of proteins that together form a “chromatin structure” that excludes human SWI/SNF. [12] Kingston found that in order to form the complex that silences chromatin remodeling, it must be stable and compact. [13] Through electron microscopy, he found that the components of PRC 1 induce compaction of nucleosomal arrays. [13] The compaction of chromatin occurs within the presence of three nucleosomes and a region of Posterior Sex Combs together. [13] His work with Polycomb proteins further extends, as he helped develop a RIP-sequence method to capture the Polycomb repressive complex 2 (PRC2) transcriptome in embryonic stem cells. [14] Noting that Polycomb proteins factor into stem cell renewal and the formation of diseases, Kingston's discovery of direct interactions (Ezh2 subunit) and PRC2 cofactors (Gtl2 RNA) really contributed to identifying the function of Polycomb proteins within the genome. [14] Dr. Kingston's heavy interest in chromatin remodeling also showed through his research regarding purifying the proteins associated with chromatin remodeling. [15] He established a protocol, Proteomics of Isolated Chromatin Segments (PICh), where a specific nucleic acid probe is used to isolate genomic DNA with regards to the quantity and purity of associated proteins. [15] The PlCh protocol was then used on telomeric chromatin to identify telomeric factors and resulted in finding a number of novel associations. [15] Professor Kingston's advancements within the field of biotechnology extend into developing eukaryotic cell transfection protocols, for he also developed two methods of calcium phosphate transfection for transient and stable transfections. [16] These two methods use a precipitate to introduce plasmid DNA into monolayer cell cultures. [16] The difference between them is that one uses a HEPES-buffered solution while the other uses a BES-buffered system, but both form a precipitate over the cells and allow for similar levels of transient expression. [16]

Macromolecular interaction in chromatin remodeling

Kingston's research surrounding chromatin remodeling dwells into understanding how long non-coding RNAs (lncRNAs) play a role on chromatin binding sites. [17] He was able to genome map NEAT1 and MALAT (both lncRNAs) and found that they localize overactive genes. [17] His research also suggests that NEAT1 and MALAT interact with complementary proteins. [17] He found that underlying DNA sequences are not responsible for targeting NEAT1 to chromatin, but it is rather transcriptional sequences that allow it to bind onto chromatin sites. [17] Robert Kingston's work with lncRNAs extends, as he also discovered that DIGIT interacts with the Bromodomain-containing protein 3 (BRD3). [18] He found that they work together to regulate endoderm differentiation transcriptionally. [18]

Kingston found another breakthrough: that a protein-protein interaction affected chromatin remodeling in the lymphoid system. [19] He discovered that the Ikaros-NURD complex is able to target chromatin remodeling and histone deacetylation complexes in vivo. [19] This allowed him to conclude that chromatin remodeling affects lymphocyte differentiation. [19]

Advances in structural and functional biochemistry

One of the biggest discoveries that Robert Kingston found was that the nucleosome structure could be arranged into different conformations so that different biophysical properties can result, including mechanisms of transcription. [20] Specifically, multiprotein complexes that were used for transcriptional regulation were found to acetylate nucleosomes, deacetylate nucleosomes, or alter nucleosome structure when ATP was present. [20] These alterations would essentially be a major way to regulate eukaryotic gene expression. [20] Kingston furthered this and discovered the novel nucleosome remodelling and deacetylating (NRD) complex. [21] Through in vitro studies with CHD3 and CHD4 proteins with ATPase domains found in chromatin remodelling factors, Dr. Kingston established that there was a functional and physical link between nucleosome remodeling proteins and histone deacetylases’ chromatin-modifying features. [21]

Selected review publications

Related Research Articles

Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in reinforcing the DNA during cell division, preventing DNA damage, and regulating gene expression and DNA replication. During mitosis and meiosis, chromatin facilitates proper segregation of the chromosomes in anaphase; the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin.

<span class="mw-page-title-main">Nucleosome</span> Basic structural unit of DNA packaging in eukaryotes

A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.

