Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

NIH Image to ImageJ: 25 years of image analysis

Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012) · Nature Methods · doi:10.1038/nmeth.2089 · Cited by 64,638 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · see citing works

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 11,930 · see citing works

Genome engineering using the CRISPR-Cas9 system

Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133 · see citing works

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

deepTools2: a next generation web server for deep-sequencing data analysis

Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096 · see citing works

Gene ontology analysis for RNA-seq: accounting for selection bias

Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-2-r14 · Cited by 7,107 · see citing works

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2016.07.002 · Cited by 3,724 · see citing works

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Durand, N. C., Robinson, J., Shamim, M. S., Machol, I., Mesirov, J. P., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2015.07.012 · Cited by 2,335 · see citing works

Formation of chromosomal domains by loop extrusion

Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003 · see citing works

MEME-ChIP: motif analysis of large DNA datasets

Machanick, P., & Bailey, T. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr189 · Cited by 1,815 · see citing works

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

Bell, A. C., & Felsenfeld, G. (2000) · Nature · doi:10.1038/35013100 · Cited by 1,746 · see citing works

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730 · see citing works

CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus

Hark, A. T., Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., & Tilghman, S. M. (2000) · Nature · doi:10.1038/35013106 · Cited by 1,547 · see citing works

A map of the cis-regulatory sequences in the mouse genome

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · see citing works

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.027 · Cited by 1,274 · see citing works

Epigenetic Regulation by Long Noncoding RNAs

Lee, J. T. (2012) · Science · doi:10.1126/science.1231776 · Cited by 1,258 · see citing works

DNA-Binding Specificities of Human Transcription Factors

Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P. M. A., Morgunova, E. Y., Enge, M., Taipale, M., Wei, G., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.009 · Cited by 1,228 · see citing works

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

Phillips-Cremins, J. E., Sauria, M. E. G., Sanyal, A., Gerasimova, T. I., Lajoie, B. R., Bell, J. S. K., Ong, C.-T., Hookway, T. A., Guo, C., Sun, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.053 · Cited by 1,187 · see citing works

Organizational principles of 3D genome architecture

Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171 · see citing works

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.016 · Cited by 1,050 · see citing works

Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982 · see citing works

Design and analysis of ChIP-seq experiments for DNA-binding proteins

Kharchenko, P., Tolstorukov, M., & Park, P. J. (2008) · Nature Biotechnology · doi:10.1038/nbt.1508 · Cited by 950 · see citing works

The 3D Genome as Moderator of Chromosomal Communication

Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937 · see citing works

DNA loop extrusion by human cohesin

Davidson, I. F., Bauer, B., Goetz, D., Tang, W., Wutz, G., & Peters, J.-M. (2019) · Science · doi:10.1126/science.aaz3418 · Cited by 863 · see citing works

The cohesin release factor WAPL restricts chromatin loop extension

Haarhuis, J. H. I., van der Weide, R. H., Blomen, V. A., Yáñez-Cuna, J. O., Amendola, M., van Ruiten, M. S., Krijger, P. H. L., Teunissen, H., Medema, R. H., van Steensel, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.04.013 · Cited by 793 · see citing works

Quantitative analysis of chromosome conformation capture assays (3C-qPCR)

Hagège, H., Klous, P., Braem, C., Splinter, E., Dekker, J., Cathala, G., de Laat, W., & Forné, T. (2007) · Nature Protocols · doi:10.1038/nprot.2007.243 · Cited by 720 · see citing works

Human cohesin compacts DNA by loop extrusion

Kim, Y., Shi, Z., Zhang, H., Finkelstein, I. J., & Yu, H. (2019) · Science · doi:10.1126/science.aaz4475 · Cited by 701 · see citing works

CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus

Splinter, E., Heath, H., Kooren, J., Palstra, R.-J., Klous, P., Grosveld, F., Galjart, N., & de Laat, W. (2006) · Genes & Development · doi:10.1101/gad.399506 · Cited by 677 · see citing works

CTCF-mediated functional chromatin interactome in pluripotent cells

Handoko, L., Han, X., Li, G., Ngan, C. Y., Chew, E. G. Y., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.857 · Cited by 614 · see citing works

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613 · see citing works

CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease

Ohlsson, R., Renkawitz, R., & Lobanenkov, V. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02366-6 · Cited by 591 · see citing works

Widespread plasticity in CTCF occupancy linked to DNA methylation

Wang, H., Maurano, M. T., Qu, H., Varley, K. E., Gertz, J., Pauli, F., Lee, K., Canfield, T., Weaver, M., Sandstrom, R., et al. (2012) · Genome Research · doi:10.1101/gr.136101.111 · Cited by 588 · see citing works

An Exceptionally Conserved Transcriptional Repressor, CTCF, Employs Different Combinations of Zinc Fingers To Bind Diverged Promoter Sequences of Avian and Mammalian c- myc Oncogenes

