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ARRAYS AND TARGETS FOR NASCENT TRANSCRIPTS

Award Number: R01CA068822
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 03/15/1992
PERIOD OF PERFORMANCE END DATE: 06/30/2010

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ARRAYS AND TARGETS FOR NASCENT TRANSCRIPTS - DESCRIPTION (provided by applicant): In microarray experiments, one way to increase the detection of rarer RNAs in a population is to use methods that label small portions of only some of the RNAs. These "low complexity representations" (LCRs) increase the sensitivity of detection of the RNAs selected and may also reduce any part of the background contributed by target complexity. We have used PCR of RNA with arbitrary primers (RAP) to enrich for subsets of RNA populations. The method selects internal amplicons in RNAs based on chance matches with the primers, and is simple and robust. We have demonstrated that LCRs can improve mRNA detection limits by an order of magnitude compared to total RNA on conventional glass slide arrays or Affymetrix arrays, while preserving the ratio of expression differences between two samples. We propose to expand the utility of LCR methods in four aims. (1) Build cheap custom arrays that are designed to maximize coverage by RAP LCRs. This will allow rare mRNAs to be detected. (2) Construct "intron" arrays for LCRs that, due to their increased sensitivity, will allow measurement of the level of nascent transcripts (hnRNAs). When hybridized to an appropriate array, each LCR may be able to detect 30% or more of the nascent transcripts in the cell, including some of the rarest. This will improve upon current methods for monitoring RNAs that, until now, have primarily focused on the abundance of the mature mRNA in the cell. (3) Generate LCRs by PCR of restriction fragment subsets of the RNA population. (4) A linear amplification strategy will be applied to make an LCR from sequences adjacent to dispersed repeats in hnRNA. This LCR will be hybridized to the appropriate custom array. The results of the four aims will be compared. Then, in Aim (5) the best LCR strategy, and the corresponding optimized array, will be applied to study nascent transcription and rare mRNAs in the cell cycle in human cell line models. Discoveries of new regulation can be integrated into this well characterized system, and previously known regulated genes can be parsed according to transcriptional vs. post-transcriptional components of their regulation by comparing nascent transcription to steady state RNA levels.


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: 2010 ( Subtotal = $0 )
2010	2008	SIDNEY KIMMEL CANCER CENTER	10905 Road To The Cure	San Diego	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	17	10/16/2009	NON-COMPETING CONTINUATION	$24,306
2010	2008	VACCINE RESEARCH INSTITUTE OF SAN DIEGO	3030 SCIENCE PARK ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	001	18	10/19/2009	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	-$24,306
														Subtotal = $0

Issue Date FY: 2008 ( Subtotal = $365,965 )
2008	2008	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	17	7/11/2008	NON-COMPETING CONTINUATION	$365,965
														Subtotal = $365,965

Issue Date FY: 2007 ( Subtotal = $365,965 )
2007	2007	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	16	5/30/2007	NON-COMPETING CONTINUATION	$365,965
														Subtotal = $365,965

Issue Date FY: 2006 ( Subtotal = $376,895 )
2006	2006	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	15	6/8/2006	NON-COMPETING CONTINUATION	$376,895
														Subtotal = $376,895

Issue Date FY: 2005 ( Subtotal = $385,965 )
2005	2005	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	14	8/30/2005	NON-COMPETING CONTINUATION	$385,965
														Subtotal = $385,965

Issue Date FY: 2004 ( Subtotal = $386,471 )
2004	2004	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	13	9/20/2004	COMPETING CONTINUATION	$386,471
														Subtotal = $386,471

Issue Date FY: 2002 ( Subtotal = $463,888 )
2002	2002	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	12	4/30/2002	NON-COMPETING CONTINUATION	$463,888
														Subtotal = $463,888

Issue Date FY: 2001 ( Subtotal = $230,064 )
2001	2001	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	11	4/27/2001	NON-COMPETING CONTINUATION	$230,064
														Subtotal = $230,064

Issue Date FY: 2000 ( Subtotal = $223,362 )
2000	2000	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	10	8/25/2000	NON-COMPETING CONTINUATION	$223,362
														Subtotal = $223,362

Issue Date FY: 1999 ( Subtotal = $192,716 )
1999	1999	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	9	6/25/1999	COMPETING CONTINUATION	$192,716
														Subtotal = $192,716

Issue Date FY: 1998 ( Subtotal = $311,556 )
1998	1998	SIDNEY KIMMEL CANCER CENTER	10835 ALTMAN ROW	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	8	1/29/1998	NON-COMPETING CONTINUATION	$311,556
														Subtotal = $311,556

Grand Total All Awards = $3,302,847

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ARRAYS AND TARGETS FOR NASCENT TRANSCRIPTS

Award Number: R01CA068822

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 03/15/1992

PERIOD OF PERFORMANCE END DATE: 06/30/2010

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