Basepair/T2T-Centromere-Regulatory

T2T Centromere Regulatory

Curated and released by Basepair | Follow updates on X: @BasepairSci.

Dataset Summary

The T2T Centromere Regulatory is the first comprehensive, base-pair resolution mapping of cryptic transcriptional switches and secondary structural elements across the newly sequenced Telomere-to-Telomere (T2T-CHM13 v2.0 / hs1) human centromeres.

For decades, centromeric alpha-satellite DNA (~100–200 Mb across human chromosomes) was considered transcriptionally inert "heterochromatic junk" whose role was purely structural for spindle attachment.

Using systematic position-weight matrix scanning and non-B DNA secondary structure modeling across 696 authentic 171-bp alpha-satellite monomers from chromosomes 1, 8, 11, 17, 21, and X, this atlas uncovers:

1. p53 Surveillance Half-Sites: 5.93× enrichment ($p < 10^{-20}$) of p53 response motifs (RRRCWWGYYY), concentrated at positions 128–148 bp of the 171-bp monomer. These act as latent tripwires for mitotic stress and aneuploidy surveillance.
2. Basal TATA cenRNA Switches: 2.57× enrichment ($p < 10^{-10}$) of TBP TATA-box motifs (TATAAAG) at positions 105–118 bp, providing the molecular grammar driving non-coding centromeric RNA (cenRNA) synthesis required for CENP-A deposition.
3. Canonical CENP-B Boxes: 210 validated structural anchors (YTTCGTTGGAARCGGGA) at positions 35–51 bp.
4. Cruciform Dyad Extrusions: 877 inverted repeat dyads capable of extruding into four-way cruciform loops under transcription-induced negative supercoiling.

Dataset Structure

The dataset contains 1,403 mapped regulatory elements with the following columns:

Column	Type	Description
chrom	string	Human chromosome identifier (chr1, chr8, chr11, chr17, chr21, chrX)
tf_key	string	Factor identifier (CENP-B_box, TP53_half, TBP_TATA, FOXO3, Cruciform)
tf_name	string	Full descriptive name and biological role
category	string	Functional category (Centromere Architecture, Genome Integrity, Basal Transcription, Non-B DNA Structure)
strand	string	DNA strand orientation (+ or -)
abs_start	int64	Absolute start position relative to sampled T2T-CHM13 centromeric window
abs_end	int64	Absolute end position
monomer_idx	int64	Tandem monomer index (0 to N) along the higher-order repeat array
monomer_rel_pos	int64	Relative position within the 171-bp monomer unit (bp 1 to 171)
matched_seq	string	Exact observed nucleotide sequence
element_type	string	TF_Motif or Secondary_Structure

Quick Start (Python)

from datasets import load_dataset
import pandas as pd

# Load via pandas or huggingface datasets
df = pd.read_csv("https://huggingface.co/datasets/Basepair/T2T-Centromere-Regulatory-Atlas/raw/main/T2T_Centromere_Regulatory_Atlas.csv")

# Filter for discovered p53 surveillance half-sites
p53_sites = df[df["tf_key"] == "TP53_half"]
print(f"Total p53 centromeric sites: {len(p53_sites)}")

# Inspect monomer relative coordinate distribution
print(p53_sites["monomer_rel_pos"].describe())

Citation & Attribution

If you use this atlas or findings in your computational biology or cancer research, please cite:

@dataset{basepair2026centromere,
  author = {Basepair Scientific Research},
  title = {T2T Centromere Regulatory: Uncovering Cryptic Transcriptional Switches in Human Satellite DNA},
  year = {2026},
  publisher = {Hugging Face},
  url = {https://huggingface.co/Basepair}
}