Filippova, G. N., Fagerlie, S. R., Klenova, E. M., Myers, C. D., Dehner, Y., Goodwin, G. H., Neiman, P. E., Collins, S. J., & Lobanenkov, V. V. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.6.2802 · Cited by 543 · see citing works

Self-organization of domain structures by DNA-loop-extruding enzymes

Alipour, E., & Marko, J. F. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks925 · Cited by 540 · see citing works

The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation

Tian, D., Sun, S., & Lee, J. T. (2010) · Cell · doi:10.1016/j.cell.2010.09.049 · Cited by 516 · see citing works

CTCF binding at the <i>H19</i> imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to <i>Igf2</i>

Kurukuti, S., Tiwari, V. K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W., & Ohlsson, R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600326103 · Cited by 511 · see citing works

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

Jeon, Y., & Lee, J. T. (2011) · Cell · doi:10.1016/j.cell.2011.06.026 · Cited by 506 · see citing works

Targeted Mutagenesis of Tsix Leads to Nonrandom X Inactivation

Lee, J. T., & Lu, N. (1999) · Cell · doi:10.1016/s0092-8674(00)80061-6 · Cited by 503 · see citing works

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

Minajigi, A., Froberg, J. E., Wei, C., Sunwoo, H., Kesner, B., Colognori, D., Lessing, D., Payer, B., Boukhali, M., Haas, W., et al. (2015) · Science · doi:10.1126/science.aab2276 · Cited by 476 · see citing works

CEAS: <i>cis</i>-regulatory element annotation system

Shin, H., Liu, T., Manrai, A. K., & Liu, X. S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp479 · Cited by 461 · see citing works

The structural basis for cohesin–CTCF-anchored loops

Li, Y., Haarhuis, J. H. I., Sedeño Cacciatore, Á., Oldenkamp, R., van Ruiten, M. S., Willems, L., Teunissen, H., Muir, K. W., de Wit, E., Rowland, B. D., et al. (2020) · Nature · doi:10.1038/s41586-019-1910-z · Cited by 459 · see citing works

The genomic binding sites of a noncoding RNA

Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., & Kingston, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113536108 · Cited by 444 · see citing works

The functional consequences of alternative promoter use in mammalian genomes

Davuluri, R. V., Suzuki, Y., Sugano, S., Plass, C., & Huang, T. H.-M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.01.008 · Cited by 408 · see citing works

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

Simon, M. D., Pinter, S. F., Fang, R., Sarma, K., Rutenberg-Schoenberg, M., Bowman, S., Kesner, B., Maier, V., Kingston, R. E., & Lee, J. T. (2013) · Nature · doi:10.1038/nature12719 · Cited by 382 · see citing works

Jpx RNA Activates Xist by Evicting CTCF

Sun, S., Rosario, B. C. D., Szántó, A., Ogawa, Y., Jeon, Y., & Lee, J. T. (2013) · Cell · doi:10.1016/j.cell.2013.05.028 · Cited by 325 · see citing works

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

Nakahashi, H., Kieffer, K.-R., Resch, W., Vian, L., Dose, M., Stavreva, D. A., Hakim, O., Pruett, N. D., Nelson, S., Yamane, A., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.04.024 · Cited by 316 · see citing works

Intersection of the RNA Interference and X-Inactivation Pathways

Ogawa, Y., Sun, B. K., & Lee, J. T. (2008) · Science · doi:10.1126/science.1157676 · Cited by 299 · see citing works

CTCF, a Conserved Nuclear Factor Required for Optimal Transcriptional Activity of the Chicken c- myc Gene, Is an 11-Zn-Finger Protein Differentially Expressed in Multiple Forms

Klenova, E. M., Nicolas, R. H., Paterson, H. F., Carne, A. F., Heath, C., Goodwin, G. H., Neiman, P. E., & Lobanenkov, V. V. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.12.7612-7624.1993 · Cited by 293 · see citing works

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

Hansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Saldaña-Meyer, R., Reinberg, D., Darzacq, X., & Tjian, R. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.039 · Cited by 279 · see citing works

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

Saldaña-Meyer, R., Rodriguez-Hernaez, J., Escobar, T. M., Nishana, M., Jácome-López, K., Nora, E. P., Bruneau, B. G., Tsirigos, A., Furlan-Magaril, M., Skok, J. A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.015 · Cited by 278 · see citing works

Function of a Foxp3 cis -Element in Protecting Regulatory T Cell Identity

Li, X., Liang, Y., Leblanc, M., Benner, C. W., & Zheng, Y. (2014) · Cell · doi:10.1016/j.cell.2014.07.030 · Cited by 268 · see citing works

Recent evidence that TADs and chromatin loops are dynamic structures

Hansen, A. S., Cattoglio, C., Darzacq, X., & Tjian, R. (2018) · Nucleus · doi:10.1080/19491034.2017.1389365 · Cited by 266 · see citing works

TERRA RNA Antagonizes ATRX and Protects Telomeres

Chu, H.-P. C., Cifuentes‐Rojas, C., Kesner, B., Aeby, E., Lee, H.-G., Wei, C., Oh, H. J., Boukhali, M., Haas, W., & Lee, J. T. (2017) · Cell · doi:10.1016/j.cell.2017.06.017 · Cited by 266 · see citing works

