Vivekanandan Ramalingam

Abstract Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression1. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions2.

Results To measure KLF1 affinity in vitro, we designed a library of 11,812 DNA sequences containing variants within the consensus nine-bp KLF motif (CCMCRCCCN). This library spans all single, all double, and some triple mutations of a high-affinity motif (CCACGCCCA), which we define as the consensus motif, extensive programmed variation in motif-flanking sequence, and negative controls lacking the motif (STAR Methods; Figure 1A).

Abstract In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria.