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Single-molecule visualization of transcription regulation mechanisms

Award Number: R01GM081648
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/15/2007
PERIOD OF PERFORMANCE END DATE: 02/29/2028

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Single-molecule visualization of transcription regulation mechanisms - Project Summary The goal of this project is to contribute to understanding of the biochemical and biophysical mechanisms by which gene expression is regulated. In particular, we seek to understand the operation of the molecular machinery that regulates production of mRNA by DNA transcription and the relationship between the composition and structures of the macromolecular complexes that make up that machinery and their functions. In this project, we have developed and applied a powerful approach to quantitatively defining the dynamic molecular mechanisms of transcription and transcription regulation in vitro. Instead of studying populations of molecules, we use multi-wavelength single-molecule fluorescence methods to directly visualize in vitro the RNA polymerase and associating regulatory proteins simultaneously on hundreds of isolated individual DNA molecules in multiplex. We propose continuing studies that apply this approach to elucidating dynamic molecular regulation mechanisms of the messenger RNA synthesis machinery from an example bacterium (E. coli) and from a model eukaryote (the budding yeast S. cerevisiae). In both systems, we have chosen for study transcription factors and regulatory activities that are general mechanisms which act during transcription of many or most protein-coding genes in the organism. Our studies will advance the field by focusing not on single regulatory factors in isolation but on understanding the emergent properties of systems in which multiple regulatory factors act together. Our immediate goals are to use multi-wavelength single-molecule fluorescence methods in vitro to 1) test the hypothesis that bacterial RNA polymerase elongation complexes are specialized by alternative modes of σ70 binding and determine how specialization dictates different combinatorial regulation by elongation factors NusA and NusG; 2) reveal the mechanisms that determine the outcome of the bacterial post- termination complex; and 3) define the pathways by which selected general elongation factors compete and cooperate for recruitment to eukaryotic RNA polymerase II elongation complexes.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $391,515 )
2025	2025	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	002	18	2/25/2025	NON-COMPETING CONTINUATION	$391,515
2025	2024	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	17	2/12/2025	COMPETING CONTINUATION	$20,967
2025	2023	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	16	2/12/2025	NON-COMPETING CONTINUATION	-$20,967
														Subtotal = $391,515

Issue Date FY: 2024 ( Subtotal = $434,647 )
2024	2024	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	17	3/28/2024	COMPETING CONTINUATION	$434,647
2024	2023	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	16	3/20/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $434,647

Issue Date FY: 2023 ( Subtotal = $432,250 )
2023	2023	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	16	2/23/2023	NON-COMPETING CONTINUATION	$432,250
														Subtotal = $432,250

Issue Date FY: 2022 ( Subtotal = $427,216 )
2022	2022	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	004	15	7/27/2022	NON-COMPETING CONTINUATION	$43,228
2022	2022	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	15	2/4/2022	NON-COMPETING CONTINUATION	$389,022
2022	2019	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	12	6/29/2022	NON-COMPETING CONTINUATION	-$5,034
2022	2018	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	003	11	6/29/2022	NON-COMPETING CONTINUATION	$0
2022	2017	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	002	10	6/29/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $427,216

Issue Date FY: 2021 ( Subtotal = $432,250 )
2021	2021	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	14	2/4/2021	NON-COMPETING CONTINUATION	$432,250
2021	2020	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	002	13	6/4/2021	COMPETING CONTINUATION	$37,853
2021	2019	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	12	6/4/2021	NON-COMPETING CONTINUATION	-$37,853
														Subtotal = $432,250

Issue Date FY: 2020 ( Subtotal = $444,250 )
2020	2020	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	13	4/8/2020	COMPETING CONTINUATION	$444,250
2020	2019	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	12	4/7/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $444,250

Issue Date FY: 2019 ( Subtotal = $416,411 )
2019	2019	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	12	2/21/2019	NON-COMPETING CONTINUATION	$416,411
														Subtotal = $416,411

Issue Date FY: 2018 ( Subtotal = $416,411 )
2018	2018	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	11	6/4/2018	NON-COMPETING CONTINUATION	$41,642
2018	2018	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	11	2/7/2018	NON-COMPETING CONTINUATION	$374,769
														Subtotal = $416,411

Issue Date FY: 2017 ( Subtotal = $416,411 )
2017	2017	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	10	8/15/2017	NON-COMPETING CONTINUATION	$41,642
2017	2017	BRANDEIS UNIVERSITY	415 SOUTH ST	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	10	2/24/2017	NON-COMPETING CONTINUATION	$374,769
														Subtotal = $416,411

Issue Date FY: 2016 ( Subtotal = $400,295 )
2016	2016	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02254		USA	Biomedical Research and Research Training	000	9	12/16/2015	COMPETING CONTINUATION	$400,295
														Subtotal = $400,295

Issue Date FY: 2015 ( Subtotal = $352,517 )
2015	2015	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02254		USA	Biomedical Research and Research Training	000	8	3/3/2015	NON-COMPETING CONTINUATION	$352,517
														Subtotal = $352,517

Issue Date FY: 2014 ( Subtotal = $351,431 )
2014	2014	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02254		USA	Biomedical Research and Research Training	000	7	5/7/2014	NON-COMPETING CONTINUATION	$351,431
														Subtotal = $351,431

Issue Date FY: 2013 ( Subtotal = $338,083 )
2013	2013	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	6	3/4/2013	NON-COMPETING CONTINUATION	$315,310
2013	2013	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	6	6/19/2013	NON-COMPETING CONTINUATION	$22,773
														Subtotal = $338,083

Issue Date FY: 2012 ( Subtotal = $348,897 )
2012	2012	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	001	5	3/1/2012	COMPETING CONTINUATION	$348,897
2012	2010	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02254		USA	Biomedical Research and Research Training	000	4	2/29/2012	NON-COMPETING CONTINUATION	$0
														Subtotal = $348,897

Issue Date FY: 2010 ( Subtotal = $315,481 )
2010	2010	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	4	6/24/2010	NON-COMPETING CONTINUATION	$315,481
														Subtotal = $315,481

Issue Date FY: 2009 ( Subtotal = $441,484 )
2009	2009	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Trans-NIH Recovery Act Research Support	001	3	9/30/2009	SUPPLEMENT FOR EXPANSION	$122,816
2009	2009	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02453	MIDDLESEX	USA	Biomedical Research and Research Training	000	3	7/8/2009	NON-COMPETING CONTINUATION	$318,668
														Subtotal = $441,484

Issue Date FY: 2008 ( Subtotal = $287,638 )
2008	2008	BRANDEIS UNIVERSITY	415 SO ST, 119 BERNSTEIN-MARCU	WALTHAM	MA	02254		USA	Biomedical Research and Research Training	000	2	7/14/2008	NON-COMPETING CONTINUATION	$287,638
														Subtotal = $287,638

Issue Date FY: 2007 ( Subtotal = $267,950 ) (Continued on the next page)
Grand Total All Awards = $6,915,137

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Single-molecule visualization of transcription regulation mechanisms

Award Number: R01GM081648

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 07/15/2007

PERIOD OF PERFORMANCE END DATE: 02/29/2028

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