CTCF, a Candidate Trans -Acting Factor for X-Inactivation Choice

Chao, W., Huynh, K. D., Spencer, R. J., Davidow, L. S., & Lee, J. T. (2002) · Science · doi:10.1126/science.1065982 · Cited by 264 · see citing works

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

Yang, F., Deng, X., Ma, W., Berletch, J. B., Rabaia, N. A., Wei, G., Moore, J. M., Filippova, G. N., Xu, J., Liu, Y., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0618-0 · Cited by 255 · see citing works

The impact of amplification on differential expression analyses by RNA-seq

Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2016) · Scientific Reports · doi:10.1038/srep25533 · Cited by 252 · see citing works

Comparative Sequence Analysis of the X-Inactivation Center Region in Mouse, Human, and BovinePreprint

Chureau, C., Prissette, M., Bourdet, A., Barbe, V., Cattolico, L., Jones, L. M., Eggen, A. A., Avner, P. R., & Duret, L. (2000) · Genome Research · doi:10.1101/gr.152902 · Cited by 250 · see citing works

Identification of a Ctcf Cofactor, Yy1, for the X Chromosome Binary Switch

Donohoe, M. E., Zhang, L., Xu, N., Shi, Y., & Lee, J. T. (2007) · Molecular Cell · doi:10.1016/j.molcel.2006.11.017 · Cited by 239 · see citing works

Isolation and Characterization of an Endonuclease from Escherichia coli Specific for Ribonucleic Acid in Ribonucleic Acid·Deoxyribonucleic Acid Hybrid Structures

Berkower, I. J., Leis, J. P., & Hurwitz, J. (1973) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)43488-1 · Cited by 223 · see citing works

Two major mechanisms of chromosome organization

Mirny, L. A., Imakaev, M., & Abdennur, N. A. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.05.001 · Cited by 222 · see citing works

Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control

Lee, J. T. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3231 · Cited by 221 · see citing works

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

Saldaña-Meyer, R., González-Buendía, E., Guerrero, G., Narendra, V., Bonasio, R., Recillas-Targa, F., & Reinberg, D. (2014) · Genes &amp; Development · doi:10.1101/gad.236869.113 · Cited by 217 · see citing works

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

Pugacheva, E. M., Kubo, N., Loukinov, D. I., Tajmul, M., Kang, S., Kovalchuk, A. L., Strunnikov, A. V., Zentner, G. E., Ren, B., & Lobanenkov, V. V. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1911708117 · Cited by 215 · see citing works

Chromatin Insulators: Linking Genome Organization to Cellular Function

Phillips‐Cremins, J. E., & Corces, V. G. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.04.018 · Cited by 213 · see citing works

Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein

Xu, N., Donohoe, M. E., Silva, S. S., & Lee, J. T. (2007) · Nature Genetics · doi:10.1038/ng.2007.5 · Cited by 192 · see citing works

Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic

Augui, S., Filion, G. J. P., Huart, S., Nora, E. P., Guggiari, M., Maresca, M., Stewart, A. F., & Heard, É. (2007) · Science · doi:10.1126/science.1149420 · Cited by 178 · see citing works

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

Naumova, N., Smith, E. M., Zhan, Y., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.07.022 · Cited by 178 · see citing works

SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X

Wang, C., Jégu, T., Chu, H.-P. C., Oh, H. J., & Lee, J. T. (2018) · Cell · doi:10.1016/j.cell.2018.05.007 · Cited by 170 · see citing works

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

Kung, J. T., Kesner, B., An, J. Y., Ahn, J. Y., Cifuentes‐Rojas, C., Colognori, D., Jeon, Y., Szántó, A., Rosario, B. C. D., Pinter, S. F., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.006 · Cited by 167 · see citing works

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stationsPreprint

Pinter, S. F., Sadreyev, R. I., Yildirim, E., Jeon, Y., Ohsumi, T. K., Borowsky, M. L., & Lee, J. T. (2012) · Genome Research · doi:10.1101/gr.133751.111 · Cited by 165 · see citing works

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Ambrosini, G., Groux, R., & Bücher, P. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty127 · Cited by 147 · see citing works

The X chromosome in space

Jégu, T., Aeby, E., & Lee, J. T. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.17 · Cited by 136 · see citing works

Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

da Rocha, S. T., & Heard, É. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3370 · Cited by 134 · see citing works

The CTCF Insulator Protein Is Posttranslationally Modified by SUMO

MacPherson, M. J., Beatty, L. G., Zhou, W., Du, M., & Sadowski, P. D. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00825-08 · Cited by 131 · see citing works

Dosage compensation of the sex chromosomes and autosomes

Distèche, C. M. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.04.013 · Cited by 125 · see citing works

Functional Phosphorylation Sites in the C-Terminal Region of the Multivalent Multifunctional Transcriptional Factor CTCF

Klenova, E. M., Chernukhin, I. V., Elkady, A. I., Lee, R. E., Pugacheva, E. M., Loukinov, D. I., Goodwin, G. H., Delgado, M. D., Filippova, G. N., León, J., et al. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.6.2221-2234.2001 · Cited by 105 · see citing works

CpG methylation regulates the Igf2/H19 insulator

Holmgren, C., Kanduri, C., Dell, G. C., Ward, A., Mukhopadhya, R., Kanduri, M., Lobanenkov, V. V., & OHLSSON, R. I. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00314-1 · Cited by 92 · see citing works

Native Purification and Analysis of Long RNAs

Chillón, I., Marcia, M., Łęgiewicz, M., Liu, F., Somarowthu, S., & Pyle, A. M. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.01.008 · Cited by 86 · see citing works

A new model for random X chromosome inactivation

Starmer, J., & Magnuson, T. (2008) · Development · doi:10.1242/dev.025908 · Cited by 82 · see citing works

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

van Bemmel, J. G., Galupa, R., Gard, C., Servant, N., Picard, C., Davies, J. O. J., Szempruch, A. J., Zhan, Y., Żylicz, J. J., Nora, E. P., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0412-0 · Cited by 76 · see citing works

Enox, a Novel Gene That Maps 10 kb Upstream of Xist and Partially Escapes X Inactivation

Johnston, C. M., Newall, A. E. T., Brockdorff, N., & Nesterova, T. B. (2002) · Genomics · doi:10.1006/geno.2002.6819 · Cited by 65 · see citing works

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation

Plasschaert, R. N., Vigneau, S., Tempera, I., Gupta, R., Maksimoska, J., Everett, L. J., Davuluri, R. V., Mamorstein, R., Lieberman, P. M., Schultz, D., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt910 · Cited by 60 · see citing works

LncRNA Jpx induces Xist expression in mice using both trans and cis mechanisms

Carmona, S., Lin, B., Chou, T., Arroyo, K., & Sun, S. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007378 · Cited by 57 · see citing works

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data

Greenwald, W. W. Y., Li, H., Smith, E. N., Benaglio, P., Nariai, N., & Frazer, K. A. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1621-0 · Cited by 48 · see citing works

Characterization of expression at the human XIST locus in somatic, embryonal carcinoma, and transgenic cell lines

Chow, J., Hall, L. L., Clemson, C., Lawrence, J. B., & Brown, C. J. (2003) · Genomics · doi:10.1016/s0888-7543(03)00170-8 · Cited by 46 · see citing works

Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence

Karner, H. M., Webb, C.-H. T., Carmona, S., Liu, Y., Lin, B., Erhard, M., Chan, D., Baldi, P., Spitale, R. C., & Sun, S. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.09.002 · Cited by 45 · see citing works

Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation

Kriz, A. J., Colognori, D., Sunwoo, H., Nabet, B., & Lee, J. T. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.02.031 · Cited by 44 · see citing works

Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition

Rosario, B. C. D., Kriz, A. J., Rosario, A. M. D., Anselmo, A. N., Fry, C. J., White, F. M., Sadreyev, R. I., & Lee, J. T. (2019) · eLife · doi:10.7554/elife.42341 · Cited by 30 · see citing works

Long non-coding RNAs: definitions, functions, challenges and recommendations

Mattick, J. S., Amaral, P., Carninci, P., Carpenter, S. B., Chang, H. Y., Chen, L., Chen, R., Dean, C., Dinger, M. E., Fitzgerald, K. A., et al. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00566-8 · Cited by 2,416 · see citing works

CTCF shapes chromatin structure and gene expression in health and disease

Dehingia, B., Milewska, M., Janowski, M., & Pękowska, A. (2022) · EMBO Reports · doi:10.15252/embr.202255146 · Cited by 128 · see citing works

G-quadruplexes associated with R-loops promote CTCF binding

Wulfridge, P., Yan, Q., Rell, N., Doherty, J. K., Jacobson, S., Offley, S. R., Deliard, S., Feng, K., Phillips‐Cremins, J. E., Gardini, A., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.07.009 · Cited by 113 · see citing works

Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo

Guo, J. K., Blanco, M. R., Walkup, W. G., Bonesteele, G., Urbinati, C. R., Banerjee, A. K., Chow, A. Y., Ettlin, O., Strehle, M. M., Peyda, P., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.01.026 · Cited by 88 · see citing works

EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes

Marakulina, D., Vorontsov, I. E., Kulakovskiy, I. V., Lennartsson, A., Drabløs, F., & Medvedeva, Y. A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac989 · Cited by 78 · see citing works

CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation

Wei, C., Jia, L., Huang, X., Jin, T., Wang, M., Niu, J., Hou, Y., Sun, J., Zeng, P., Wang, J., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00676-0 · Cited by 64 · see citing works

Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

Huang, W., Xiong, T., Zhao, Y., Heng, J., Han, G., Wang, P., Zhao, Z., Shi, M., Li, J., Wang, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-023-01620-7 · Cited by 60 · see citing works

Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations

Friedman, M. J., Wagner, T., Lee, H., Rosenfeld, M. G., & Oh, S. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01233-y · Cited by 64 · see citing works

Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome

Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01322-2 · Cited by 51 · see citing works

LNCing RNA to immunity

Peltier, D., Roberts, A., & Reddy, P. R. (2022) · Trends in Immunology · doi:10.1016/j.it.2022.04.002 · Cited by 44 · see citing works

Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity

Sharma, S., Houfani, A. A., & Foster, L. J. (2024) · Journal of Biomedical Science · doi:10.1186/s12929-024-01038-1 · Cited by 42 · see citing works

CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors

Liu, Y., Wan, X., Li, H., Chen, Y., Hu, X., Chen, H., Zhu, D., Li, C., & Zhang, Y. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113259 · Cited by 38 · see citing works

Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer

Quiroga, I. Y., Ahn, J. H., Wang, G. G., & Phanstiel, D. H. (2022) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2022.101901 · Cited by 32 · see citing works

Long-distance association of topological boundaries through nuclear condensates

Gamliel, A., Meluzzi, D., Oh, S., Jiang, N., Destici, E., Rosenfeld, M. G., & Nair, S. J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2206216119 · Cited by 35 · see citing works

CTCF: A misguided jack-of-all-trades in cancer cells

Segueni, J., & Noordermeer, D. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.044 · Cited by 28 · see citing works

CTCF and Its Partners: Shaper of 3D Genome during Development

Sun, X., Zhang, J., & Cao, C. (2022) · Genes · doi:10.3390/genes13081383 · Cited by 31 · see citing works

The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation

Farhadova, S., Ghousein, A., Charon, F., Surcis, C., Gomez-Velazques, M., Roidor, C., Michele, F. D., Borensztein, M., Sario, A. D., Esnault, C., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae247 · Cited by 29 · see citing works

A biophysical basis for the spreading behavior and limited diffusion of Xist

Ding, M., Wang, D., Chen, H., Kesner, B., Grimm, N.-B., Weissbein, U., Lappala, A., Jiang, J., Rivera, C., Lou, J., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.004 · Cited by 29 · see citing works

lncRNA JPX-Enriched Chromatin Microenvironment Mediates Vascular Smooth Muscle Cell Senescence and Promotes Atherosclerosis

Gu, J., Chen, J., Yin, Q., Dong, M., Zhang, Y., Chen, M., Chen, X., Min, J., He, X., Tan, Y., et al. (2023) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.122.319250 · Cited by 28 · see citing works

CTCF and Its Multi-Partner Network for Chromatin Regulation

del Moral-Morales, A., Salgado-Albarrán, M., Sánchez-Pérez, Y., Wenke, N., Baumbach, J., & Soto-Reyes, E. (2023) · Cells · doi:10.3390/cells12101357 · Cited by 27 · see citing works

Regulatory principles and mechanisms governing the onset of random X-chromosome inactivation

Schwämmle, T., & Schulz, E. G. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102063 · Cited by 24 · see citing works

Long non-coding RNA-targeting therapeutics: discovery and development update

Khorkova, O., Stahl, J., Joji, A., Volmar, C., Zeier, Z. R., & Wahlestedt, C. (2023) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2023.2236552 · Cited by 21 · see citing works

Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion

Corin, A. J., Nora, E. P., & Ramani, V. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102298 · Cited by 19 · see citing works

Chromatin Reorganization during Myoblast Differentiation Involves the Caspase-Dependent Removal of SATB2

Bell, R. A. V., Al-Khalaf, M. H., Brunette, S., Alsowaida, D., Chu, A., Bandukwala, H., Dechant, G., Apostolova, G., Dilworth, F. J., & Megeney, L. A. (2022) · Cells · doi:10.3390/cells11060966 · Cited by 18 · see citing works

Exploring new roles for RNA-binding proteins in epigenetic and gene regulation

Ávila-López, P. A., & Lauberth, S. M. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102136 · Cited by 15 · see citing works

The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation

Tang, X., Zeng, P., Liu, K., Li, Q., Sun, Y., Liu, X., Lu, L., Wei, C., Wang, J., Jiang, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47048-3 · Cited by 17 · see citing works

Enhancer Function in the 3D Genome

Razin, S. V., Ulianov, S. V., & Iarovaia, O. V. (2023) · Genes · doi:10.3390/genes14061277 · Cited by 15 · see citing works

RNA-binding proteins mediate the maturation of chromatin topology during differentiation

Dehingia, B., Milewska, M., Janowski, M., Rafiee, M., Abbas, M., Piotrowska, A., Senge, J. F., Blaut, P., Walsh, D., Severino, J., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01735-5 · Cited by 16 · see citing works

CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation

Tajmul, M., Bhatt, D. N., Ruje, L., Price, E., Ji, Y. J., Loukinov, D. I., Teif, V. B., Lobanenkov, V. V., & Pugacheva, E. M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf587 · Cited by 14 · see citing works

