An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Summary

Gene expression is regulated by interactions of gene promoters with distal regulatory elements. Here, we descirbe how low input Capture Hi-C (liCHi-C) allows the identification of these interactions in rare cell types, which were previously unmeasurable.

Abstract

Spatiotemporal gene transcription is tightly regulated by distal regulatory elements, such as enhancers and silencers, which rely on physical proximity with their target gene promoters to control transcription. Although these regulatory elements are easy to identify, their target genes are difficult to predict, since most of them are cell-type specific and may be separated by hundreds of kilobases in the linear genome sequence, skipping over other non-target genes. For several years, Promoter Capture Hi-C (PCHi-C) has been the gold standard for the association of distal regulatory elements to their target genes. However, PCHi-C relies on the availability of millions of cells, prohibiting the study of rare cell populations such as those commonly obtained from primary tissues. To overcome this limitation, low input Capture Hi-C (liCHi-C), a cost-effective and customizable method to identify the repertoire of distal regulatory elements controlling each gene of the genome, has been developed. liCHi-C relies on a similar experimental and computational framework as PCHi-C, but by employing minimal tube changes, modifying the reagent concentration and volumes, and swapping or eliminating steps, it accounts for minimal material loss during library construction. Collectively, liCHi-C enables the study of gene regulation and spatiotemporal genome organization in the context of developmental biology and cellular function.

Introduction

Temporal gene expression drives cell differentiation and, ultimately, organism development, and its alteration is closely related to a wide plethora of diseases^1,2,3,4,5. Gene transcription is finely regulated by the action of regulatory elements, which can be classified as proximal (i.e., gene promoters) and distal (e.g., enhancers or silencers), the latter of which are frequently located afar from their target genes and physically interact with them through chromatin looping to modulate gene expression

Protocol

To ensure minimal material loss, (1) work with DNA low-binding tubes and tips (see Table of Materials), (2) place reagents on the tube wall instead of introducing the tip inside the sample and, (3) if possible, mix the sample by inversion instead of pipetting the sample up and down, and spin down afterward to recover the sample.

1. Cell fixation

1. Cells growing in suspension
   1. Harvest 50,000 to one million cells and place them in a DNA low-.......

Discussion

liCHi-C offers the capability of generating high-resolution promoter interactome libraries using a similar experimental framework from PCHi-C's but with a vastly reduced cell number. This is greatly achieved by eliminating unnecessary steps, such as phenol purification and biotin removal. In the classical in-nucleus ligation Hi-C protocol⁵⁷ and its subsequent derivative technique PCHi-C, biotin is removed from non-ligated restriction fragments to avoid pulling down DNA fragments that are after.......