A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation of gene expression is an essential feature of all living organisms and viruses.

RSC is a member of the ATP-dependent chromatin remodeler family. The activity of the RSC complex allows for chromatin to be remodeled by altering the structure of the nucleosome.

<span class="mw-page-title-main">SWI/SNF</span> Subfamily of ATP-dependent chromatin remodeling complexes

In molecular biology, SWI/SNF, is a subfamily of ATP-dependent chromatin remodeling complexes, which is found in eukaryotes. In other words, it is a group of proteins that associate to remodel the way DNA is packaged. This complex is composed of several proteins – products of the SWI and SNF genes, as well as other polypeptides. It possesses a DNA-stimulated ATPase activity that can destabilize histone-DNA interactions in reconstituted nucleosomes in an ATP-dependent manner, though the exact nature of this structural change is unknown. The SWI/SNF subfamily provides crucial nucleosome rearrangement, which is seen as ejection and/or sliding. The movement of nucleosomes provides easier access to the chromatin, enabling binding of specific transcription factors, and allowing genes to be activated or repressed.

In genetics and cell biology, repression is a mechanism often used to decrease or inhibit the expression of a gene. Removal of repression is called derepression. This mechanism may occur at different stages in the expression of a gene, with the result of increasing the overall RNA or protein products. Dysregulation of derepression mechanisms can result in altered gene expression patterns, which may lead to negative phenotypic consequences such as disease.

<span class="mw-page-title-main">Eukaryotic transcription</span> Transcription is heterocatalytic function of DNA

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes. Besides actively regulating gene expression, dynamic remodeling of chromatin imparts an epigenetic regulatory role in several key biological processes, egg cells DNA replication and repair; apoptosis; chromosome segregation as well as development and pluripotency. Aberrations in chromatin remodeling proteins are found to be associated with human diseases, including cancer. Targeting chromatin remodeling pathways is currently evolving as a major therapeutic strategy in the treatment of several cancers.

<span class="mw-page-title-main">SMARCA4</span> Protein-coding gene in the species Homo sapiens

Transcription activator BRG1 also known as ATP-dependent chromatin remodeler SMARCA4 is a protein that in humans is encoded by the SMARCA4 gene.

<span class="mw-page-title-main">SMARCB1</span> Protein-coding gene in the species Homo sapiens

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 is a protein that in humans is encoded by the SMARCB1 gene.

<span class="mw-page-title-main">SMARCA2</span> Protein-coding gene in the species Homo sapiens

Probable global transcription activator SNF2L2 is a protein that in humans is encoded by the SMARCA2 gene.

<span class="mw-page-title-main">SMARCA5</span> Protein-coding gene in the species Homo sapiens

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 is a protein that in humans is encoded by the SMARCA5 gene.

<span class="mw-page-title-main">ACTL6A</span> Protein-coding gene in the species Homo sapiens

Actin-like protein 6A is a protein that in humans is encoded by the ACTL6A gene.

<span class="mw-page-title-main">ARID1A</span> Protein-coding gene in humans

AT-rich interactive domain-containing protein 1A is a protein that in humans is encoded by the ARID1A gene.

<span class="mw-page-title-main">SMARCE1</span> Protein-coding gene in the species Homo sapiens

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 is a protein that in humans is encoded by the SMARCE1 gene.

<span class="mw-page-title-main">SMARCC2</span> Protein-coding gene in the species Homo sapiens

SWI/SNF complex subunit SMARCC2 is a protein that in humans is encoded by the SMARCC2 gene.

<span class="mw-page-title-main">SMARCD1</span> Protein-coding gene in the species Homo sapiens

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 is a protein that in humans is encoded by the SMARCD1 gene.

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

ISWI is one of the five major DNA chromatin remodeling complex types, or subfamilies, found in most eukaryotic organisms. ISWI remodeling complexes place nucleosomes along segments of DNA at regular intervals. The placement of nucleosomes by ISWI protein complexes typically results in the silencing of the DNA because the nucleosome placement prevents transcription of the DNA. ISWI, like the closely related SWI/SNF subfamily, is an ATP-dependent chromatin remodeler. However, the chromatin remodeling activities of ISWI and SWI/SNF are distinct and mediate the binding of non-overlapping sets of DNA transcription factors.