Re-analysis of CLAP data affirms PRC2 as an RNA binding proteinPreprint

Lee, Y., Das, P., Kesner, B., Rosenberg, M., Blum, R., & Lee, J. T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.19.613009 · Cited by 14 · see citing works

HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation

Mazurov, E., Sizykh, A., & Medvedeva, Y. A. (2022) · Non-Coding RNA · doi:10.3390/ncrna8010018 · Cited by 13 · see citing works

Profiling and characterization of constitutive chromatin-enriched RNAs

Shen, W., Zhang, Y., Shi, M., Ye, B., Yin, M., Li, P., Shi, S., Jin, Y., Zhang, Z., Zhang, M. Q., et al. (2022) · iScience · doi:10.1016/j.isci.2022.105349 · Cited by 12 · see citing works

Plumbing mysterious RNAs in “dark genome” for the conquest of human diseases

Huang, L. A., Lin, C., & Yang, L. (2023) · Molecular Therapy · doi:10.1016/j.ymthe.2023.05.003 · Cited by 12 · see citing works

Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology

Antonazzo, G., Gaudet, P., Lovering, R. C., & Attrill, H. L. (2024) · RNA Biology · doi:10.1080/15476286.2024.2408523 · Cited by 11 · see citing works

3D genome alterations and editing in pathology

Tiukacheva, E. A., Ulianov, S. V., Karpukhina, A. A., Razin, S. V., & Vassetzky, Y. S. (2023) · Molecular Therapy · doi:10.1016/j.ymthe.2023.02.005 · Cited by 11 · see citing works

Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies

Sen, D., Maniyadath, B., Chowdhury, S., Kaur, A., Khatri, S., Chakraborty, A., Mehendale, N., Nadagouda, S., Sandra, U. S., Kamat, S. S., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107128 · Cited by 10 · see citing works

B cell stimulation changes the structure and higher-order organization of the inactive X chromosome

Sierra, I., Toothacre, N. E., van der Weide, R. H., Lovell, C. D., Nguyen, S. C., Barnett, R. J., Cook, A. L., Ryu, H.-S., Pyfrom, S., Wang, H., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115351 · Cited by 9 · see citing works

Emerging role of long non-coding RNA JPX in malignant processes and potential applications in cancers

Wang, Y., Bai, H., Jiang, M., Zhou, C., & Gong, Z. (2023) · Chinese Medical Journal · doi:10.1097/cm9.0000000000002392 · Cited by 9 · see citing works

T-Cadherin (CDH13) and Non-Coding RNAs: The Crosstalk Between Health and Disease

Rubina, K. A., Maier, A., Сергеевна, К. П., Sysoeva, V., Romashin, D. D., Semina, E. V., & Va, T. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26136127 · Cited by 9 · see citing works

Xist in X chromosome inactivation: mechanisms and disease relevance

Zhang, X., Mu, Q., Wang, J., Sun, Y., Cao, R., Guo, L., Han, Q., Gao, J., Yu, B., Wang, X. N., et al. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02534-z · Cited by 10 · see citing works

Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment

Huber, J., Tanasie, N.-L., Zernia, S., & Stigler, J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae391 · Cited by 8 · see citing works

7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress

Bujisic, B., Lee, H.-G., Xu, L., Weissbein, U., Rivera, C., Topisirović, I., & Lee, J. T. (2025) · Nature Communications · doi:10.1038/s41467-025-56351-6 · Cited by 8 · see citing works

Uncovering the functions and mechanisms of regulatory elements-associated non-coding RNAs

Fosseprez, O., & Cuvier, O. (2024) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2024.195059 · Cited by 6 · see citing works

Aberrant chromatin organization at the nexus of laminopathy disease pathways

Santini, G. T., Shah, P. P., Karnay, A. M., & Jain, R. (2022) · Nucleus · doi:10.1080/19491034.2022.2153564 · Cited by 8 · see citing works

Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers

Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00533-x · Cited by 6 · see citing works

Repair of DNA double-strand breaks leaves heritable impairment to genome functionPreprint

Bantele, S. C. S., Mordini, I., Biran, A., Alcaraz, N., Wenger, A., Krietenstein, N., Groth, A., & Lukas, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.29.555258 · Cited by 6 · see citing works

Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure

Xie, B., & Dean, A. (2025) · Non-Coding RNA · doi:10.3390/ncrna11050068 · Cited by 6 · see citing works

X Chromosome Inactivation Timing is Not eXACT: Implications for Autism Spectrum Disorders

LaSalle, J. M. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.864848 · Cited by 7 · see citing works

Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells

Hyle, J. W., Qi, W., Djekidel, M. N., Rosikiewicz, W., Xu, B., & Li, C. (2025) · Genome biology · doi:10.1186/s13059-025-03582-x · Cited by 5 · see citing works

