# Exploring a Functional Role of Chromosome Loop Extrusion Direction on Regulating Genome Biology

> **NIH NIH R21** · CHILDREN'S HOSP OF PHILADELPHIA · 2024 · $267,000

## Abstract

ABSTRACT/PROJECT SUMMARY
Elucidating mechanisms that control chromosome topology is of much interest as ~10% of human diseases arise
from changes in genomic architecture. The Cohesin and CTCF proteins establish and revise chromosome loops
to direct promoter/enhancer contacts that mediate tissue- and developmental stage-specific gene transcription.
In a cell population, loops can form through uni- or bi-directional cohesin-mediated loop extrusion between CTCF
binding elements (CBEs) bound by CTCF. Yet, any potential role for the directionality of loop formation has not
been considered. Antigen receptor (AgR) loci are great models for studying functions of chromosome topology
because changes in their architectures during lymphocyte development help establish AgR repertoires vital for
immunity. The recombination of AgR locus variable (V), diversity (D), and joining (J) gene segments produces
AgR diversity. Thus, studying AgR loci also yields mechanistic insights into how chromosome topology controls
the initiation of V(D)J recombination and the cellular response to DNA damage that suppresses transformation
of all cells. AgR loci contain many V segments and CBEs spanning vast genomic distances located far upstream
of (D)J clusters flanked by CBEs of convergent orientation with V CBEs. When an AgR locus activates, the RAG
endonuclease binds (D)J segments to establish a recombination center (RC) and CTCF and Cohesin form loops
that reposition all V segments within similar spatial proximity to the RC. Early studies formulated a model wherein
Cohesin/CTCF-mediated loops between V and RC CBEs generate compacted locus structures that drive long-
distance V-to-RC recombination by increasing the chance for diffusion-based collisions between V segments
and the RC (structural synapsis). This mechanism would support recombination by deletion or inversion. More
recent next generation sequencing (NGS) studies of Igh and Tcra/d show that cohesin-directed loop extrusion
from the RC directs V-to-RC recombination by allowing RAG to unidirectionally scan the locus and capture a V
RSS (scanning synapsis). This mechanism dictates that recombination occurs only by deletion and uses V CBEs
to impede loop extrusion. While scanning synapsis might mediate V-to-RC rearrangements by deletion at all loci,
it cannot direct long-range V-to-RC rearrangements that occur through inversion in Tcrb and Igk loci. Based on
differences between published Igh studies and unpublished Tcrb data of the applicant, he hypothesizes that the
direction of cohesin-mediated loop extrusion across a locus determines whether scanning or structural synapsis
mediates long-range rearrangement. To test this hypothesis, the applicant proposes to: Aim 1) determine the
extents that scanning and structural synapsis operate within Tcrb and Aim 2) elucidate the impacts of Vb CBE
modifications on long-range synapsis by each mechanism. The expected outcomes would yield a major advance
by providing strong evidence ...

## Key facts

- **NIH application ID:** 10737648
- **Project number:** 5R21AI174545-02
- **Recipient organization:** CHILDREN'S HOSP OF PHILADELPHIA
- **Principal Investigator:** CRAIG H BASSING
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $267,000
- **Award type:** 5
- **Project period:** 2022-11-08 → 2025-10-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10737648

## Citation

> US National Institutes of Health, RePORTER application 10737648, Exploring a Functional Role of Chromosome Loop Extrusion Direction on Regulating Genome Biology (5R21AI174545-02). Retrieved via AI Analytics 2026-05-31 from https://api.ai-analytics.org/grant/nih/10737648. Licensed CC0.

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