Transgenerational epigenetic inheritance in plants involves mechanisms for the passing of epigenetic marks from parent to offspring that differ from those reported in animals. There are several kinds of epigenetic markers, but they all provide a mechanism to facilitate greater phenotypic plasticity by influencing the expression of genes without altering the DNA code. These modifications represent responses to environmental input and are reversible changes to gene expression patterns that can be passed down through generations. In plants, transgenerational epigenetic inheritance could potentially represent an evolutionary adaptation for sessile organisms to quickly adapt to their changing environment.

References

  1. 1 2 3 4 5 6 7 8 "Robert Kingston". www.nasonline.org.
  2. 1 2 3 4 "Genetics". genetics.hms.harvard.edu. Retrieved 2021-04-16.
  3. ↑ mghresearch (2023-01-31). "Kingston Ready for New Challenges as Mass General's First Chief Academic Officer". Bench Press. Retrieved 2024-01-28.
  4. 1 2 Kingston, Robert E.; Chamberlin, Michael J. (1981-12-01). "Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli". Cell. 27 (3): 523–531. doi:10.1016/0092-8674(81)90394-9. ISSN   0092-8674. PMID   6086107. S2CID   19331708.
  5. ↑ Kingston, Robert E.; Baldwin, Albert S.; Sharp, Phillip A. (November 1984). "Regulation of heat shock protein 70 gene expression by c- myc". Nature. 312 (5991): 280–282. doi:10.1038/312280a0. ISSN   1476-4687. PMID   6438521. S2CID   2336314.
  6. 1 2 Wu, B. J.; Kingston, R. E.; Morimoto, R. I. (1986-02-01). "Human HSP70 promoter contains at least two distinct regulatory domains". Proceedings of the National Academy of Sciences. 83 (3): 629–633. doi: 10.1073/pnas.83.3.629 . ISSN   0027-8424. PMC   322917 . PMID   3456160.
  7. ↑ "Google Scholar". scholar.google.com. Retrieved 2021-04-16.
  8. ↑ Larson, Jeffrey S.; Schuetz, Thomas J.; Kingston, Robert E. (September 1988). "Activation in vitro of sequence-specific DNA binding by a human regulatory factor". Nature. 335 (6188): 372–375. doi:10.1038/335372a0. ISSN   1476-4687. PMID   3419505. S2CID   4336885.
  9. 1 2 3 Kadam, Shilpa; McAlpine, Glenn S.; Phelan, Michael L.; Kingston, Robert E.; Jones, Katherine A.; Emerson, Beverly M. (2000-10-01). "Functional selectivity of recombinant mammalian SWI/SNF subunits". Genes & Development. 14 (19): 2441–2451. doi: 10.1101/gad.828000 . ISSN   0890-9369. PMC   316972 . PMID   11018012.
  10. 1 2 3 Imbalzano, Anthony N.; Kwon, Hyockman; Green, Michael R.; Kingston, Robert E. (August 1994). "Facilitated binding of TATA-binding protein to nucleosomal DNA". Nature. 370 (6489): 481–485. doi:10.1038/370481a0. ISSN   1476-4687. PMID   8047170. S2CID   4337727.
  11. ↑ Kwon, Hyockman; Imbalzano, Anthony N.; Khavari, Paul A.; Kingston, Robert E.; Green, Michael R. (August 1994). "Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex". Nature. 370 (6489): 477–481. doi:10.1038/370477a0. ISSN   1476-4687. PMID   8047169. S2CID   4337725.