Materials

Name	Company	Catalog Number	Comments
0.4 mM Biotin-14-dATP	Invitrogen	19524-016
0.5 M EDTA pH 8.0	Invitrogen	AM9260G
1 M Tris pH 8.0	Invitrogen	AM9855G
10x NEBuffer 2	New England Biolabs	B7002S	Referenced as restriction buffer 2 in the manuscript
10x PBS	Fisher Scientific	BP3994
10x T4 DNA ligase reaction buffer	New England Biolabs	B0202S
16% formaldehyde solution (w/v), methanol-free	Thermo Scientific	28908
20 mg/mL Bovine Serum Albumin	New England Biolabs	B9000S
5 M NaCl	Invitrogen	AM9760G
5PRIME Phase Lock Gel Light tubes	Qiuantabio	2302820	For phenol-chloroform purification in section 4 (DNA purification). Phase Lock Gel tubes are a commercial type of tubes specially designed to maximize DNA recovery after phenol-chloroform purifications while avoiding carryover of contaminants in the organic phase by containing a resin of intermediate density which settles between the organic and aqueous phase and isolates them. PLG tubes should be spun at 12,000 x g for 30 s before use to ensure that the resin is well-placed at the bottom of the tube
Adapters and PCR primers for library amplification	Integrated DNA Technologies	-	Bought as individual primers with PAGE purification for NGS
Cell scrappers	Nunc	179693	Or any other brand
Centrifuge (fixed-angle rotor for 1.5 mL tubes)	Any brand
CHiCAGO R package	1.14.0
CleanNGS beads	CleanNA	CNGS-0050
dATP, dCTP, dGTP, dTTP	Promega	U120A, U121A, U122A, U123A	Or any other brand
DNA LoBind tube, 1.5 mL	Eppendorf	30108051
DNA LoBind tube, 2 mL	Eppendorf	30108078
DNA polymerase I large (Klenow) fragment 5000 units/mL	New England Biolabs	M0210L
Dynabeads MyOne Streptavidin C1 beads	Invitrogen	65002	For biotin pull-down of the pre-captured library in section 8 (biotin pull-down)
Dynabeads MyOne Streptavidin T1 beads	Invitrogen	65602	For biotin pull-down of the post-captured library in section 11 (biotin pull-down and PCR amplification)
DynaMag-2	Invitrogen	12321D	Or any other magnet suitable for 1.5 ml tubeL
Ethanol absolute	VWR	20821.321
FBS, qualified	Gibco	10270-106	Or any other brand
Glycine	Fisher BioReagents	BP381-1
GlycoBlue Coprecipitant	Invitrogen	AM9515	Used for DNA coprecipitation in section 4 (DNA purification)
HiCUP	0.8.2
HindIII, 100 U/µL	New England Biolabs	R0104T
IGEPAL CA-630	Sigma-Aldrich	I8896-50ML
Klenow EXO- 5000 units/mL	New England Biolabs	M0212L
Low-retention filter tips (10 µL, 20 µL, 200 µL and 1000 µL)	ZeroTip	PMT233010, PMT252020, PMT231200, PMT252000
M220 Focused-ultrasonicator	Covaris	500295
Micro TUBE AFA Fiber Pre-slit snap cap 6 x 16 mm vials	Covaris	520045	For sonication in section 6 (sonication)
NheI-HF, 100 U/µL	New England Biolabs	R3131M
Nuclease-free molecular biology grade water	Sigma-Aldrich	W4502
PCR primers for quality controls	Integrated DNA Technologies	-
PCR strips and caps	Agilent Technologies	410022, 401425
Phenol: Chloroform: Isoamyl Alcohol 25:24:1, Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA	Sigma-Aldrich	P3803
Phusion High-Fidelity PCR Master Mix with HF Buffer	New England Biolabs	M0531L	For amplification of the library in sections 9 (dATP-tailing, adapter ligation and PCR amplification) and 11 (biotin pull-down and PCR amplification)
Protease inhibitor cocktail (EDTA-free)	Roche	11873580001
Proteinase K, recombinant, PCR grade	Roche	3115836001
Qubit 1x dsDNA High Sensitivity kit	Invitrogen	Q33230	For DNA quantification after precipitation in section 4 (DNA purification)
Qubit assay tubes	Invitrogen	Q32856
rCutsmart buffer	New England Biolabs	B6004S
RPMI Medium 1640 1x + GlutaMAX	Gibco	61870-010	Or any other brand
SDS - Solution 10% for molecular biology	PanReac AppliChem	A0676
Sodium acetate pH 5.2	Sigma-Aldrich	S7899-100ML
SureSelect custom 3-5.9 Mb library	Agilent Technologies	5190-4831	Custom designed mouse or human capture system, used for the capture
SureSelect Target Enrichment Box 1	Agilent Technologies	5190-8645	Used for the capture
SureSelect Target Enrichment Kit ILM PE Full Adapter	Agilent Technologies	931107	Used for the capture
T4 DNA ligase 1 U/µL	Invitrogen	15224025	For ligation in section 3 (ligation and decrosslink)
T4 DNA ligase 2000000/mL	New England Biolabs	M0202T	For ligation in section 9 (dATP-tailing, adapter ligation and PCR amplification)
T4 DNA polymerase 3000 units/mL	New England Biolabs	M0203L
T4 PNK 10000 units/mL	New England Biolabs	M0201L
Tapestation 4200 instrument	Agilent Technologies		For automated electrophoresis in section 9 (dATP-tailing, adapter ligation, and PCR amplification) and section 11 (Biotin pull-down and PCR amplification). Any other automated electrophoresis system is valid
Tapestation reagents	Agilent Technologies	5067-5582, 5067-5583, 5067-5584, 5067-5585,	For automated electrophoresis in section 9 (dATP-tailing, adapter ligation, and PCR amplification) and section 11 (Biotin pull-down and PCR amplification). Any other automated electrophoresis system is valid
Triton X-100 for molecular biology	PanReac AppliChem	A4975
Tween 20	Sigma-Aldrich	P9416-50ML