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Locus-Scale Massively Parallel Reporter Assays

McGee, A. V.; Biar, C. G.; Martin, B. K.; Li, T.; Lalanne, J.-B.; Kim, H.; Shendure, J.

2026-07-25 genomics
10.64898/2026.07.24.740649 bioRxiv
Show abstract

Interactions among cis-regulatory elements (CREs) are central to mammalian gene regulation. Long @$$ massively parallel reporter assays (LAMPRAs) integrate combinatorial cloning, molecular barcoding and long- and short-read sequencing, to scalably measure how CRE identities, numbers, spacings, orders, orientations, and interactions shape regulatory output at multi-kilobase length scales. As a proof-of-concept, we assay 36,000 x 5-kb synthetic cis-regulatory loci (sCRLs), each a 5 x 1-kb random combination of enhancers, insulators and spacers, to model how locus composition drives gene expression.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Nature Communications
○ 5641 papers in training set
Top 9%
18.4%
Similar papers in this journal
2
Nature Genetics
○ 286 papers in training set
Top 0.5%
11.9%
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3
Molecular Cell
○ 350 papers in training set
Top 0.7%
7.9%
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4
Nature
○ 645 papers in training set
Top 2%
7.9%
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5
Cell Genomics
○ 172 papers in training set
Top 0.6%
6.2%
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50% of probability mass above
6
Nature Structural & Molecular Biology
236 papers in training set
Top 0.9%
5.3%
7
Nature Biotechnology
○ 172 papers in training set
Top 0.8%
4.8%
8
Science
● 477 papers in training set
Top 2%
4.3%
9
Nucleic Acids Research
◐ 1281 papers in training set
Top 5%
4.0%
10
eLife
● 5828 papers in training set
Top 39%
2.7%
11
Genome Biology
○ 637 papers in training set
Top 5%
2.4%
12
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 24%
2.1%
13
Nature Plants
○ 94 papers in training set
Top 1%
1.7%
14
Cell
○ 431 papers in training set
Top 7%
1.5%
15
Nature Methods
○ 385 papers in training set
Top 5%
1.5%
16
Genome Research
● 468 papers in training set
Top 4%
1.5%
17
Nature Cell Biology
○ 118 papers in training set
Top 2%
1.4%
18
Nature Ecology & Evolution
131 papers in training set
Top 1%
1.4%
19
Nature Chemical Biology
○ 119 papers in training set
Top 2%
1.1%
20
Science Advances
● 1243 papers in training set
Top 27%
1.0%
21
Cell Reports
○ 1498 papers in training set
Top 25%
1.0%
22
Nature Neuroscience
○ 252 papers in training set
Top 5%
0.8%
23
Nature Cancer
○ 39 papers in training set
Top 1%
0.8%
24
Molecular Systems Biology
○ 162 papers in training set
Top 3%
0.8%
25
Cell Systems
○ 201 papers in training set
Top 5%
0.8%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.