  12. ↑ Francis, Nicole J.; Saurin, Andrew J.; Shao, Zhaohui; Kingston, Robert E. (2001-09-01). "Reconstitution of a Functional Core Polycomb Repressive Complex". Molecular Cell. 8 (3): 545–556. doi: 10.1016/S1097-2765(01)00316-1 . ISSN   1097-2765. PMID   11583617.
  13. 1 2 3 Francis, Nicole J.; Kingston, Robert E.; Woodcock, Christopher L. (2004-11-26). "Chromatin Compaction by a Polycomb Group Protein Complex". Science. 306 (5701): 1574–1577. doi:10.1126/science.1100576. ISSN   0036-8075. PMID   15567868. S2CID   29551452.
  14. 1 2 Zhao, Jing; Ohsumi, Toshiro K.; Kung, Johnny T.; Ogawa, Yuya; Grau, Daniel J.; Sarma, Kavitha; Song, Ji Joon; Kingston, Robert E.; Borowsky, Mark; Lee, Jeannie T. (2010-12-22). "Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq". Molecular Cell. 40 (6): 939–953. doi:10.1016/j.molcel.2010.12.011. ISSN   1097-2765. PMC   3021903 . PMID   21172659.
  15. 1 2 3 Déjardin, Jérôme; Kingston, Robert E. (2009-01-09). "Purification of Proteins Associated with Specific Genomic Loci". Cell. 136 (1): 175–186. doi:10.1016/j.cell.2008.11.045. ISSN   0092-8674. PMC   3395431 . PMID   19135898.
  16. 1 2 3 Kingston, Robert E.; Chen, Claudia A.; Rose, John K. (2003). "Calcium Phosphate Transfection". Current Protocols in Molecular Biology. 63 (1): 9.1.1–9.1.11. doi:10.1002/0471142727.mb0901s63. ISSN   1934-3647. PMID   18265332. S2CID   46188175.
  17. 1 2 3 4 West, Jason A.; Davis, Christopher P.; Sunwoo, Hongjae; Simon, Matthew D.; Sadreyev, Ruslan I.; Wang, Peggy I.; Tolstorukov, Michael Y.; Kingston, Robert E. (2014-09-04). "The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites". Molecular Cell. 55 (5): 791–802. doi: 10.1016/j.molcel.2014.07.012 . ISSN   1097-2765. PMC   4428586 . PMID   25155612.
  18. 1 2 Daneshvar, Kaveh; Ardehali, M. Behfar; Klein, Isaac A.; Hsieh, Fu-Kai; Kratkiewicz, Arcadia J.; Mahpour, Amin; Cancelliere, Sabrina O. L.; Zhou, Chan; Cook, Brett M.; Li, Wenyang; Pondick, Joshua V. (October 2020). "lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation". Nature Cell Biology. 22 (10): 1211–1222. doi:10.1038/s41556-020-0572-2. ISSN   1476-4679. PMC   8008247 . PMID   32895492.
  19. 1 2 3 Kim, John; Sif, Saïd; Jones, Beverly; Jackson, Audrey; Koipally, Joseph; Heller, Elizabeth; Winandy, Susan; Viel, Alain; Sawyer, Alan; Ikeda, Toru; Kingston, Robert; Georgopoulos, Katia (1999-03-01). "Ikaros DNA-Binding Proteins Direct Formation of Chromatin Remodeling Complexes in Lymphocytes". Immunity. 10 (3): 345–355. doi: 10.1016/S1074-7613(00)80034-5 . ISSN   1074-7613. PMID   10204490.
  20. 1 2 3 Workman, J. L.; Kingston, R. E. (June 1998). "Alteration of Nucleosome Structure as a Mechanism of Transcriptional Regulation". Annual Review of Biochemistry. 67 (1): 545–579. doi: 10.1146/annurev.biochem.67.1.545 . ISSN   0066-4154. PMID   9759497.
  21. 1 2 Tong, Jeffrey K.; Hassig, Christian A.; Schnitzler, Gavin R.; Kingston, Robert E.; Schreiber, Stuart L. (October 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–921. doi:10.1038/27699. ISSN   1476-4687. PMID   9804427. S2CID   4355885.
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