Massively parallel dissection of RNA in RNA–protein interactions in vivo

Lee, Y. H., Hass, E. P., Campodonico-Burnett, W., Lee, Y. K., Lasda, E. L., Shah, J. S., Rinn, J. L., & Hwang, T. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae334 · Cited by 5 · see citing works

An EGFR co-amplified lncRNA HELDR promotes glioblastoma malignancy through KAT7-driven gene programs

Yu, X., Song, X., Schäfer, R. A., Meng, Q., Tiek, D. M., Wu, R., He, Q. Q., Walker, M. N., Cao, Q., Yang, R., et al. (2026) · Nature Cell Biology · doi:10.1038/s41556-026-01924-w · Cited by 4 · see citing works

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

Lucero, K., Han, S., Huang, P., Qiu, X., Mazzoni, E. O., & Reinberg, D. (2025) · Science Advances · doi:10.1126/sciadv.ady5507 · Cited by 6 · see citing works

Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion

Thorvaldsen, J. L., Juan, A. M., Lan, Y., Krapp, C. J., & Bartolomei, M. S. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011834 · Cited by 3 · see citing works

Widespread DNA off-targeting confounds RNA chromatin occupancy studies

Goldrich, M. J., Delhaye, L., Bekaert, S.-L., Decaesteker, B., Nieuwerburgh, F. V., Speleman, F., Eyckerman, S., Mestdagh, P., & Ulitsky, I. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03130-3 · Cited by 3 · see citing works

HDAC4‐AS1/CTCF Transcriptionally Represses HDAC4 Under Stress, Whereas HDAC4 Inhibits Stress‐Induced Syncytiotrophoblast Cellular Pyroptosis by Deacetylating NLRP3 and GSDMD

Du, J., Ji, Q., Dong, L., Wang, L., & Xin, G. (2025) · Cell Biochemistry and Function · doi:10.1002/cbf.70064 · Cited by 3 · see citing works

High CTCF expression mediated by FGD5-AS1/miR-19a-3p axis is associated with immunosuppression and pancreatic cancer progression

Liu, Y., Qi, W., Yin, J., He, X., Duan, S., Bao, H., Li, C., Shi, M., Wang, J., & Song, S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e22584 · Cited by 3 · see citing works

Regulation of loop extrusion on the interphase genome

Shin, H., & Kim, Y. (2023) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2023.2182273 · Cited by 3 · see citing works

Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Ma, F., Ollikainen, N., Du, H., Braikia, F.-Z., Cui, N., Bianchi, A. H., Dunn, C., Nguyen, C., Fan, J., De, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57373-w · Cited by 2 · see citing works

Role of RNA in genome folding: It's all about affinity

Czapiewski, R., & Gilbert, N. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103136 · Cited by 2 · see citing works

Re-analysis of CLAP supports prior evidence of PRC2 as an RNA-binding protein

Lee, Y., Das, P., Kesner, B., Rosenberg, M., Blum, R., & Lee, J. T. (2026) · Patterns · doi:10.1016/j.patter.2026.101641 · Cited by 2 · see citing works

The Potential Links between lncRNAs and Drug Tolerance in Lung Adenocarcinoma

Davis, W. J. H., Drummond, C. J., Diermeier, S. D., & Reid, G. (2024) · Genes · doi:10.3390/genes15070906 · Cited by 2 · see citing works

Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center

Oh, H. J., Das, P., Blum, R., Kriz, A. J., Lee, H.-G., Lee, Y.-W., & Lee, J. T. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.06.028 · Cited by 2 · see citing works

Identification of chromatin-associated RNAs at human centromeresPreprint

Fryer, K. A., Limouse, C., & Straight, A. F. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.05.658139 · Cited by 2 · see citing works

Comparative Analysis of RNA-Chromatin Interactome Data: Resolution, Completeness, and Specificity

Ryabykh, G. K., Nikolskaya, A. I., Garkul, L., & Mironov, A. A. (2025) · Biochemistry (Moscow) · doi:10.1134/s0006297925601923 · Cited by 1 · see citing works

The anti-aging drug Senolytics alleviates vascular endothelial cell senescence by antagonizing the JPX-BRD4-p65 complex

Mao, K., Zhu, W., Sun, H., Zheng, H., & Fu, Z. (2025) · Cellular Signalling · doi:10.1016/j.cellsig.2025.112342 · Cited by 1 · see citing works

NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture

Sun, W., Wu, N., Xia, M., Pan, Y., Liu, M., Fan, S., Wang, J., Zeng, Y., Fan, L., Chen, J., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.05.010 · Cited by 1 · see citing works

Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function

Bag, I., Chen, Y., D’Orazio, K. N., Lopez, P., Wenzel, S., Takagi, Y., & Lei, E. P. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac152 · Cited by 1 · see citing works

Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective TranscriptionPreprint

Wagner, T., Priyanka, P., Micheletti, R., Friedman, M. J., Nair, S. J., Gamliel, A., Taylor, H., Song, X., Cho, M., Oh, S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.17.594600 · Cited by 1 · see citing works

Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism of XistPreprint

Kadam, S., & Tamar Schlick, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.20.700676 · Cited by 1 · see citing works

Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiationPreprint

Thapa, C., Oh, E., Sirkin, D., Lahey, J., de León‐Guerrero, S. D., McCarroll, A., Gowda, P., Zhang, H., Barishman, A., Peyton, L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.27.708613 · Cited by 1 · see citing works

Additional file 2 of Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome

Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20047163

Epigenetic Control of Cell Fate Decisions by Enhancer-Derived Long Noncoding RNAs

Mattick, J. S. (2024) · Springer eBooks · doi:10.1007/978-3-031-59286-7_2

MARBP-lncRNA Complexes Alter Gene Function Through Modulation of Epigenetic Landscape

Maji, N., Dutta, A., Anand, A., Chatterjee, S., & Chattopadhyay, S. (2025) · Molecular and Cellular Biology · doi:10.1080/10985549.2025.2519156

COMPARATIVE ANALYSIS OF THE RNA-CHROMATIN INTERACTOME DATAPreprint

Ryabykh, G. K., Nikolskaya, A. I., Garkul, L., & Mironov, A. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.16.668492

Alternative Splicing And Global Transcriptome Changes Associated With LPS Stimulation In Human Peripheral Blood Mononuclear CellsPreprint

Chavez-Iglesias, E., Sucher, A., Thati, N., Trudeau, J., Yom, S. S., Sirota, M., Olshen, A. B., Cho, N. W., & Kober, K. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.09.687437

Beyond DNA binding: CTCF at the crossroads of chromatin architecture and epitranscriptomic regulation

Mukherjee, O., & Sarkar, K. (2025) · Epigenomics · doi:10.1080/17501911.2025.2591875

Long Non-Coding RNA JPX: Structure, Functions, and Role in Chromatin Architecture

Selivanovskiy, A. V., Sivkina, A. L., Ulianov, S. V., & Razin, S. V. (2025) · Biochemistry (Moscow) · doi:10.1134/s0006297925602692

Additional file 1 of Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome

Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20047160

Long noncoding RNAs as key regulators of autoimmunity

Yang-Fischer, R., Shearer, A., & Ghosh, S. (2025) · Advances in genetics · doi:10.1016/bs.adgen.2025.11.005

Rôles de très longs ARNs non codants intergéniques dans la réorganisation 3D du génome au cours de la sénescence

Ouvrard, J. (2023) · theses.fr (ABES) · doi:10.70675/f1618134z102ez441cz9ff8zade45dc23aa9

DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cells

Segueni, J. (2024) · doi:10.70675/abf007fbz8adcz4c68zb9faz5f550f134b2a

Dissecting the role of long non-coding RNA in multiple myeloma

Zocchi, S. (2024) · theses.fr (ABES) · doi:10.70675/22f35f26z6442z47d6z8cdaz153527b5df6e

Context-dependent roles of lncRNA JPX in human cancers

Li, Y., Li, T., Li, J. S., Su, Y., Liu, Y., Chen, L., Pan, Y., Ma, J., Gong, T., & Hu, H. (2026) · Discover Oncology · doi:10.1007/s12672-026-05419-w

Detection of Long Non-Coding RNA Localization by RNA Fluorescence In Situ Hybridization (FISH)

Shin, H., & Oh, H. J. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5352-4_11

Female iPSC X chromosome inactivation erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation.

Thapa, C., Oh, E. K., Sirkin, D., Lahey, J., de León-Guerrerro, S. D., McCarroll, A., Gowda, P., Zhang, H.-W., Barishman, A., Peyton, L., et al. (2026) · Stem Cell Reports · doi:10.1016/j.stemcr.2026.103120

Poster #192 FROM INTRUSIONS TO OBSESSIONS TO PSYCHOSIS. MEDIATED BY DELUSIONS?

Dael, F. V., van Os, J., Lieb, R., Wïttchen, H., & Myin‐Germeys, I. (2012) · Schizophrenia Research · doi:10.1016/s0920-9964(12)71024-1

Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center

Oh, H. J., Das, P., Blum, R., Kriz, A. J., Lee, H.-G., Lee, Y.-W., & Lee, J. T. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.06.028 · Cited by 2 · see citing works

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

Kung, J. T., Kesner, B., An, J. Y., Ahn, J. Y., Cifuentes‐Rojas, C., Colognori, D., Jeon, Y., Szántó, A., Rosario, B. C. D., Pinter, S. F., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.006 · Cited by 167 · see citing works

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

Lucero, K., Han, S., Huang, P., Qiu, X., Mazzoni, E. O., & Reinberg, D. (2025) · Science Advances · doi:10.1126/sciadv.ady5507 · Cited by 6 · see citing works

Jpx RNA Activates Xist by Evicting CTCF

Sun, S., Rosario, B. C. D., Szántó, A., Ogawa, Y., Jeon, Y., & Lee, J. T. (2013) · Cell · doi:10.1016/j.cell.2013.05.028 · Cited by 325 · see citing works