Papers by Andrey Shlyakhtenko
G3 (Bethesda, Md.), 2012
Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promo... more Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserv...
This report provides a compendium of ongoing leading initiatives and activities designed to accel... more This report provides a compendium of ongoing leading initiatives and activities designed to accelerate private investment flows in low-emission projects. The research identifies current investment challenges of green projects and summarizes the extensive body of work that has been evolving over the past few years. The report presents a number of conclusions that emerged from the research, along with an identification of additional work needed to move the agenda forward. Research has shown that climate change is heightening the importance of accelerating investments in low-emission projects. However, many such projects are financially unattractive when compared with traditional but less eco-friendly alternatives. Further, private sector investments have fallen far short of the amounts required to stabilize CO2 emissions at levels that will ensure sustainable development. While there is much hope that carbon markets can be revived, there is also great uncertainty regarding the breadth...
This report builds on the conclusions of the Green Infrastructure Finance: Leading Initiatives an... more This report builds on the conclusions of the Green Infrastructure Finance: Leading Initiatives and Research report and lays out a simple and elegant way in which scarce public financing can leverage market interest in “greening” infrastructure, particularly in the East Asia and Pacific Region. The framework introduced in the report bridges ideas and concepts between environmental economics and project fi nance practices and consists largely of an analytical methodology for determining the financial viability gap of low-emission projects, as well as an approach for assessing and strengthening the green investment climate in a given country environment. The report argues that the solution to the financing challenge of low-emission investments lies in understanding the causes of a given project’s fi nancial viability gap, and then investigating how specific actions—including concessional financing, strategic subsidies, and other public policy interventions and reforms—can be deployed i...
Genome Research, 2004
We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long... more We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression. 3 Corresponding author. E-MAIL [email protected]; FAX (301) 496-8419. Article and publication are at
BMC Genomics, 2008
The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP) in different tissu... more The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP) in different tissues. Although the promoters of these genes are known to contain CpG islands, the specific DNA sequences that are associated with high RNAP binding to housekeeping promoters has not been described.
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Papers by Andrey Shlyakhtenko