Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs. Overall design: Cleavage Under Targets and Tagmentation DNA-sequencing (CUT&Tag-Seq) for histone modifications H4K16ac, H3K27ac, H3K122ac, H4K12ac, H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9me3 and IgG in H9 hPSCs, Transformed dermal fibroblasts (TDF), HEK293T, HeLa, K562, LnCaP, PC3, RWPE and ShSY5Y. For H9 and all cancer lines, wild type cells were used. For TDFs, wild type (iacs9) iCAS9 line, MSL1 knockout (MSL1 KO) line and MSL3 KO lines were used. For each cell line and histone modification, samples were processed in a minimum of two biological replicates (except for TDF MSL3 KO, TDF H3K27ac, IgGs for cancer lines, LnCaP H4K16ac and RWPE).