Transcriptional regulation – A primer
Books
Many excellent books can be read online through:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=books
This includes the latest edition of one of the main textbooks on molecular biology of the cell by
Alberts et al:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2
In particular, see Chapters 6 and 7:
6. How Cells Read the Genome: From DNA to Protein
7. Control of Gene Expression
Reviews
T.I. Lee and R.A. Young, Transcription of eukaryotic protein-coding genes. Annual Review of
Genetics, 2000. 34: 77-137.
G. Stormo, DNA binding sites: representation and discovery. Bioinformatics, 2000. 16: 16-23.
R. Schleif, DNA Looping. Annual Review of Biochemistry, 1992. 61: 199-223.
M. Bulyk, Computational prediction of transcription-factor binding site locations. Genome Biology,
2003. 5: 201.
Some nice papers
M.A. Beer and S. Tavazoie, Predicting gene expression from sequence. Cell, 2004. 117: 185-98
O. Hallikas, K. Palin, N. Sinjushina, R. Rautiainen, J. Partanen, E. Ukkonen and J. Taipale,
Genome-wide Prediction of Mammalian Enhancers Based on Analysis of TranscriptionFactor Binding Affinity. Cell, 2006. 124: 47-59.
X. Xie, et al., Systematic discovery of regulatory motifs in human promoters and 3' UTRs by
comparison of several mammals. Nature, 2005. 434: 338-45.
G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. De Moor, P. Rouze and Y. Moreau, A Gibbs
sampling method to detect overrepresented motifs in the upstream regions of
coexpressed genes. Journal of Computational Biology, 2002. 9: 447-464.
M. Nobrega, I. Ovcharenko, V. Afzal and E. Rubin, Scanning human gene deserts for long-range
enhancers. Science, 2003. 302: 413.
Some of my work
G. Kreiman, Identification of sparsely distributed clusters of cis-regulatory elements in sets of coexpressed genes. Nucleic Acids Research, 2004. 32: 2889-2900.
A. Su, et al., A gene atlas of the mouse and human protein-encoding transcriptomes. PNAS,
2004. 101: 6062-6067.
D. Tropea, G. Kreiman, A. Lychman, S. Mukherjee, H. Yu, S. Horng and M. Sur, Gene expression
changes and molecular pathways mediating activity-dependent plasticity in visual cortex.
Nature Neuroscience, 2006. 9: 660-668.
G. Yeo, D. Holste, G. Kreiman and C. Burge, Variation in alternative splicing across human
tissues. Genome Biology, 2004. 5: R74.