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The increasing sequence divergence of different [http://en.wikipedia.org/wiki/Oxalosuccinic_acid Oxalosuccinic acid] Alu elements, along with decreasing substitution rate of an Alu element within the same subfamily over time, indicates divergence of mutational direction across different Alu elements (e.g., different Alu elements may harbor different TF motifs), hence functional divergence among different Alu elements and functional selection. Although gene duplication contributes to the generation of new genes, de novo gene birth from proto-genes in the noncoding genomic regions also contributes significantly toward the evolution of new genes (Carvunis et?al., 2012, Li et?al., 2010?and?Wu et?al., 2011). Similarly, although sequence duplication and transcriptional network rewiring are important mechanisms during the evolution of new enhancers (Li and Johnson, 2010?and?Tuch et?al., 2008), the de novo birth of new enhancers from the enormous number of proto-enhancers harbored by Alu may play a critical role in shaping the transcriptome and regulatory network of the primate genomes. Human RefSeq genes and the RepeatMasker track were obtained from http://genome.ucsc.edu in March 2006; all other data sets are summarized in the Supplemental Experimental Procedures. For MNase-seq and ChIP-seq, unmapped tags in FASTQ format were first filtered to remove low complexity tags with a dusty-score >20 using the DUST algorithm in the ��ShortRead�� R package. SOAP2 (Li et?al., 2009) was then used to align filtered tags to hg18 genome sequences. For redundant all reads mapping, multiple [http://www.selleckchem.com/products/AP24534.html Ponatinib] mapped tags were reported randomly to a matching coordinate. For unique-reads mapping, all multiple mapped tags were discarded. For a specific histone modification mod, its preferencemod on a certain family of transposon elements, whose total copy number is N, was calculated as Preferencemod=log2[(��1NReadsi,mod/TotalReadsmod)/(��1NReadsi,bg/TotalReadsbg)],where Readsi,mod stands for ChIP-seq tag counts for the histone modification mod on the transposable element i. Nucleosome mapping [http://www.selleckchem.com/products/mi-773-sar405838.html MI-773] MNase-seq, histone H3 ChIP-seq, or IgG control experiment was used for the background distribution of histones, indicated by bg. For IMR90 and H1 data from NREMC, no MNase-seq data were available, so input data were used as background. We only used Hi-C tag pairs that mapped to the same chromosome and removed tag pairs that were