REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-Bub1	Abcam	Cat# ab227228
Rabbit monoclonal anti-BubR1	Abcam	Cat# ab254326
Mouse monoclonal anti-CENP-A	Abcam	Cat# ab13939; RRID: AB_300766
Mouse monoclonal anti-CENP-A	MBL	Cat# D115-3; RRID: AB_591074
Rabbit monoclonal anti-CENP-C	Abcam	Cat# ab193666
Guinea pig monoclonal anti-CENP-C	MBL	Cat# PD030; RRID: AB_10693556
Mouse monoclonal anti-Flag	Sigma	Cat# F1804; RRID: AB_262044
Rabbit polyclonal anti-GAPDH	Abcam	Cat# ab37168; RRID: AB_732652
Mouse monoclonal anti-GFP	BioVision	Cat# 3992-100; RRID: AB_1121019
Normal rabbit IgG antibody	Cell Signaling Technology	Cat# 2729; RRID: AB_1031062
Mouse monoclonal anti-β-actin	Abcam	Cat# ab8226; RRID: AB_306371
CREST antiserum	kind gift from Li lab	N/A
Bacterial and Virus Strains
E. coli DH5α	Biomed	Cat# BC116
E. coli DL21 (DE3)	Transgen	Cat# CD601-02
Chemicals, Peptides, and Recombinant Proteins
SNAP-Cell® Block (bromothenylpteridine, BTP)	New England BioLabs	Cat# S9106S
SNAP-Cell® TMR-star (tetramethylrhodamine)	New England BioLabs	Cat# S9105S
4’-aminomethyltrioxsalen (AMT)	Sigma	Cat# A4330
6 x His-CENP-C	This paper	N/A
Critical Commercial Assays
Chemiluminescent Nucleic Acid Detection Module Kit	Thermo	Cat# 89880
DIG Northern Starter Kit	Roche	Cat# 12039672910
FirstChoice RLM-RACE RNA Ligase Mediated RACE Kit	Ambion	Cat# AM1700
GeneArt™ Precision gRNA Synthesis Kit	Thermo	Cat# A29377
His-Tag Protein Purification Kit	Qiagen	Cat# 31314
PARIS Kit	Life Technologies	Cat# AM1921
Deposited Data
Human reference genome NCBI build 38, GRCh38	Genome Reference Consortium	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
CCTT AMT-ChIRP-seq data	This paper	GEO: GSE149534
CCTT irCLIP-seq data	This paper	GEO: GSE149534
CCTT SHAPE-MaP data	This paper	GEO: GSE149534
CENP-C RIP-seq data	This paper	GEO: GSE149534
Experimental Models: Cell Lines
HCT116	ATCC	Cat# CCL-247
HeLa	ATCC	Cat# CCL-2
Oligonucleotides
PCR primers, siRNAs, ASOs, sgRNAs target sequences, and probes	This paper	See Table S1 and Star Methods
Recombinant DNA
CENP-CSNAP	gift from Li lab	N/A
CMV10-Flag-CENP-C full length	This paper	N/A
CMV10-Flag-CENP-C 1-292 aa	This paper	N/A
CMV10-Flag-CENP-C 295-551 aa	This paper	N/A
CMV10-Flag-CENP-C 552-825 aa	This paper	N/A
CMV10-Flag-CENP-C 826-943 aa	This paper	N/A
CMV10-Flag-CENP-C 1-825 aa	This paper	N/A
pcDNA3.1-CCTT full length	This paper	N/A
pcDNA3.1-CCTT ORF1-GFP	This paper	N/A
pcDNA3.1-CCTT ORF2-GFP	This paper	N/A
pcDNA3.1-CCTT ΔAlu	This paper	N/A
pcDNA3.1-CCTT Δ43-79 (ΔDBD)	This paper	N/A
pcDNA3.1-CCTT Δ127-177	This paper	N/A
pcDNA3.1-GFP	This paper	N/A
pET-28a-CENP-C full length	This paper	N/A
pLenti-U6-spgRNA v2.0-CMV-Puro-P2A-3Flag-s pCas9	Obio	Cat# H7548
Software and Algorithms
BEDTools	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
Bowtie2	Langmead and Salzberg, 2012	http://bowtiebio.sourceforge.net/bowtie2/indexs.html
BWA-MEM	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
CNCI	Sun et al., 2013	http://www.bioinfo.org/software/cnci/
CPAT	Wang et al., 2013	http://rna-cpat.sourceforge.net/
CPC	Kong et al., 2007	http://cpc.cbi.pku.edu.cn
DeepTools	Ramirez et al., 2016	https://deeptools.readthedocs.io/en/develop/
deltaSHAPE	Smola et al., 2015	https://weekslab.com/software/
DNA/RNA Copy Number Calculator	N/A	http://endmemo.com/bio/dnacopynum.php/
edgeR	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
Fastq-dump	N/A	https://ncbi.github.io/sra-tools/fastq-dump.html
FASTX-Toolkit	N/A	http://hannonlab.cshl.edu/fastx_toolkit/
FeatureCounts	Liao et al., 2014	http://bioinf.wehi.edu.au/featureCounts/
GraphPad Prism	GraphPad Software	http://www.graphpad.com/scientifificsoftware/prism/
IMARIS	Bitplane	N/A
Limma	Ritchie et al., 2015	https://www.bioconductor.org/packages/release/bioc/html/limma.html
MEME	Bailey et al., 2009	http://meme-suite.org
PEAR	Zhang et al., 2013	https://cme.h-its.org/exelixis/web/software/pear/
Pfam	El-Gebali et al., 2019	http://pfam.xfam.org
PhyloSCF	Lin et al., 2011	https://github.com/mlin/PhyloCSF/
Picard	N/A	http://broadinstitute.github.io/picard/
RNAstructure web server	DiChiacchio and Mathews, 2016	https://rna.urmc.rochester.edu/RNAstructureWeb/
ShapeMapper	Busan and Weeks, 2018	https://help.rc.ufl.edu/doc/ShapeMapper
SICER	Xu et al., 2014	http://gensoft.pasteur.fr/docs/SICER/1.1/SICER-README.pdf
SortMeRNA	Kopylova et al., 2012	http://bioinfo.lifl.fr/RNA/sortmerna/
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
TDF	Kuo et al., 2019	https://www.regulatory-genomics.org/tdf/basic-introduction/
Trimmomatic	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
Triplexator	Buske et al., 2012	http://abacus.qfab.org/tools/triplexator/manual.html
UCSC	N/A	http://genome.ucsc.edu/
Volocity Demo (x 64)	Volocity Software	N/A