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. Author manuscript; available in PMC: 2010 Nov 1.
Published in final edited form as: Nat Struct Mol Biol. 2010 Apr 25;17(5):620–628. doi: 10.1038/nsmb.1801

Table 1.

Pol III Genes and Pol III-related Repeats in the Human Genome and Enrichment with Pol III Initiation Machinery in HeLa ChIP-seq

Pol III Promoter Type Class of RNA Subclassa Number in Human hg18 Reference Genomeb Number and Percent with Attributec Number and Percent Occupied with Pol III or BRF1/2 (FDR<1%) in HeLa
Type 1 5S Consensus 17 17d 100.0% 17e 100.0%
5S-related 1,260 175d 13.9% 0e 0%
Type 2 tRNA Consensus 513 490f 95.5% 242 47.1%
tRNA-pseudogeneg 172 120f 69.8% 2 1.2%
tRNA-relatedg 1,224 227f 18.5% 0 0%
Alu Dimerh 1,099,242 638,006f 58.0% 13 0.001%
Monomerh 90,882 30,301f 33.3% 2 0.002%
MIR MIR 587,443 65,530f 11.5% 1 0.0002%
snaR Consensus 21 21f 100.0% 21e 100.0%
snaR-related 7 5f 71.4% 2e 28.5%
HVG or Vault Consensus 3 3f 100.0% 3 100.0%
HVG-related 1 1f 100.0% 0 0%
7SL or SRP Consensus 2 0f 0% 1 50%
7SL-related 954 128f 13.4% 0 0%
BC200 Consensus 1 1f 100.0% 1i 100.0%
BC200-related 253 141f 55.9% 0 0%
Type 3 Y Consensus 4 4j 100.0% 4 100.0%
Y-related 1,123 0j 0% 0 0%
U6 Consensus 9 5j 55.5% 5 55.5%
U6-related 1,670 0j 0% 0 0%
7SK Consensus 1 1j 100.0% 1 100.0%
7SK-related 713 1j 0.1% 0 0%
RNase P Consensus 1 1j 100.0% 1 100.0%
RNase P-related 1 0j 0% 0 0%
RNase MRP Consensus 1 1j 100.0% 1 100.0%
RNase MRP-related 6 0j 0% 0 0%
U6atac Consensus 1 1j 100.0% 1 100.0%
U6atac-related 39 0j 0% 0 0%
tRNASeC Consensus 3k 1f,j 33.3% 1k 33.3%
a

‘Consensus’ subclass is based on high sequence identity (using BLAT, genome.ucsc.edu) to the validated RNA, except tRNAs from the Genomic tRNA database (GtRNAdb, gtrnadb.ucsc.edu) and snaRs from others31.

b

Based on UCSC Genome Browser (genome.ucsc.edu) tracks ‘RNA Genes’ and ‘RepeatMasker’ (www.repeatmasker.org) (except for tRNAs and snaRs, see footnote a).

c

Attributes determined with ‘Consensus’ and ‘Patser’ programs (rsat.ulb.ac.be/rsat; see Methods). See Supplementary Data 1 for consensus matrices.

d

Contains an internal C-box

e

Mapped allowing multiple alignments with Bowtie (bowtie-bio.sourceforge.net; see Methods and Supplementary Data 1.)

f

Contains an internal B-box

g

‘tRNA-pseudogene’ from GtRNAdb and ‘RNA Genes’; ‘tRNA-related’ from ‘RepeatMasker’ track (genome.ucsc.edu), not overlapping ‘Consensus’ or ‘tRNA-pseudogene.’

h

‘Monomer’ refers to free left and right element (FLAM, FRAM); ‘Dimer’ means the Alu has a FLAM and a FRAM

i

Enriched in Pol III ChIP-array but not ChIP-seq

j

Contains a TATA (within 50 bp upstream) and PSE (between 100 bp and 25 bp upstream)

k

These are a subset of the tRNAs in Type 2 Promoter section.